codealmanac 0.1.0 → 0.1.1

package/dist/codealmanac.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../src/cli.ts","../src/commands/bootstrap.ts","../src/agent/auth.ts","../src/agent/prompts.ts","../src/agent/sdk.ts","../src/paths.ts","../src/commands/init.ts","../src/slug.ts","../src/registry/index.ts","../src/commands/capture.ts","../src/indexer/frontmatter.ts","../src/commands/hook.ts","../src/commands/health.ts","../src/indexer/duration.ts","../src/indexer/index.ts","../src/topics/yaml.ts","../src/indexer/paths.ts","../src/indexer/schema.ts","../src/indexer/wikilinks.ts","../src/indexer/resolveWiki.ts","../src/topics/dag.ts","../src/commands/info.ts","../src/commands/list.ts","../src/commands/path.ts","../src/commands/reindex.ts","../src/commands/search.ts","../src/commands/show.ts","../src/topics/frontmatterRewrite.ts","../src/topics/paths.ts","../src/commands/tag.ts","../src/commands/topics.ts","../src/registry/autoregister.ts","../bin/codealmanac.ts"],"sourcesContent":["import { basename } from \"node:path\";\n\nimport { Command } from \"commander\";\n\nimport { runBootstrap } from \"./commands/bootstrap.js\";\nimport { runCapture } from \"./commands/capture.js\";\nimport {\n  runHookInstall,\n  runHookStatus,\n  runHookUninstall,\n} from \"./commands/hook.js\";\nimport { runHealth } from \"./commands/health.js\";\nimport { initWiki } from \"./commands/init.js\";\nimport { runInfo } from \"./commands/info.js\";\nimport { listWikis } from \"./commands/list.js\";\nimport { runPath } from \"./commands/path.js\";\nimport { runReindex } from \"./commands/reindex.js\";\nimport { runSearch } from \"./commands/search.js\";\nimport { runShow } from \"./commands/show.js\";\nimport { runTag, runUntag } from \"./commands/tag.js\";\nimport {\n  runTopicsCreate,\n  runTopicsDelete,\n  runTopicsDescribe,\n  runTopicsLink,\n  runTopicsList,\n  runTopicsRename,\n  runTopicsShow,\n  runTopicsUnlink,\n} from \"./commands/topics.js\";\nimport { autoRegisterIfNeeded } from \"./registry/autoregister.js\";\n\n/**\n * Entry point. `bin/codealmanac.ts` hands us `process.argv` and any errors\n * bubble up to the shim for a uniform \"almanac: <message>\" output format.\n *\n * Auto-registration runs before most commands. Two exceptions:\n *   - `init` registers explicitly, so auto-register would be redundant and\n *     would race with init's own write.\n *   - `list --drop <name>` shouldn't silently re-register the repo whose\n *     entry the user is trying to remove.\n */\nexport async function run(argv: string[]): Promise<void> {\n  const program = new Command();\n\n  // Both `almanac` and `codealmanac` point at the same entry (see\n  // `package.json#bin`). Match the help header to whatever the user\n  // invoked so `codealmanac --help` doesn't incongruously read\n  // `Usage: almanac …`. Fall back to `almanac` when argv[1] isn't\n  // available (programmatic invocation, tests).\n  const invoked = argv[1] !== undefined ? basename(argv[1]) : \"almanac\";\n  const programName =\n    invoked === \"codealmanac\" ? \"codealmanac\" : \"almanac\";\n\n  program\n    .name(programName)\n    .description(\n      \"codealmanac — a living wiki for codebases, maintained by AI agents\",\n    )\n    .version(\"0.1.0\", \"-v, --version\", \"print version\");\n\n  program\n    .command(\"init\")\n    .description(\"scaffold .almanac/ in the current directory and register it\")\n    .option(\"--name <name>\", \"wiki name (defaults to the directory name)\")\n    .option(\"--description <text>\", \"one-line description of this wiki\")\n    .action(async (opts: { name?: string; description?: string }) => {\n      const result = await initWiki({\n        cwd: process.cwd(),\n        name: opts.name,\n        description: opts.description,\n      });\n      const verb = result.created ? \"initialized\" : \"updated\";\n      process.stdout.write(\n        `${verb} wiki \"${result.entry.name}\" at ${result.almanacDir}\\n`,\n      );\n    });\n\n  program\n    .command(\"list\")\n    .description(\"list registered wikis\")\n    .option(\"--json\", \"emit structured JSON\")\n    .option(\n      \"--drop <name>\",\n      \"remove a wiki from the registry (the only way entries are ever removed)\",\n    )\n    .action(async (opts: { json?: boolean; drop?: string }) => {\n      // Auto-register only makes sense for default/JSON listing. Skipping\n      // it on --drop keeps the removal operation predictable — the user's\n      // intent is to shrink the registry, not grow it mid-command.\n      if (opts.drop === undefined) {\n        await autoRegisterIfNeeded(process.cwd());\n      }\n      const result = await listWikis(opts);\n      process.stdout.write(result.stdout);\n      if (result.exitCode !== 0) {\n        process.exitCode = result.exitCode;\n      }\n    });\n\n  program\n    .command(\"search [query]\")\n    .description(\"query pages by text, topic, file mentions, or freshness\")\n    .option(\n      \"--topic <name...>\",\n      \"filter by topic (repeat for intersection)\",\n      collectOption,\n      [] as string[],\n    )\n    .option(\n      \"--mentions <path>\",\n      \"pages referencing this file or folder (trailing / = folder)\",\n    )\n    .option(\n      \"--since <duration>\",\n      \"updated within duration, by file mtime (e.g. 2w, 30d)\",\n    )\n    .option(\n      \"--stale <duration>\",\n      \"NOT updated within duration, by file mtime\",\n    )\n    .option(\"--orphan\", \"pages with no topics\")\n    .option(\"--include-archive\", \"include archived pages\")\n    .option(\"--archived\", \"archived pages only\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .option(\"--json\", \"emit structured JSON\")\n    .option(\"--limit <n>\", \"cap results\", parsePositiveInt)\n    .action(\n      async (\n        query: string | undefined,\n        opts: {\n          topic?: string[];\n          mentions?: string;\n          since?: string;\n          stale?: string;\n          orphan?: boolean;\n          includeArchive?: boolean;\n          archived?: boolean;\n          wiki?: string;\n          json?: boolean;\n          limit?: number;\n        },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runSearch({\n          cwd: process.cwd(),\n          query,\n          topics: opts.topic ?? [],\n          mentions: opts.mentions,\n          since: opts.since,\n          stale: opts.stale,\n          orphan: opts.orphan,\n          includeArchive: opts.includeArchive,\n          archived: opts.archived,\n          wiki: opts.wiki,\n          json: opts.json,\n          limit: opts.limit,\n        });\n        if (result.stderr.length > 0) process.stderr.write(result.stderr);\n        process.stdout.write(result.stdout);\n        if (result.exitCode !== 0) process.exitCode = result.exitCode;\n      },\n    );\n\n  program\n    .command(\"show [slug]\")\n    .description(\"print the markdown content of a page\")\n    .option(\"--stdin\", \"read slugs from stdin (one per line)\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (\n        slug: string | undefined,\n        opts: { stdin?: boolean; wiki?: string },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runShow({\n          cwd: process.cwd(),\n          slug,\n          stdin: opts.stdin,\n          stdinInput: opts.stdin === true ? await readStdin() : undefined,\n          wiki: opts.wiki,\n        });\n        if (result.stderr.length > 0) process.stderr.write(result.stderr);\n        process.stdout.write(result.stdout);\n        if (result.exitCode !== 0) process.exitCode = result.exitCode;\n      },\n    );\n\n  program\n    .command(\"path [slug]\")\n    .description(\"resolve a slug to its absolute file path\")\n    .option(\"--stdin\", \"read slugs from stdin (one per line)\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (\n        slug: string | undefined,\n        opts: { stdin?: boolean; wiki?: string },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runPath({\n          cwd: process.cwd(),\n          slug,\n          stdin: opts.stdin,\n          stdinInput: opts.stdin === true ? await readStdin() : undefined,\n          wiki: opts.wiki,\n        });\n        if (result.stderr.length > 0) process.stderr.write(result.stderr);\n        process.stdout.write(result.stdout);\n        if (result.exitCode !== 0) process.exitCode = result.exitCode;\n      },\n    );\n\n  program\n    .command(\"info [slug]\")\n    .description(\"print metadata for a page (topics, refs, links, lineage)\")\n    .option(\"--stdin\", \"read slugs from stdin (one per line)\")\n    .option(\"--json\", \"emit structured JSON\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (\n        slug: string | undefined,\n        opts: { stdin?: boolean; json?: boolean; wiki?: string },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runInfo({\n          cwd: process.cwd(),\n          slug,\n          stdin: opts.stdin,\n          stdinInput: opts.stdin === true ? await readStdin() : undefined,\n          json: opts.json,\n          wiki: opts.wiki,\n        });\n        if (result.stderr.length > 0) process.stderr.write(result.stderr);\n        process.stdout.write(result.stdout);\n        if (result.exitCode !== 0) process.exitCode = result.exitCode;\n      },\n    );\n\n  program\n    .command(\"reindex\")\n    .description(\"force a full rebuild of .almanac/index.db\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(async (opts: { wiki?: string }) => {\n      await autoRegisterIfNeeded(process.cwd());\n      const result = await runReindex({\n        cwd: process.cwd(),\n        wiki: opts.wiki,\n      });\n      process.stdout.write(result.stdout);\n      if (result.exitCode !== 0) process.exitCode = result.exitCode;\n    });\n\n  // ─── topics (sub-tree) ────────────────────────────────────────────\n  const topics = program\n    .command(\"topics\")\n    .description(\"manage the topic DAG (list, create, link, rename, delete)\");\n\n  // Default action for `almanac topics` with no subcommand: list.\n  topics\n    .command(\"list\", { isDefault: true })\n    .description(\"list all topics with page counts\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .option(\"--json\", \"emit structured JSON\")\n    .action(async (opts: { wiki?: string; json?: boolean }) => {\n      await autoRegisterIfNeeded(process.cwd());\n      const result = await runTopicsList({\n        cwd: process.cwd(),\n        wiki: opts.wiki,\n        json: opts.json,\n      });\n      emit(result);\n    });\n\n  topics\n    .command(\"show <slug>\")\n    .description(\"print a topic's metadata, parents, children, and pages\")\n    .option(\"--descendants\", \"include pages tagged with descendant topics\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .option(\"--json\", \"emit structured JSON\")\n    .action(\n      async (\n        slug: string,\n        opts: { descendants?: boolean; wiki?: string; json?: boolean },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runTopicsShow({\n          cwd: process.cwd(),\n          slug,\n          descendants: opts.descendants,\n          wiki: opts.wiki,\n          json: opts.json,\n        });\n        emit(result);\n      },\n    );\n\n  topics\n    .command(\"create <name>\")\n    .description(\"create a topic (rejects if --parent slug does not exist)\")\n    .option(\n      \"--parent <slug>\",\n      \"parent topic slug (repeat for multiple parents)\",\n      collectOption,\n      [] as string[],\n    )\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (\n        name: string,\n        opts: { parent?: string[]; wiki?: string },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runTopicsCreate({\n          cwd: process.cwd(),\n          name,\n          parents: opts.parent,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  topics\n    .command(\"link <child> <parent>\")\n    .description(\"add a DAG edge (cycle-checked)\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (child: string, parent: string, opts: { wiki?: string }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runTopicsLink({\n          cwd: process.cwd(),\n          child,\n          parent,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  topics\n    .command(\"unlink <child> <parent>\")\n    .description(\"remove a DAG edge\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (child: string, parent: string, opts: { wiki?: string }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runTopicsUnlink({\n          cwd: process.cwd(),\n          child,\n          parent,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  topics\n    .command(\"rename <old> <new>\")\n    .description(\"rename a topic; rewrites every affected page's frontmatter\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (oldSlug: string, newSlug: string, opts: { wiki?: string }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runTopicsRename({\n          cwd: process.cwd(),\n          oldSlug,\n          newSlug,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  topics\n    .command(\"delete <slug>\")\n    .description(\"delete a topic; untags every affected page\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(async (slug: string, opts: { wiki?: string }) => {\n      await autoRegisterIfNeeded(process.cwd());\n      const result = await runTopicsDelete({\n        cwd: process.cwd(),\n        slug,\n        wiki: opts.wiki,\n      });\n      emit(result);\n    });\n\n  topics\n    .command(\"describe <slug> <text>\")\n    .description(\"set a topic's one-line description\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (slug: string, text: string, opts: { wiki?: string }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runTopicsDescribe({\n          cwd: process.cwd(),\n          slug,\n          description: text,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  // ─── tag / untag ─────────────────────────────────────────────────\n  program\n    .command(\"tag [page] [topics...]\")\n    .description(\"add topics to a page (auto-creates missing topics)\")\n    .option(\"--stdin\", \"read page slugs from stdin (one per line)\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (\n        page: string | undefined,\n        topicsArg: string[],\n        opts: { stdin?: boolean; wiki?: string },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        // `--stdin <topic> [<topic>...]` shape: no positional page,\n        // all positionals are topics. commander gives us `page` =\n        // first positional and `topicsArg` = rest, so in --stdin mode\n        // we prepend whatever landed in `page` to the topics list.\n        const resolvedTopics = opts.stdin === true\n          ? [page, ...topicsArg].filter(\n              (t): t is string => typeof t === \"string\" && t.length > 0,\n            )\n          : topicsArg;\n        const result = await runTag({\n          cwd: process.cwd(),\n          page: opts.stdin === true ? undefined : page,\n          topics: resolvedTopics,\n          stdin: opts.stdin,\n          stdinInput: opts.stdin === true ? await readStdin() : undefined,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  program\n    .command(\"untag <page> <topic>\")\n    .description(\"remove a topic from a page's frontmatter\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (page: string, topic: string, opts: { wiki?: string }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runUntag({\n          cwd: process.cwd(),\n          page,\n          topic,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  // ─── bootstrap ───────────────────────────────────────────────────\n  // Slice 4: first Claude Agent SDK integration. Spawns the bootstrap\n  // agent on the current repo to create initial entity pages + README +\n  // topic DAG. Requires ANTHROPIC_API_KEY; refuses on populated wikis\n  // unless --force.\n  program\n    .command(\"bootstrap\")\n    .description(\n      \"spawn an agent to scan the repo and create initial wiki stubs (requires ANTHROPIC_API_KEY)\",\n    )\n    .option(\"--quiet\", \"suppress per-tool streaming; print only the final line\")\n    .option(\"--model <model>\", \"override the agent model\")\n    .option(\n      \"--force\",\n      \"overwrite an existing populated wiki (default: refuse)\",\n    )\n    .action(\n      async (opts: { quiet?: boolean; model?: string; force?: boolean }) => {\n        // No auto-register here: if this is a fresh repo the bootstrap\n        // command handles init (and therefore registration) itself. If\n        // the repo is already a wiki, capture/init have already\n        // registered it.\n        const result = await runBootstrap({\n          cwd: process.cwd(),\n          quiet: opts.quiet,\n          model: opts.model,\n          force: opts.force,\n        });\n        emit(result);\n      },\n    );\n\n  // ─── capture ─────────────────────────────────────────────────────\n  // Slice 5: writer + reviewer subagent on a Claude Code session\n  // transcript. Refuses if no `.almanac/` exists (capture is for\n  // maintaining wikis, not creating them). Transcript path resolution:\n  //  - explicit positional arg wins\n  //  - `--session <id>` matches by filename under ~/.claude/projects/\n  //  - otherwise auto-resolve the most recent transcript whose cwd\n  //    matches this repo\n  program\n    .command(\"capture [transcript]\")\n    .description(\n      \"capture knowledge from a Claude Code session transcript \" +\n        \"(auto-resolves the most recent session for this repo when no \" +\n        \"path is given; requires ANTHROPIC_API_KEY)\",\n    )\n    .option(\"--session <id>\", \"target a specific session by ID\")\n    .option(\n      \"--quiet\",\n      \"suppress per-tool streaming; print only the final summary\",\n    )\n    .option(\"--model <model>\", \"override the agent model\")\n    .action(\n      async (\n        transcript: string | undefined,\n        opts: { session?: string; quiet?: boolean; model?: string },\n      ) => {\n        // Auto-register the repo on capture: the user may have cloned a\n        // repo with `.almanac/` committed but never run init.\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runCapture({\n          cwd: process.cwd(),\n          transcriptPath: transcript,\n          sessionId: opts.session,\n          quiet: opts.quiet,\n          model: opts.model,\n        });\n        emit(result);\n      },\n    );\n\n  // ─── hook ─────────────────────────────────────────────────────────\n  // Wires codealmanac into Claude Code's SessionEnd hook via\n  // ~/.claude/settings.json. Non-interactive install/uninstall/status.\n  const hook = program\n    .command(\"hook\")\n    .description(\n      \"install, uninstall, or inspect the SessionEnd hook in ~/.claude/settings.json\",\n    );\n\n  hook\n    .command(\"install\")\n    .description(\"add a SessionEnd entry that runs 'almanac capture' on session end\")\n    .action(async () => {\n      const result = await runHookInstall();\n      emit(result);\n    });\n\n  hook\n    .command(\"uninstall\")\n    .description(\"remove codealmanac's SessionEnd entry; leaves foreign entries alone\")\n    .action(async () => {\n      const result = await runHookUninstall();\n      emit(result);\n    });\n\n  hook\n    .command(\"status\")\n    .description(\"report whether the SessionEnd hook is installed\")\n    .action(async () => {\n      const result = await runHookStatus();\n      emit(result);\n    });\n\n  // ─── health ──────────────────────────────────────────────────────\n  program\n    .command(\"health\")\n    .description(\"report wiki problems (orphans, dead refs, broken links, …)\")\n    .option(\"--topic <name>\", \"scope to a topic + its descendants\")\n    .option(\"--stale <duration>\", \"stale threshold (default 90d)\")\n    .option(\"--stdin\", \"read page slugs from stdin (limit to these pages)\")\n    .option(\"--json\", \"emit structured JSON\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (opts: {\n        topic?: string;\n        stale?: string;\n        stdin?: boolean;\n        json?: boolean;\n        wiki?: string;\n      }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runHealth({\n          cwd: process.cwd(),\n          topic: opts.topic,\n          stale: opts.stale,\n          stdin: opts.stdin,\n          stdinInput: opts.stdin === true ? await readStdin() : undefined,\n          json: opts.json,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  await program.parseAsync(argv);\n}\n\n/**\n * Uniform writer for commands that produce `{stdout, stderr, exitCode}`.\n * Used by the slice-3 topics/tag/health commands; older commands still\n * inline the same three lines and can be collapsed in a follow-up.\n */\nfunction emit(result: {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}): void {\n  if (result.stderr.length > 0) process.stderr.write(result.stderr);\n  if (result.stdout.length > 0) process.stdout.write(result.stdout);\n  if (result.exitCode !== 0) process.exitCode = result.exitCode;\n}\n\n/**\n * Commander's built-in collectable option helper. Repeatable `--topic`\n * appends; a bare call with no previous value starts a fresh array.\n */\nfunction collectOption(value: string, previous: string[]): string[] {\n  return [...previous, value];\n}\n\nfunction parsePositiveInt(value: string): number {\n  const n = Number.parseInt(value, 10);\n  if (!Number.isFinite(n) || n < 0) {\n    throw new Error(`invalid --limit \"${value}\" (expected a non-negative integer)`);\n  }\n  return n;\n}\n\n/**\n * Drain stdin to a string. Used by the `--stdin` flag on show/path/info.\n * We require an explicit opt-in rather than auto-detect TTY because\n * relying on `process.stdin.isTTY` makes the behavior surprising when\n * invoked from scripts with stdin redirected.\n */\nasync function readStdin(): Promise<string> {\n  if (process.stdin.isTTY === true) return \"\";\n  const chunks: Buffer[] = [];\n  for await (const chunk of process.stdin) {\n    chunks.push(Buffer.isBuffer(chunk) ? chunk : Buffer.from(chunk));\n  }\n  return Buffer.concat(chunks).toString(\"utf8\");\n}\n","import { createWriteStream, existsSync, type WriteStream } from \"node:fs\";\nimport { readdir } from \"node:fs/promises\";\nimport { join, relative } from \"node:path\";\n\nimport type { SDKMessage } from \"@anthropic-ai/claude-agent-sdk\";\n\nimport { assertClaudeAuth, type SpawnCliFn } from \"../agent/auth.js\";\nimport { loadPrompt } from \"../agent/prompts.js\";\nimport {\n  runAgent,\n  type AgentResult,\n  type RunAgentOptions,\n} from \"../agent/sdk.js\";\nimport { findNearestAlmanacDir, getRepoAlmanacDir } from \"../paths.js\";\nimport { initWiki } from \"./init.js\";\n\nexport interface BootstrapOptions {\n  cwd: string;\n  /** Suppress per-tool-use streaming output; print only errors + final line. */\n  quiet?: boolean;\n  /** Override the agent model. Defaults to the SDK default (sonnet-4-6). */\n  model?: string;\n  /** Overwrite a populated wiki. Default refuses with a pointer at `capture`. */\n  force?: boolean;\n  /** Injectable agent runner — tests replace this with a fake. */\n  runAgent?: (opts: RunAgentOptions) => Promise<AgentResult>;\n  /**\n   * Injectable subprocess spawner for the Claude auth-status check.\n   * Tests substitute a stub that emits canned JSON without running the\n   * bundled CLI. Production leaves this undefined and `assertClaudeAuth`\n   * falls through to `defaultSpawnCli`.\n   */\n  spawnCli?: SpawnCliFn;\n  /**\n   * Clock injection, for tests. Otherwise `Date.now()` timestamps the\n   * transcript log filename and defaults to the SDK's session_id once\n   * we receive one (the filename is chosen BEFORE the agent starts so\n   * we can stream to it).\n   */\n  now?: () => Date;\n}\n\nexport interface BootstrapResult {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * Tools the bootstrap agent is permitted to use. Bootstrap reads the repo\n * (Read/Glob/Grep), runs quick inspection commands (Bash — scoped by the\n * prompt, not by the SDK — the agent isn't expected to do anything\n * destructive), and writes scaffolding (Write/Edit). Notably absent:\n *   - `Agent` — bootstrap has no subagents (reviewer is slice 5).\n *   - `WebFetch` / `WebSearch` — prompt is explicit that we work from the\n *     repo, not the internet. Adding these would invite drift.\n *   - MCP servers — none needed for a local filesystem scan.\n */\nconst BOOTSTRAP_TOOLS = [\"Read\", \"Write\", \"Edit\", \"Glob\", \"Grep\", \"Bash\"];\n\n/**\n * `almanac bootstrap` — first Claude Agent SDK integration.\n *\n * Flow:\n *   1. Auth gate (ANTHROPIC_API_KEY). Fail fast with a clean error.\n *   2. Resolve repo root (existing `.almanac/` or cwd).\n *   3. Refuse-if-populated unless --force.\n *   4. Auto-init silently if `.almanac/` doesn't exist yet.\n *   5. Load `prompts/bootstrap.md`.\n *   6. Run the agent with BOOTSTRAP_TOOLS, cwd = repo root.\n *   7. Stream tool-uses to stdout (unless --quiet); write the full raw\n *      transcript to `.almanac/.bootstrap-<session>.log`.\n *   8. Print a final `[done]` / `[failed]` line with cost + turns.\n *\n * Non-zero exit on failure so shell users can pipe into `&&`.\n */\nexport async function runBootstrap(\n  options: BootstrapOptions,\n): Promise<BootstrapResult> {\n  // Fail before loading prompts so we don't do filesystem work on a request\n  // that can't succeed. `assertClaudeAuth` accepts either subscription\n  // OAuth (via the bundled SDK CLI) or `ANTHROPIC_API_KEY`; missing both\n  // surfaces a two-option error and MUST exit non-zero so the SessionEnd\n  // hook (which backgrounds the process and ignores stderr) doesn't\n  // treat silent auth failure as success.\n  try {\n    await assertClaudeAuth(options.spawnCli);\n  } catch (err: unknown) {\n    const msg = err instanceof Error ? err.message : String(err);\n    return {\n      stdout: \"\",\n      stderr: `almanac: ${msg}\\n`,\n      exitCode: 1,\n    };\n  }\n\n  // Repo root: honor an already-initialized wiki anywhere above us.\n  // Otherwise treat `cwd` as the root for a fresh wiki.\n  const repoRoot = findNearestAlmanacDir(options.cwd) ?? options.cwd;\n  const almanacDir = getRepoAlmanacDir(repoRoot);\n  const pagesDir = join(almanacDir, \"pages\");\n\n  // Refuse to clobber a populated wiki. `almanac capture` is the tool for\n  // maintaining wikis after bootstrap.\n  if (options.force !== true && existsSync(pagesDir)) {\n    const existing = await countMarkdownPages(pagesDir);\n    if (existing > 0) {\n      return {\n        stdout: \"\",\n        stderr:\n          `almanac: .almanac/ already initialized with ${existing} page${existing === 1 ? \"\" : \"s\"}. ` +\n          \"Use 'almanac capture' instead, or --force to overwrite.\\n\",\n        exitCode: 1,\n      };\n    }\n  }\n\n  // Auto-init silently if missing. `initWiki` is idempotent — re-running\n  // on an existing wiki is a no-op for the README / pages dir.\n  if (!existsSync(almanacDir)) {\n    try {\n      await initWiki({ cwd: repoRoot });\n    } catch (err: unknown) {\n      // Per the slice spec: auto-init failures should be loud. The user\n      // needs to know init is broken, not see a cascading agent error.\n      const msg = err instanceof Error ? err.message : String(err);\n      return {\n        stdout: \"\",\n        stderr: `almanac: init failed during bootstrap: ${msg}\\n`,\n        exitCode: 1,\n      };\n    }\n  }\n\n  const systemPrompt = await loadPrompt(\"bootstrap\");\n\n  // Transcript log filename: timestamp-based so it's sortable. The session\n  // ID from the SDK isn't known until the first message arrives — by then\n  // we'd already want somewhere to stream to. Use a clock-derived prefix\n  // that's still meaningful even on a run that fails before producing a\n  // session_id.\n  const now = options.now?.() ?? new Date();\n  const logName = `.bootstrap-${formatTimestamp(now)}.log`;\n  const logPath = join(almanacDir, logName);\n  const logStream = createWriteStream(logPath, { flags: \"w\" });\n\n  // The streaming formatter is what the user sees on stdout unless\n  // --quiet is set. The raw log captures EVERYTHING (including\n  // `stream_event` partials) for postmortem.\n  const out = process.stdout;\n  const formatter = new StreamingFormatter({\n    write: (line: string) => {\n      if (options.quiet !== true) out.write(line);\n    },\n  });\n\n  const onMessage = (msg: SDKMessage): void => {\n    // Write the raw message to the transcript. Keep one JSON per line so\n    // the log is grep-able and can be re-parsed if needed.\n    try {\n      logStream.write(`${JSON.stringify(msg)}\\n`);\n    } catch {\n      // Serialization failures are non-fatal — we'd rather keep streaming\n      // to stdout than crash because one message had a circular ref.\n    }\n    formatter.handle(msg);\n  };\n\n  const runner = options.runAgent ?? runAgent;\n\n  const userPrompt = `Begin the bootstrap now. Working directory: ${repoRoot}.`;\n\n  let result: AgentResult;\n  try {\n    result = await runner({\n      systemPrompt,\n      prompt: userPrompt,\n      allowedTools: BOOTSTRAP_TOOLS,\n      cwd: repoRoot,\n      model: options.model,\n      onMessage,\n    });\n  } finally {\n    await closeStream(logStream);\n  }\n\n  const finalLine = formatFinalLine(result, logPath, repoRoot);\n\n  if (result.success) {\n    return {\n      stdout: `${finalLine}\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  return {\n    stdout: options.quiet === true ? \"\" : `${finalLine}\\n`,\n    stderr: `almanac: bootstrap failed: ${result.error ?? \"unknown error\"}\\n`,\n    exitCode: 1,\n  };\n}\n\n/**\n * Format the final line the user sees. On success it's a one-liner with\n * cost + turns; on failure we still print the cost/turns so the user\n * knows what the partial run used. The log path is shown relative to\n * `repoRoot` to keep the line short.\n */\nfunction formatFinalLine(\n  result: AgentResult,\n  logPath: string,\n  repoRoot: string,\n): string {\n  const status = result.success ? \"done\" : \"failed\";\n  const rel = relative(repoRoot, logPath);\n  const cost = `$${result.cost.toFixed(3)}`;\n  return `[${status}] cost: ${cost}, turns: ${result.turns} (transcript: ${rel})`;\n}\n\nasync function countMarkdownPages(pagesDir: string): Promise<number> {\n  try {\n    const entries = await readdir(pagesDir, { withFileTypes: true });\n    return entries.filter((e) => e.isFile() && e.name.endsWith(\".md\")).length;\n  } catch {\n    return 0;\n  }\n}\n\nfunction closeStream(stream: WriteStream): Promise<void> {\n  return new Promise((resolve) => {\n    stream.end(() => resolve());\n  });\n}\n\nfunction formatTimestamp(d: Date): string {\n  // YYYYMMDD-HHMMSS, local time. Collision-proof enough for human use\n  // (one bootstrap per second, per repo is an acceptable ceiling).\n  const pad = (n: number): string => n.toString().padStart(2, \"0\");\n  const y = d.getFullYear();\n  const mo = pad(d.getMonth() + 1);\n  const da = pad(d.getDate());\n  const h = pad(d.getHours());\n  const mi = pad(d.getMinutes());\n  const s = pad(d.getSeconds());\n  return `${y}${mo}${da}-${h}${mi}${s}`;\n}\n\n/**\n * Translates SDK messages into one-line-per-tool-use output.\n *\n * Design rules:\n *   - One line per `tool_use` block, not per token. Users scanning the\n *     output want to see \"what the agent did\", not a tail of the\n *     assistant's prose.\n *   - `Bash` gets special formatting because the input is most usefully\n *     rendered as the command being run.\n *   - On final `result`, emit a summary line. Callers can suppress all\n *     intermediate output via `--quiet` and still get the summary.\n *   - Tool paths are shown relative to the cwd (not implemented here\n *     because the SDK doesn't give us cwd on every message; users get\n *     the raw input). The cwd-relative rendering is a nice-to-have that\n *     we can layer on later without changing the API.\n *\n * Exported for testing — `StreamingFormatter` is easier to unit-test in\n * isolation than the whole command.\n */\nexport class StreamingFormatter {\n  private readonly sink: { write: (line: string) => void };\n  /**\n   * Current agent label. Starts as \"bootstrap\"; switches when we see an\n   * `Agent` tool-use (slice 5 will exercise this). We still track it here\n   * so the formatter can stay shared between bootstrap and capture.\n   */\n  private currentAgent = \"bootstrap\";\n\n  constructor(sink: { write: (line: string) => void }) {\n    this.sink = sink;\n  }\n\n  /**\n   * Swap the top-level agent label. `capture` uses this to relabel from\n   * the default \"bootstrap\" to \"writer\" — otherwise the writer's tool-use\n   * output would render as `[bootstrap] …`, which is confusing when you're\n   * reading capture logs.\n   */\n  setAgent(name: string): void {\n    this.currentAgent = name;\n  }\n\n  handle(msg: SDKMessage): void {\n    if (msg.type === \"assistant\") {\n      for (const block of msg.message.content) {\n        if (block.type !== \"tool_use\") continue;\n        this.handleToolUse(block.name, block.input);\n      }\n      return;\n    }\n\n    if (msg.type === \"result\") {\n      // The command-level finalLine is what the user sees at the end of\n      // stdout; the formatter also emits one here so live-tailing a\n      // transcript log shows the full run. Kept terse.\n      const status =\n        msg.subtype === \"success\" ? \"done\" : `failed (${msg.subtype})`;\n      this.sink.write(\n        `[${status}] cost: $${msg.total_cost_usd.toFixed(3)}, turns: ${msg.num_turns}\\n`,\n      );\n      return;\n    }\n  }\n\n  private handleToolUse(name: string, rawInput: unknown): void {\n    const input = normalizeToolInput(rawInput);\n\n    if (name === \"Agent\") {\n      // Subagent dispatch. Track the label so subsequent tool-uses show\n      // up under the right agent bracket. The label is whatever the\n      // parent passed as `subagent_type`, falling back to \"subagent\" if\n      // the input was malformed (shouldn't happen, but defensively).\n      const sub =\n        typeof input.subagent_type === \"string\" ? input.subagent_type : \"subagent\";\n      this.currentAgent = sub;\n      this.sink.write(`[${sub}] starting\\n`);\n      return;\n    }\n\n    const summary = formatToolSummary(name, input);\n    this.sink.write(`[${this.currentAgent}] ${summary}\\n`);\n  }\n}\n\n/**\n * SDK quirk: `tool_use.input` arrives as either an object OR a\n * JSON-encoded string. Always normalize before touching fields.\n */\nfunction normalizeToolInput(raw: unknown): Record<string, unknown> {\n  if (typeof raw === \"string\") {\n    try {\n      const parsed = JSON.parse(raw);\n      if (parsed !== null && typeof parsed === \"object\") {\n        return parsed as Record<string, unknown>;\n      }\n    } catch {\n      // Fall through to empty object.\n    }\n    return {};\n  }\n  if (raw !== null && typeof raw === \"object\") {\n    return raw as Record<string, unknown>;\n  }\n  return {};\n}\n\n/**\n * Render a tool call as a single human-readable line. Not exhaustive —\n * we cover the tools bootstrap actually invokes and fall back to the\n * tool name + a terse input summary for anything else.\n */\nfunction formatToolSummary(\n  name: string,\n  input: Record<string, unknown>,\n): string {\n  switch (name) {\n    case \"Read\": {\n      const target = stringField(input, \"file_path\") ?? \"?\";\n      return `reading ${target}`;\n    }\n    case \"Write\": {\n      const target = stringField(input, \"file_path\") ?? \"?\";\n      return `writing ${target}`;\n    }\n    case \"Edit\": {\n      const target = stringField(input, \"file_path\") ?? \"?\";\n      return `editing ${target}`;\n    }\n    case \"Glob\": {\n      const pattern = stringField(input, \"pattern\") ?? \"?\";\n      return `glob ${pattern}`;\n    }\n    case \"Grep\": {\n      const pattern = stringField(input, \"pattern\") ?? \"?\";\n      return `grep ${pattern}`;\n    }\n    case \"Bash\": {\n      const command = stringField(input, \"command\") ?? \"?\";\n      // Truncate long commands so one tool-use stays one line.\n      const trimmed =\n        command.length > 80 ? `${command.slice(0, 77)}...` : command;\n      return `bash ${trimmed}`;\n    }\n    default: {\n      // Unknown or MCP tool. Show the name; omit the input to avoid\n      // spamming the terminal with arbitrary JSON.\n      return name;\n    }\n  }\n}\n\nfunction stringField(\n  input: Record<string, unknown>,\n  key: string,\n): string | undefined {\n  const value = input[key];\n  return typeof value === \"string\" ? value : undefined;\n}\n","import { spawn, type ChildProcess } from \"node:child_process\";\nimport { createRequire } from \"node:module\";\nimport { dirname, join } from \"node:path\";\n\n/**\n * Claude auth gate — accepts either an active Claude subscription login\n * OR an `ANTHROPIC_API_KEY` environment variable.\n *\n * The Claude Agent SDK delegates authentication to its bundled `cli.js`,\n * which reads OAuth credentials from `~/.claude/credentials/` (the same\n * store Claude Code uses). Users who are logged in via `claude auth login\n * --claudeai` should be able to run bootstrap/capture without ever\n * exporting an API key. Conversely, users on pay-per-token API keys\n * shouldn't be required to go through the OAuth flow.\n *\n * We spawn the bundled SDK's `cli.js auth status --json` to answer \"are\n * we logged in?\" rather than poking at the credentials file directly —\n * that's the SDK's contract, and it handles all the edge cases (token\n * expiry, org switching, consoleloginpath, …) for us.\n *\n * The CLI path is resolved via `require.resolve(\"@anthropic-ai/claude-\n * agent-sdk/package.json\")` + the `cli.js` sibling. Going through\n * `createRequire` keeps this compatible with both ESM dev mode (tsx) and\n * the bundled dist (tsup externalizes the SDK, so Node's own resolver\n * does the lookup at runtime). If the SDK isn't installed at all we fall\n * back to treating the user as unauthenticated — the assert will then\n * surface the familiar two-path error so they can at least fix it via\n * `ANTHROPIC_API_KEY`.\n */\n\nexport interface ClaudeAuthStatus {\n  loggedIn: boolean;\n  email?: string;\n  subscriptionType?: string;\n  authMethod?: string;\n}\n\nexport interface SpawnedProcess {\n  stdout: { on: (event: \"data\", cb: (data: Buffer | string) => void) => void };\n  stderr: { on: (event: \"data\", cb: (data: Buffer | string) => void) => void };\n  on: (event: \"close\" | \"error\", cb: (arg: number | null | Error) => void) => void;\n  kill: (signal?: string) => void;\n}\n\n/**\n * The subprocess spawner is injectable so tests can replace it with a\n * fake that emits canned JSON without touching the filesystem. Production\n * code uses `defaultSpawnCli` which invokes the bundled SDK CLI.\n */\nexport type SpawnCliFn = (args: string[]) => SpawnedProcess;\n\nconst AUTH_TIMEOUT_MS = 10_000;\n\n/**\n * Resolve `cli.js` from the bundled `@anthropic-ai/claude-agent-sdk`\n * install. Uses `createRequire` so the lookup works regardless of\n * whether we're running from `dist/` (where tsup externalized the SDK)\n * or directly from source.\n *\n * Throws if the SDK can't be located — `checkClaudeAuth` catches this\n * and treats the user as not-logged-in, which lets the env-var path\n * still work for users with a borked install.\n */\nfunction resolveCliJsPath(): string {\n  // `import.meta.url` points at this module (dev or dist). `createRequire`\n  // from that URL can then resolve sibling packages the same way Node's\n  // own CJS resolver would.\n  const require = createRequire(import.meta.url);\n  const pkgJsonPath = require.resolve(\n    \"@anthropic-ai/claude-agent-sdk/package.json\",\n  );\n  return join(dirname(pkgJsonPath), \"cli.js\");\n}\n\n/**\n * Default subprocess spawner for production use — invokes the bundled\n * SDK's `cli.js` via the same Node runtime that's running codealmanac.\n * Tests inject a fake via the `spawnCli` parameter.\n */\nexport const defaultSpawnCli: SpawnCliFn = (args: string[]) => {\n  const cliPath = resolveCliJsPath();\n  // Use `process.execPath` so we inherit the Node runtime codealmanac\n  // itself is running under — avoids PATH weirdness on systems where\n  // `node` isn't on PATH but codealmanac was installed via npm.\n  const child = spawn(process.execPath, [cliPath, ...args], {\n    stdio: [\"ignore\", \"pipe\", \"pipe\"],\n  });\n  return child as unknown as SpawnedProcess;\n};\n\n/**\n * Check whether the user is authenticated via Claude subscription OAuth.\n *\n * Spawns the bundled SDK CLI's `auth status --json`. On any failure\n * (spawn error, non-JSON stdout, non-zero exit, timeout) we return\n * `{ loggedIn: false }` rather than propagating the error — the caller\n * will fall back to the `ANTHROPIC_API_KEY` path and, if that's also\n * missing, produce a clean two-option error message.\n *\n * The 10s timeout guards against the CLI hanging on a broken network or\n * keychain prompt. In practice `auth status` is a cheap local read.\n */\nexport async function checkClaudeAuth(\n  spawnCli: SpawnCliFn = defaultSpawnCli,\n): Promise<ClaudeAuthStatus> {\n  let child: SpawnedProcess;\n  try {\n    child = spawnCli([\"auth\", \"status\", \"--json\"]);\n  } catch {\n    return { loggedIn: false };\n  }\n\n  return new Promise<ClaudeAuthStatus>((resolve) => {\n    let stdout = \"\";\n    let stderr = \"\";\n    let settled = false;\n\n    const settle = (value: ClaudeAuthStatus): void => {\n      if (settled) return;\n      settled = true;\n      clearTimeout(timer);\n      resolve(value);\n    };\n\n    const timer = setTimeout(() => {\n      try {\n        child.kill(\"SIGTERM\");\n      } catch {\n        // Kill can fail if the process already exited; nothing we can do.\n      }\n      settle({ loggedIn: false });\n    }, AUTH_TIMEOUT_MS);\n\n    child.stdout.on(\"data\", (data) => {\n      stdout += data.toString();\n    });\n    child.stderr.on(\"data\", (data) => {\n      stderr += data.toString();\n    });\n\n    child.on(\"error\", () => {\n      settle({ loggedIn: false });\n    });\n\n    child.on(\"close\", (code) => {\n      // The SDK writes `{\"loggedIn\": false, ...}` to stdout with a zero\n      // exit code when the user isn't signed in, so we only reject on\n      // non-zero + empty stdout. An empty stdout with zero exit (shouldn't\n      // happen in practice) also fails safely to `loggedIn: false`.\n      if (code !== 0 && stdout.trim().length === 0) {\n        // `stderr` isn't surfaced to the user here — the caller's error\n        // message covers both auth paths — but it would be captured by\n        // `stderr` if we ever wanted to log it for debugging.\n        void stderr;\n        settle({ loggedIn: false });\n        return;\n      }\n      try {\n        const parsed = JSON.parse(stdout.trim()) as Record<string, unknown>;\n        const loggedIn = parsed.loggedIn === true;\n        const out: ClaudeAuthStatus = { loggedIn };\n        if (typeof parsed.email === \"string\") out.email = parsed.email;\n        if (typeof parsed.subscriptionType === \"string\") {\n          out.subscriptionType = parsed.subscriptionType;\n        }\n        if (typeof parsed.authMethod === \"string\") {\n          out.authMethod = parsed.authMethod;\n        }\n        settle(out);\n      } catch {\n        settle({ loggedIn: false });\n      }\n    });\n  });\n}\n\n/**\n * Human-readable error when neither auth path is available. The text is\n * deliberately verbose — users hitting this wall for the first time\n * deserve both options in front of them, not a terse hint.\n */\nexport const UNAUTHENTICATED_MESSAGE =\n  \"not authenticated to Claude.\\n\\n\" +\n  \"Option 1 — use your Claude subscription (Pro/Max):\\n\" +\n  \"  claude auth login --claudeai\\n\\n\" +\n  \"Option 2 — use a pay-per-token API key:\\n\" +\n  \"  Get one at https://console.anthropic.com\\n\" +\n  \"  export ANTHROPIC_API_KEY=sk-ant-...\\n\\n\" +\n  \"Verify with: claude auth status\";\n\n/**\n * Assert that at least one auth path is satisfied. Prefers subscription\n * auth (fewer surprises for Claude Pro/Max users) but accepts\n * `ANTHROPIC_API_KEY` as a fallback. On failure throws with\n * `code = \"CLAUDE_AUTH_MISSING\"` so callers can distinguish this from\n * other errors if they ever want to.\n *\n * Returns the resolved auth status so callers that want to display the\n * logged-in email in a preamble can do so without a second subprocess.\n */\nexport async function assertClaudeAuth(\n  spawnCli: SpawnCliFn = defaultSpawnCli,\n): Promise<ClaudeAuthStatus> {\n  const status = await checkClaudeAuth(spawnCli);\n  if (status.loggedIn) {\n    return status;\n  }\n  const apiKey = process.env.ANTHROPIC_API_KEY;\n  if (apiKey !== undefined && apiKey.length > 0) {\n    // Signal to callers that we're on the API-key path. Not \"loggedIn\"\n    // in the OAuth sense, but the SDK will pick up the env var and\n    // succeed — so we return a status that tells bootstrap/capture the\n    // gate is open.\n    return { loggedIn: true, authMethod: \"apiKey\" };\n  }\n  const err = new Error(UNAUTHENTICATED_MESSAGE);\n  (err as { code?: string }).code = \"CLAUDE_AUTH_MISSING\";\n  throw err;\n}\n\n// Internal re-export — helps keep the public type surface minimal while\n// still letting tests import the `ChildProcess` shape when needed.\nexport type { ChildProcess };\n","import { existsSync } from \"node:fs\";\nimport { readFile } from \"node:fs/promises\";\nimport path from \"node:path\";\nimport { fileURLToPath } from \"node:url\";\n\n/**\n * Loads bundled prompt text from the `prompts/` directory that ships with\n * the npm package. Used by `almanac bootstrap` (slice 4) and `almanac\n * capture` (slice 5).\n *\n * ## Why not embed the prompts as TS string literals?\n *\n * The non-negotiable from the spec (see CLAUDE.md → \"Non-negotiables\"):\n * \"Prompts are shipped from the npm package. They live in `prompts/` at\n * repo root, are bundled into `files` in `package.json`, and the agent\n * harness reads them from the package install path at runtime.\"\n *\n * Keeping them as separate files means they can be reviewed as prose,\n * diffed meaningfully, and (in the future) edited by users without\n * rebuilding the package.\n *\n * ## Path resolution\n *\n * Two runtime layouts need to work:\n *\n *   1. **Installed (`npm i -g codealmanac`).** The entry point lives at\n *      `dist/codealmanac.js`; prompts at `prompts/*.md`. Walking up from\n *      `import.meta.url` (`.../<pkg>/dist/codealmanac.js`) one level and\n *      into `prompts/` hits the right directory.\n *\n *   2. **Source dev.** During `npm run dev`, tsup emits to `dist/` just\n *      like in production, so case 1 applies. Tests import\n *      `src/agent/prompts.ts` directly via tsx/vitest; `import.meta.url`\n *      points at `src/agent/prompts.ts`. Walking up two levels from there\n *      lands at the repo root, where `prompts/` also lives.\n *\n * We probe a small list of candidates in order and use the first that\n * contains all three expected prompt files. This keeps a single source of\n * truth — the `prompts/` directory on disk — without baking in whether\n * we're running from `dist/` or `src/`.\n */\n\nexport type PromptName = \"bootstrap\" | \"writer\" | \"reviewer\";\n\nconst PROMPT_NAMES: readonly PromptName[] = [\n  \"bootstrap\",\n  \"writer\",\n  \"reviewer\",\n];\n\n/**\n * Override the prompts directory, for tests. Production code should never\n * call this — the auto-resolution handles both installed + source layouts.\n */\nlet overrideDir: string | null = null;\n\nexport function setPromptsDirForTesting(dir: string | null): void {\n  overrideDir = dir;\n}\n\n/**\n * Resolve the prompts directory by probing candidate locations. Cached\n * after the first call so repeated `loadPrompt()` calls don't stat the\n * filesystem more than once per process.\n */\nlet resolvedDir: string | null = null;\n\nexport function resolvePromptsDir(): string {\n  if (overrideDir !== null) return overrideDir;\n  if (resolvedDir !== null) return resolvedDir;\n\n  const here = path.dirname(fileURLToPath(import.meta.url));\n\n  // Candidates, most-specific first. Each path is where `prompts/` MIGHT\n  // live given some plausible bundle layout. The first one that exists\n  // and contains our three expected files wins.\n  const candidates = [\n    // Bundled dist layout: `.../<pkg>/dist/codealmanac.js` → `../prompts`\n    path.resolve(here, \"..\", \"prompts\"),\n    // Source layout: `.../<pkg>/src/agent/prompts.ts` → `../../prompts`\n    path.resolve(here, \"..\", \"..\", \"prompts\"),\n    // Defensive fallback: if tsup someday emits a nested `dist/src/agent`,\n    // walk up three levels.\n    path.resolve(here, \"..\", \"..\", \"..\", \"prompts\"),\n  ];\n\n  for (const dir of candidates) {\n    if (isPromptsDir(dir)) {\n      resolvedDir = dir;\n      return dir;\n    }\n  }\n\n  // If none matched, give a helpful error with the candidates we tried.\n  // This typically means the package was installed without the `prompts/`\n  // dir included — shouldn't happen unless someone broke `files` in\n  // package.json.\n  throw new Error(\n    \"could not locate bundled prompts/ directory. Tried:\\n\" +\n      candidates.map((c) => `  - ${c}`).join(\"\\n\"),\n  );\n}\n\nfunction isPromptsDir(dir: string): boolean {\n  if (!existsSync(dir)) return false;\n  // Require all three prompts to be present. A half-populated directory\n  // is worse than not finding one — we'd rather error early.\n  return PROMPT_NAMES.every((name) =>\n    existsSync(path.join(dir, `${name}.md`)),\n  );\n}\n\nexport async function loadPrompt(name: PromptName): Promise<string> {\n  const dir = resolvePromptsDir();\n  return readFile(path.join(dir, `${name}.md`), \"utf8\");\n}\n","import { query } from \"@anthropic-ai/claude-agent-sdk\";\nimport type {\n  AgentDefinition,\n  SDKMessage,\n} from \"@anthropic-ai/claude-agent-sdk\";\n\n/**\n * Thin wrapper around `@anthropic-ai/claude-agent-sdk`'s `query()`. This is\n * the ONLY module that imports from the SDK — every other command imports\n * from here. Slice 5 (capture) reuses this wrapper unchanged.\n *\n * Why a wrapper at all:\n *   1. Sets defaults (`maxTurns`, `includePartialMessages`, model) once so\n *      commands stay small.\n *   2. Translates the SDK's rich message types into a {cost, turns, result}\n *      summary the commands actually care about.\n *\n * The auth gate lives in `src/agent/auth.ts`. Commands call\n * `assertClaudeAuth()` BEFORE `runAgent` so we fail with a clean two-path\n * error before the SDK generator spins up. `runAgent` itself doesn't\n * re-check — the SDK reads whichever of (subscription OAuth,\n * `ANTHROPIC_API_KEY`) is present.\n *\n * Keep this module SMALL. If a feature can live in the caller, it should.\n */\n\nexport interface RunAgentOptions {\n  /** Full system prompt text — usually loaded from `prompts/*.md`. */\n  systemPrompt: string;\n  /** User prompt / kick-off message. */\n  prompt: string;\n  /** Tool allowlist, e.g. `[\"Read\", \"Write\", \"Edit\", \"Glob\", \"Grep\", \"Bash\"]`. */\n  allowedTools: string[];\n  /**\n   * Subagent definitions (slice 5 passes `{ reviewer: ... }`). Defaults to\n   * `{}` — bootstrap has no subagents.\n   */\n  agents?: Record<string, AgentDefinition>;\n  /** Working directory the agent's tools operate in (repo root). */\n  cwd: string;\n  /**\n   * Model override. Defaults to `claude-sonnet-4-6`. Note the FULL form —\n   * `options.model` requires `claude-sonnet-4-6`, not `sonnet`.\n   */\n  model?: string;\n  /**\n   * Hard cap on turns. Defaults to 100. SDK enforces this as a strict stop\n   * (no graceful wrap-up turn), so set generously.\n   */\n  maxTurns?: number;\n  /**\n   * Observer called for every SDK message. The formatter (streaming\n   * output, transcript log) runs here.\n   */\n  onMessage?: (msg: SDKMessage) => void;\n}\n\nexport interface AgentResult {\n  /** `true` when the SDK emitted a `result` with `subtype: \"success\"`. */\n  success: boolean;\n  /** Total USD cost reported by the final `result` message. */\n  cost: number;\n  /** Number of turns the agent used. */\n  turns: number;\n  /** The assistant's final textual result, if any. */\n  result: string;\n  /** Session ID captured from the first assistant/result message. */\n  sessionId?: string;\n  /** Populated when `success === false`. */\n  error?: string;\n}\n\n/**\n * Run an agent to completion. Iterates the SDK's `AsyncGenerator` and\n * returns a summary. Any thrown error in the `for await` becomes a\n * `success: false` result with the error message attached — we don't\n * propagate because the caller wants to write transcripts + print\n * formatted output regardless of outcome.\n *\n * The caller is responsible for running `assertClaudeAuth()` BEFORE\n * loading prompts or printing progress — see `bootstrap.ts`/`capture.ts`.\n * `runAgent` itself no longer re-checks; the SDK will happily pick up\n * whichever of (subscription OAuth, `ANTHROPIC_API_KEY`) the environment\n * provides.\n */\nexport async function runAgent(opts: RunAgentOptions): Promise<AgentResult> {\n\n  const q = query({\n    prompt: opts.prompt,\n    options: {\n      systemPrompt: opts.systemPrompt,\n      allowedTools: opts.allowedTools,\n      agents: opts.agents ?? {},\n      cwd: opts.cwd,\n      model: opts.model ?? \"claude-sonnet-4-6\",\n      maxTurns: opts.maxTurns ?? 100,\n      // REQUIRED for streaming text deltas. Without it, `stream_event`\n      // messages never fire and the CLI has no progress visibility during\n      // long turns. See docs/research/agent-sdk.md §12 pitfall #1.\n      includePartialMessages: true,\n    },\n  });\n\n  let cost = 0;\n  let turns = 0;\n  let result = \"\";\n  let sessionId: string | undefined;\n  let success = false;\n  let errorMsg: string | undefined;\n\n  try {\n    for await (const msg of q) {\n      opts.onMessage?.(msg);\n\n      // Capture session_id from the first message that carries it.\n      // Per the research doc, it appears on the first `assistant` or on\n      // the `result` — whichever arrives first.\n      if (\n        sessionId === undefined &&\n        typeof (msg as { session_id?: unknown }).session_id === \"string\"\n      ) {\n        sessionId = (msg as { session_id: string }).session_id;\n      }\n\n      if (msg.type === \"result\") {\n        // `SDKResultMessage = SDKResultSuccess | SDKResultError`. Both\n        // carry `total_cost_usd` and `num_turns`; only success has\n        // `result` (the final assistant text).\n        cost = msg.total_cost_usd;\n        turns = msg.num_turns;\n        if (msg.subtype === \"success\") {\n          success = true;\n          result = msg.result;\n        } else {\n          success = false;\n          errorMsg =\n            // `SDKResultError` variants don't carry a `result` string; the\n            // useful detail lives in `errors` (array of strings) or the\n            // subtype itself (e.g. \"error_max_turns\").\n            (msg.errors?.join(\"; \") ?? \"\") || `agent error: ${msg.subtype}`;\n        }\n      }\n    }\n  } catch (err: unknown) {\n    errorMsg = err instanceof Error ? err.message : String(err);\n    success = false;\n  }\n\n  return { success, cost, turns, result, sessionId, error: errorMsg };\n}\n","import { existsSync } from \"node:fs\";\nimport { homedir } from \"node:os\";\nimport { dirname, isAbsolute, join, resolve } from \"node:path\";\n\n/**\n * Absolute path to the user-level `~/.almanac/` directory.\n *\n * All global state (the registry, future global config) lives here, not in\n * the repo. We resolve this via `os.homedir()` rather than `$HOME` so the\n * CLI behaves the same on macOS, Linux, and Windows.\n */\nexport function getGlobalAlmanacDir(): string {\n  return join(homedir(), \".almanac\");\n}\n\n/**\n * Absolute path to the global registry file.\n *\n * The registry is the single source of truth for \"which wikis exist on this\n * machine.\" It is intentionally stored outside any repo so it survives\n * branch switches, clones, and repo deletions.\n */\nexport function getRegistryPath(): string {\n  return join(getGlobalAlmanacDir(), \"registry.json\");\n}\n\n/**\n * Repo-level `.almanac/` path for a given working directory (not resolved —\n * just `join(cwd, \".almanac\")`). Use `findNearestAlmanacDir` when you need\n * to walk upward like git does.\n */\nexport function getRepoAlmanacDir(cwd: string): string {\n  return join(cwd, \".almanac\");\n}\n\n/**\n * Walk upward from `startDir` looking for a directory that contains\n * `.almanac/`. Returns the absolute path to the repo root (the directory\n * containing `.almanac/`), or `null` if none is found before hitting the\n * filesystem root.\n *\n * Mirrors how `git` locates the enclosing repository. This lets `almanac`\n * work from any subdirectory inside a repo, not just the root.\n *\n * We explicitly skip the global `~/.almanac/` directory. It shares the\n * `.almanac` name with the per-repo wiki dir, but it's not a wiki — it\n * only holds the registry and global state. If the user runs `almanac\n * init` anywhere inside their home directory (outside a real wiki), we\n * must NOT treat `~` as an enclosing wiki root. Otherwise init would try\n * to register the home dir itself as a wiki.\n */\nexport function findNearestAlmanacDir(startDir: string): string | null {\n  const globalDir = getGlobalAlmanacDir();\n  let current = isAbsolute(startDir) ? startDir : resolve(startDir);\n\n  // Walk until we hit the filesystem root. `dirname(\"/\")` returns `\"/\"`,\n  // so the loop terminates when we stop ascending.\n  while (true) {\n    const candidate = join(current, \".almanac\");\n    if (candidate !== globalDir && existsSync(candidate)) {\n      return current;\n    }\n    const parent = dirname(current);\n    if (parent === current) {\n      return null;\n    }\n    current = parent;\n  }\n}\n","import { existsSync } from \"node:fs\";\nimport { mkdir, readFile, writeFile } from \"node:fs/promises\";\nimport { basename, join } from \"node:path\";\n\nimport { findNearestAlmanacDir, getRepoAlmanacDir } from \"../paths.js\";\nimport { toKebabCase } from \"../slug.js\";\nimport {\n  addEntry,\n  ensureGlobalDir,\n  type RegistryEntry,\n} from \"../registry/index.js\";\n\nexport interface InitOptions {\n  cwd: string;\n  name?: string;\n  description?: string;\n}\n\nexport interface InitResult {\n  entry: RegistryEntry;\n  almanacDir: string;\n  created: boolean; // false if .almanac/ already existed (idempotent re-init)\n}\n\n/**\n * Scaffold `.almanac/` in the repo and register it globally.\n *\n * Idempotent: running `init` on a repo that already has `.almanac/` is\n * fine — we re-register (refreshing the name/description) and skip\n * anything that already exists. We never overwrite a user-authored\n * `README.md` or touch existing pages.\n *\n * If `cwd` lives inside a subdirectory of an existing wiki, we walk up to\n * the wiki root and operate there. `almanac init` from `src/nested/`\n * should update the enclosing wiki, not create a nested one at\n * `src/nested/.almanac/` (which would fragment the registry and leave a\n * confusing orphan `.almanac/` on disk).\n */\nexport async function initWiki(options: InitOptions): Promise<InitResult> {\n  // If cwd is already inside a wiki, prefer that root. Otherwise treat\n  // cwd as the new wiki root.\n  const repoRoot = findNearestAlmanacDir(options.cwd) ?? options.cwd;\n\n  const almanacDir = getRepoAlmanacDir(repoRoot);\n  const pagesDir = join(almanacDir, \"pages\");\n  const readmePath = join(almanacDir, \"README.md\");\n\n  const alreadyExisted = existsSync(almanacDir);\n\n  await mkdir(pagesDir, { recursive: true });\n\n  if (!existsSync(readmePath)) {\n    await writeFile(readmePath, starterReadme(), \"utf8\");\n  }\n\n  await ensureGitignoreHasIndexDb(repoRoot);\n\n  const name = toKebabCase(options.name ?? basename(repoRoot));\n  if (name.length === 0) {\n    throw new Error(\n      \"could not derive a wiki name from the current directory; pass --name\",\n    );\n  }\n\n  const description = (options.description ?? \"\").trim();\n\n  await ensureGlobalDir();\n  const entry: RegistryEntry = {\n    name,\n    description,\n    path: repoRoot,\n    registered_at: new Date().toISOString(),\n  };\n  await addEntry(entry);\n\n  return { entry, almanacDir, created: !alreadyExisted };\n}\n\n/**\n * Ensure `.gitignore` in the repo root contains the codealmanac-derived\n * files that should never be committed.\n *\n * We ignore three paths:\n *   - `.almanac/index.db`        — the SQLite index (derived)\n *   - `.almanac/index.db-wal`    — WAL mode sidecar (present during writes)\n *   - `.almanac/index.db-shm`    — shared-memory sidecar (WAL mode)\n *\n * All three are derived from the markdown pages. The sidecars only show\n * up while better-sqlite3 has the DB open and can vanish between `git\n * status` calls, but explicitly ignoring them prevents \"dirty worktree\"\n * noise during active reindexing.\n *\n * We add the block regardless of whether the file exists (creating\n * `.gitignore` if needed), and we add any target lines that aren't\n * already present. Existing targets are left alone. If none of the\n * target lines need adding, the file is not touched at all.\n *\n * Formatting: when we do append, we guarantee exactly one blank line\n * between the prior content and our appended block. If the `# codealmanac`\n * header is already present but new targets need adding, we just append\n * the missing lines (no duplicate header).\n */\nasync function ensureGitignoreHasIndexDb(cwd: string): Promise<void> {\n  const path = join(cwd, \".gitignore\");\n  const targets = [\n    \".almanac/index.db\",\n    \".almanac/index.db-wal\",\n    \".almanac/index.db-shm\",\n  ];\n\n  let existing = \"\";\n  if (existsSync(path)) {\n    existing = await readFile(path, \"utf8\");\n  }\n\n  // Normalize to line comparison to avoid false negatives on trailing\n  // whitespace or CRLF line endings.\n  const lines = existing.split(/\\r?\\n/).map((l) => l.trim());\n  const missing = targets.filter((t) => !lines.includes(t));\n  if (missing.length === 0) return;\n\n  const hasHeader = lines.includes(\"# codealmanac\");\n  const block = hasHeader\n    ? missing.join(\"\\n\") + \"\\n\"\n    : `# codealmanac\\n${missing.join(\"\\n\")}\\n`;\n\n  // Three cases for the separator before the appended block:\n  //  - empty file: no separator needed\n  //  - ends with newline: one more newline produces a single blank line\n  //  - no trailing newline: two newlines (one to terminate the last line,\n  //    one for the blank separator)\n  const sep =\n    existing.length === 0 ? \"\" : existing.endsWith(\"\\n\") ? \"\\n\" : \"\\n\\n\";\n  await writeFile(path, `${existing}${sep}${block}`, \"utf8\");\n}\n\n/**\n * The starter `.almanac/README.md` content. Based on the \"Wiki README\" and\n * \"Notability bar\" sections of the design spec. Kept opinionated but short\n * (~70 lines) — the user is expected to edit it to fit the repo.\n */\nfunction starterReadme(): string {\n  return `# Wiki\n\nThis is the codealmanac wiki for this repository. It captures the knowledge\nthe code itself can't say — decisions, flows, invariants, gotchas, incidents.\n\nThe primary reader is an AI coding agent. The secondary reader is a human\nskimming to understand the shape of the codebase. Write accordingly: dense,\nfactual, linked.\n\n## Notability bar\n\nWrite a page when there is **non-obvious knowledge that will help a future\nagent**. Specifically:\n\n- A decision that took discussion, research, or trial-and-error\n- A gotcha discovered through failure\n- A cross-cutting flow that spans multiple files and isn't obvious from any\n  one of them\n- A constraint or invariant not visible from the code\n- An entity (technology, service, system) referenced by multiple pages\n\nDo not write pages that restate what the code does. Do not write pages of\ninference — only of observation. Silence is an acceptable outcome.\n\n## Topic taxonomy\n\nTopics form a DAG; pages can belong to multiple topics. Start with these and\ngrow as the wiki does:\n\n- \\`stack\\` — technologies and services we use (frameworks, databases, APIs)\n- \\`systems\\` — custom systems we built (auth, billing, search)\n- \\`flows\\` — multi-file processes end-to-end (checkout-flow, publish-flow)\n- \\`decisions\\` — \"why X over Y\"\n- \\`incidents\\` — recorded failures and their fixes\n- \\`concepts\\` — shared vocabulary specific to this codebase\n\nDomain topics (\\`auth\\`, \\`payments\\`, \\`frontend\\`, \\`backend\\`) live alongside\nthese. A page about JWT rotation belongs to both \\`auth\\` and \\`decisions\\`.\n\n## Page shapes\n\nFour shapes cover most of what gets written. They are suggestions, not a\nschema — a page that fits none of them is fine.\n\n- **Entity** — a stable named thing (Supabase, Stripe, the search service)\n- **Decision** — why we chose X over Y\n- **Flow** — how a multi-file process works end-to-end\n- **Gotcha** — a specific surprise, failure, or constraint\n\n## Writing conventions\n\n- Every sentence contains a specific fact. If it doesn't, cut it.\n- Neutral tone. \"is\", not \"serves as\". No \"plays a pivotal role\", no\n  interpretive \"-ing\" clauses, no vague attribution (\"experts argue\").\n- No hedging or knowledge-gap disclaimers. If you don't know, don't write\n  the sentence.\n- Prose first. Bullets for genuine lists. Tables only for structured\n  comparison.\n- No formulaic conclusions. End with the last substantive fact.\n\n## Linking\n\nOne \\`[[...]]\\` syntax for everything, disambiguated by content:\n\n- \\`[[checkout-flow]]\\` — page slug\n- \\`[[src/checkout/handler.ts]]\\` — file reference\n- \\`[[src/checkout/]]\\` — folder reference (trailing slash)\n- \\`[[other-wiki:slug]]\\` — cross-wiki reference\n\nEvery page should link to at least one entity when possible. A page with no\nentity link is suspect.\n\n## Pages live in \\`.almanac/pages/\\`\n\nOne markdown file per page, kebab-case slug. Frontmatter carries \\`topics:\\`\nand optional \\`files:\\`. The rest is prose.\n`;\n}\n","/**\n * Canonical kebab-case slugifier used across the codebase.\n *\n * One function, three callers:\n *   - `registry/index.ts` — wiki name slugs (both auto-derived and\n *     user-supplied via `--name`)\n *   - `indexer/index.ts` — page filename → slug and topic → slug\n *   - `indexer/wikilinks.ts` — wikilink target → slug for resolution\n *\n * All three want the same behavior: lowercased, non-alphanumeric runs\n * collapse to a single hyphen, leading/trailing hyphens trimmed. Keeping\n * this in one place avoids a class of bug where an unusual input (e.g.\n * `Checkout_Flow`) produces different slugs depending on which layer\n * slugified it.\n *\n * Rules:\n *   - Lowercase\n *   - Non-alphanumeric runs collapse to a single hyphen\n *   - Leading/trailing hyphens trimmed\n */\nexport function toKebabCase(input: string): string {\n  return input\n    .toLowerCase()\n    .replace(/[^a-z0-9]+/g, \"-\")\n    .replace(/^-+|-+$/g, \"\");\n}\n","import { mkdir, readFile, rename, writeFile } from \"node:fs/promises\";\nimport { dirname } from \"node:path\";\n\nimport { getGlobalAlmanacDir, getRegistryPath } from \"../paths.js\";\nimport { toKebabCase } from \"../slug.js\";\n\n// Re-export so existing import sites (`from \"../registry/index.js\"`) keep\n// working without a mechanical fan-out. The canonical home is `../slug.js`.\nexport { toKebabCase };\n\n/**\n * One entry in `~/.almanac/registry.json`.\n *\n * `name` is the canonical kebab-case slug the user types. `path` is the\n * absolute repo root (the directory that contains `.almanac/`). We store\n * absolute paths so cross-wiki resolution works regardless of the caller's\n * cwd.\n */\nexport interface RegistryEntry {\n  name: string;\n  description: string;\n  path: string;\n  registered_at: string;\n}\n\n/**\n * Read the registry file into memory.\n *\n * A missing file is not an error — it's the first-run state, which we\n * treat as an empty registry. A malformed file IS an error; we surface it\n * rather than silently clobbering the user's data.\n */\nexport async function readRegistry(): Promise<RegistryEntry[]> {\n  const path = getRegistryPath();\n  let raw: string;\n  try {\n    raw = await readFile(path, \"utf8\");\n  } catch (err: unknown) {\n    if (isNodeError(err) && err.code === \"ENOENT\") {\n      return [];\n    }\n    throw err;\n  }\n\n  const trimmed = raw.trim();\n  if (trimmed.length === 0) {\n    return [];\n  }\n\n  let parsed: unknown;\n  try {\n    parsed = JSON.parse(trimmed);\n  } catch (err: unknown) {\n    const message = err instanceof Error ? err.message : String(err);\n    throw new Error(`registry at ${path} is not valid JSON: ${message}`);\n  }\n\n  if (!Array.isArray(parsed)) {\n    throw new Error(`registry at ${path} must be a JSON array`);\n  }\n\n  // Validate every entry. We do NOT silently coerce missing `name` or\n  // `path` — an entry with `name: \"\"` would be unremovable via `--drop`\n  // and an empty `path` would match any `findEntry({ path: \"\" })` call.\n  // If someone hand-edited the registry into a bad state, surfacing the\n  // error is strictly better than limping along with corrupt data.\n  return parsed.map((item, idx) => {\n    if (typeof item !== \"object\" || item === null) {\n      throw new Error(`registry entry ${idx} is not an object`);\n    }\n    const e = item as Record<string, unknown>;\n    const name = typeof e.name === \"string\" ? e.name : \"\";\n    const path = typeof e.path === \"string\" ? e.path : \"\";\n    if (name.length === 0) {\n      throw new Error(`registry entry ${idx} is missing a non-empty \"name\"`);\n    }\n    if (path.length === 0) {\n      throw new Error(`registry entry ${idx} is missing a non-empty \"path\"`);\n    }\n    return {\n      name,\n      description: typeof e.description === \"string\" ? e.description : \"\",\n      path,\n      registered_at:\n        typeof e.registered_at === \"string\" ? e.registered_at : \"\",\n    };\n  });\n}\n\n/**\n * Persist the registry to disk. Creates `~/.almanac/` if it doesn't exist.\n *\n * We write with a trailing newline and 2-space indentation so the file is\n * diff-friendly if someone ever commits or inspects it manually.\n *\n * The write is atomic: we write to `registry.json.tmp` and then rename,\n * which is an atomic operation on every mainstream filesystem. This\n * matters because two concurrent `almanac init` (or autoregister) calls\n * from different shells would otherwise race on a partial write and\n * corrupt the file — a single `rename` means one wins cleanly and the\n * other's contents are simply dropped.\n */\nexport async function writeRegistry(entries: RegistryEntry[]): Promise<void> {\n  const path = getRegistryPath();\n  await mkdir(dirname(path), { recursive: true });\n  const body = `${JSON.stringify(entries, null, 2)}\\n`;\n  const tmpPath = `${path}.tmp`;\n  await writeFile(tmpPath, body, \"utf8\");\n  await rename(tmpPath, path);\n}\n\n/**\n * macOS (HFS+/APFS default) and Windows (NTFS default) are case-insensitive\n * but case-preserving. `/Users/x/Project` and `/Users/x/project` are the\n * same directory. We must treat them as the same registry entry, or a\n * single `almanac init` from a differently-cased cwd would duplicate the\n * row. Linux is case-sensitive — do not normalize there.\n *\n * Callers still store the original casing; only comparisons are lowercased.\n */\nfunction pathsEqual(a: string, b: string): boolean {\n  if (process.platform === \"darwin\" || process.platform === \"win32\") {\n    return a.toLowerCase() === b.toLowerCase();\n  }\n  return a === b;\n}\n\n/**\n * Add (or replace) an entry in the registry.\n *\n * Uniqueness is enforced on BOTH `name` and `path`: a repo can only appear\n * once, and a name can only refer to one repo. If either matches, we\n * replace the existing entry rather than creating a duplicate. This is\n * what makes auto-registration idempotent.\n */\nexport async function addEntry(entry: RegistryEntry): Promise<RegistryEntry[]> {\n  const existing = await readRegistry();\n  const filtered = existing.filter(\n    (e) => e.name !== entry.name && !pathsEqual(e.path, entry.path),\n  );\n  filtered.push(entry);\n  await writeRegistry(filtered);\n  return filtered;\n}\n\n/**\n * Remove an entry by name. Returns the removed entry (or `null` if none\n * matched). Only `almanac list --drop <name>` calls this — we never drop\n * automatically, even for unreachable paths.\n */\nexport async function dropEntry(name: string): Promise<RegistryEntry | null> {\n  const existing = await readRegistry();\n  const idx = existing.findIndex((e) => e.name === name);\n  if (idx === -1) {\n    return null;\n  }\n  const [removed] = existing.splice(idx, 1);\n  await writeRegistry(existing);\n  return removed ?? null;\n}\n\n/**\n * Find an entry by either name or absolute path. Used by auto-registration\n * to decide whether the current repo is already known.\n *\n * Path comparison is case-insensitive on macOS/Windows (see `pathsEqual`).\n */\nexport async function findEntry(params: {\n  name?: string;\n  path?: string;\n}): Promise<RegistryEntry | null> {\n  const entries = await readRegistry();\n  for (const entry of entries) {\n    if (params.name !== undefined && entry.name === params.name) return entry;\n    if (params.path !== undefined && pathsEqual(entry.path, params.path)) {\n      return entry;\n    }\n  }\n  return null;\n}\n\n/**\n * Ensure the global `.almanac/` directory exists. Safe to call repeatedly;\n * `mkdir recursive` is a no-op when the directory already exists.\n */\nexport async function ensureGlobalDir(): Promise<void> {\n  await mkdir(getGlobalAlmanacDir(), { recursive: true });\n}\n\nfunction isNodeError(err: unknown): err is NodeJS.ErrnoException {\n  return err instanceof Error && \"code\" in err;\n}\n","import { createHash } from \"node:crypto\";\nimport {\n  createWriteStream,\n  existsSync,\n  statSync,\n  type WriteStream,\n} from \"node:fs\";\nimport { readFile, readdir, stat } from \"node:fs/promises\";\nimport { homedir } from \"node:os\";\nimport { basename, join, relative } from \"node:path\";\n\nimport type { AgentDefinition, SDKMessage } from \"@anthropic-ai/claude-agent-sdk\";\n\nimport { assertClaudeAuth, type SpawnCliFn } from \"../agent/auth.js\";\nimport { loadPrompt } from \"../agent/prompts.js\";\nimport {\n  runAgent,\n  type AgentResult,\n  type RunAgentOptions,\n} from \"../agent/sdk.js\";\nimport { parseFrontmatter } from \"../indexer/frontmatter.js\";\nimport { findNearestAlmanacDir, getRepoAlmanacDir } from \"../paths.js\";\nimport { StreamingFormatter } from \"./bootstrap.js\";\n\nexport interface CaptureOptions {\n  cwd: string;\n  /** Explicit transcript path. Skips auto-resolution. */\n  transcriptPath?: string;\n  /** Target a specific session ID. */\n  sessionId?: string;\n  /** Suppress per-tool-use streaming; print only the final summary line. */\n  quiet?: boolean;\n  /** Model override. Defaults to the SDK default (sonnet-4-6). */\n  model?: string;\n  /** Injectable agent runner — tests replace this with a fake. */\n  runAgent?: (opts: RunAgentOptions) => Promise<AgentResult>;\n  /**\n   * Injectable spawner for the Claude auth-status subprocess. Tests pass\n   * a stub; production uses `defaultSpawnCli` which shells out to the\n   * bundled SDK's `cli.js`.\n   */\n  spawnCli?: SpawnCliFn;\n  /** Clock injection for deterministic log filenames in tests. */\n  now?: () => Date;\n  /**\n   * Override the Claude Code projects directory when auto-resolving a\n   * transcript. Production code leaves this undefined and we fall back to\n   * `~/.claude/projects`; tests point it at a fixture dir.\n   */\n  claudeProjectsDir?: string;\n}\n\nexport interface CaptureResult {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * Tools the writer agent is permitted to use.\n *\n *   - `Read` — read the session transcript, existing wiki pages, source files\n *   - `Write` / `Edit` — create and update pages under `.almanac/pages/`\n *   - `Glob` / `Grep` — navigate the wiki and source code\n *   - `Bash` — interrogate the wiki via `almanac search/show/info/list`\n *   - `Agent` — invoke the reviewer subagent\n *\n * `WebFetch`/`WebSearch` are intentionally absent: the writer should work\n * from the transcript + repo, not the open internet.\n */\nconst WRITER_TOOLS = [\"Read\", \"Write\", \"Edit\", \"Glob\", \"Grep\", \"Bash\", \"Agent\"];\n\n/**\n * Tools the reviewer subagent is permitted to use. The absence of\n * `Write`/`Edit`/`Agent` is the *only* thing preventing the reviewer from\n * editing files or chaining to further subagents — the SDK enforces this\n * based on the `tools` field in the `AgentDefinition`.\n */\nconst REVIEWER_TOOLS = [\"Read\", \"Grep\", \"Glob\", \"Bash\"];\n\nconst REVIEWER_DESCRIPTION =\n  \"Reviews proposed wiki changes against the full knowledge base for \" +\n  \"cohesion, duplication, missing links, notability, and writing conventions.\";\n\n/**\n * `almanac capture` — writer agent + reviewer subagent on a session transcript.\n *\n * Flow:\n *   1. Auth gate (ANTHROPIC_API_KEY).\n *   2. Resolve repo root (walk up for `.almanac/`). Refuse if none.\n *   3. Resolve transcript path (arg, --session, or auto-resolve from\n *      Claude Code's session storage).\n *   4. Snapshot `.almanac/pages/` BEFORE the agent runs so we can compute\n *      a created/updated/archived summary when it finishes.\n *   5. Load `prompts/writer.md` + `prompts/reviewer.md`. Build a reviewer\n *      `AgentDefinition` with read-only tools.\n *   6. Run the writer agent with the reviewer registered under `agents`.\n *   7. Stream tool-uses via the shared `StreamingFormatter` (unless --quiet).\n *   8. Diff the snapshot → emit `[done] N updated, M created, K archived …`.\n *\n * Empty outcomes (writer wrote nothing) exit 0 with a clear \"notability bar\"\n * message — per the writer prompt, silence is a valid output.\n */\nexport async function runCapture(\n  options: CaptureOptions,\n): Promise<CaptureResult> {\n  // Fail before any filesystem work. `assertClaudeAuth` accepts either\n  // subscription OAuth (via the bundled SDK CLI) or `ANTHROPIC_API_KEY`;\n  // missing both surfaces a two-option error with exit 1 so the\n  // SessionEnd hook (which backgrounds + redirects to a sidecar log)\n  // doesn't silently treat auth failure as a successful capture.\n  try {\n    await assertClaudeAuth(options.spawnCli);\n  } catch (err: unknown) {\n    const msg = err instanceof Error ? err.message : String(err);\n    return {\n      stdout: \"\",\n      stderr: `almanac: ${msg}\\n`,\n      exitCode: 1,\n    };\n  }\n\n  // Resolve the repo root by walking up for `.almanac/`. Unlike bootstrap,\n  // capture refuses to run when no wiki exists — the writer needs existing\n  // pages to read against, and auto-initing here would hide the fact that\n  // the user skipped `almanac bootstrap`.\n  const repoRoot = findNearestAlmanacDir(options.cwd);\n  if (repoRoot === null) {\n    return {\n      stdout: \"\",\n      stderr:\n        \"almanac: no .almanac/ found in this directory or any parent. \" +\n        \"Run 'almanac init' or 'almanac bootstrap' first.\\n\",\n      exitCode: 1,\n    };\n  }\n\n  const almanacDir = getRepoAlmanacDir(repoRoot);\n  const pagesDir = join(almanacDir, \"pages\");\n\n  // Resolve the transcript path up front. Doing this before we open a log\n  // stream keeps bad-arg errors uncluttered by side effects.\n  const transcriptResolution = await resolveTranscript({\n    repoRoot,\n    explicit: options.transcriptPath,\n    sessionId: options.sessionId,\n    claudeProjectsDir: options.claudeProjectsDir,\n  });\n  if (!transcriptResolution.ok) {\n    return {\n      stdout: \"\",\n      stderr: `almanac: ${transcriptResolution.error}\\n`,\n      exitCode: 1,\n    };\n  }\n  const transcriptPath = transcriptResolution.path;\n\n  // Snapshot the pages dir BEFORE the writer runs. We compare against it\n  // after the agent exits to compute a created/updated/archived tally.\n  // Doing this in TS (not via the agent's self-reporting) means the summary\n  // stays trustworthy even if the writer gets confused about what it did.\n  const snapshotBefore = await snapshotPages(pagesDir);\n\n  // Load the two prompts. Kept sequential rather than parallel — both files\n  // are tiny and the second read is cache-warm.\n  const systemPrompt = await loadPrompt(\"writer\");\n  const reviewerPrompt = await loadPrompt(\"reviewer\");\n\n  const agents: Record<string, AgentDefinition> = {\n    reviewer: {\n      description: REVIEWER_DESCRIPTION,\n      prompt: reviewerPrompt,\n      tools: REVIEWER_TOOLS,\n    },\n  };\n\n  // Transcript log filename: timestamp-based so repeated runs don't clobber\n  // each other. We don't have the SDK session_id yet (it's on the first\n  // message), and filesystem writes need a destination before the stream\n  // begins.\n  const now = options.now?.() ?? new Date();\n  const logName = `.capture-${formatTimestamp(now)}.log`;\n  const logPath = join(almanacDir, logName);\n  const logStream = createWriteStream(logPath, { flags: \"w\" });\n\n  const out = process.stdout;\n  const formatter = new StreamingFormatter({\n    write: (line: string) => {\n      if (options.quiet !== true) out.write(line);\n    },\n  });\n  // The shared StreamingFormatter defaults its currentAgent to \"bootstrap\"\n  // because bootstrap was the first command to use it. For capture the\n  // writer owns the top-level turn, so relabel.\n  formatter.setAgent(\"writer\");\n\n  const onMessage = (msg: SDKMessage): void => {\n    try {\n      logStream.write(`${JSON.stringify(msg)}\\n`);\n    } catch {\n      // Best-effort: one unserializable message shouldn't kill the whole\n      // stream. Humans read the log; if a line is missing they can re-run.\n    }\n    formatter.handle(msg);\n  };\n\n  // Pass an ABSOLUTE path for the transcript so the writer doesn't have to\n  // guess at cwd semantics. Everything else (`.almanac/pages/`) is already\n  // relative to the cwd the SDK gives its tools.\n  const userPrompt =\n    `Capture this coding session.\\n` +\n    `Transcript: ${transcriptPath}.\\n` +\n    `Working directory: ${repoRoot}.`;\n\n  const runner = options.runAgent ?? runAgent;\n\n  let result: AgentResult;\n  try {\n    result = await runner({\n      systemPrompt,\n      prompt: userPrompt,\n      allowedTools: WRITER_TOOLS,\n      agents,\n      cwd: repoRoot,\n      model: options.model,\n      // Capture sessions can touch many pages; give it more headroom than\n      // bootstrap. The SDK treats `maxTurns` as a hard stop — better to\n      // overshoot than to cut off mid-review.\n      maxTurns: 150,\n      onMessage,\n    });\n  } finally {\n    await closeStream(logStream);\n  }\n\n  const snapshotAfter = await snapshotPages(pagesDir);\n  const delta = diffSnapshots(snapshotBefore, snapshotAfter);\n\n  if (!result.success) {\n    return {\n      stdout: \"\",\n      stderr:\n        `almanac: capture failed: ${result.error ?? \"unknown error\"}\\n` +\n        `(transcript: ${relative(repoRoot, logPath)})\\n`,\n      exitCode: 1,\n    };\n  }\n\n  const summary = formatSummary(result, delta, logPath, repoRoot);\n\n  return {\n    stdout: `${summary}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\n// ─── Transcript resolution ────────────────────────────────────────────────\n\ninterface ResolvedTranscript {\n  ok: true;\n  path: string;\n}\ninterface FailedTranscript {\n  ok: false;\n  error: string;\n}\n\n/**\n * Resolve the transcript path from the three possible sources, in priority:\n *   1. Explicit positional arg (`almanac capture <path>`).\n *   2. `--session <id>`: find the single `.jsonl` matching that ID.\n *   3. Auto-resolve: most recent `.jsonl` under Claude Code's projects dir\n *      whose parent directory hashes to `repoRoot`. If multiple candidates\n *      or none match, return an error directing the user to pass a path.\n *\n * Claude Code names the per-project directory with a path-hash that we\n * can't deterministically reproduce without reading Claude Code's source.\n * Rather than guess at the hashing scheme, we scan all project dirs, pick\n * the one whose most recent transcript mentions the `repoRoot` in its\n * `cwd` field, and take the newest `.jsonl` from there.\n */\nasync function resolveTranscript(args: {\n  repoRoot: string;\n  explicit?: string;\n  sessionId?: string;\n  claudeProjectsDir?: string;\n}): Promise<ResolvedTranscript | FailedTranscript> {\n  if (args.explicit !== undefined && args.explicit.length > 0) {\n    if (!existsSync(args.explicit)) {\n      return {\n        ok: false,\n        error: `transcript not found: ${args.explicit}`,\n      };\n    }\n    return { ok: true, path: args.explicit };\n  }\n\n  const projectsDir =\n    args.claudeProjectsDir ?? join(homedir(), \".claude\", \"projects\");\n  if (!existsSync(projectsDir)) {\n    return {\n      ok: false,\n      error:\n        `could not auto-resolve transcript; ${projectsDir} does not exist. ` +\n        `Pass --session <id> or <transcript-path>.`,\n    };\n  }\n\n  const allTranscripts = await collectTranscripts(projectsDir);\n\n  if (args.sessionId !== undefined && args.sessionId.length > 0) {\n    const expected = `${args.sessionId}.jsonl`;\n    const match = allTranscripts.find((t) => basename(t.path) === expected);\n    if (match === undefined) {\n      return {\n        ok: false,\n        error:\n          `no transcript found for session ${args.sessionId} under ${projectsDir}`,\n      };\n    }\n    return { ok: true, path: match.path };\n  }\n\n  // Auto-resolve: prefer transcripts whose `cwd` field matches `repoRoot`,\n  // then fall back to the most recently modified if no cwd match is found.\n  // We read a peek of each transcript (not the whole file) to check the\n  // cwd — JSONL's first line typically carries it.\n  const matches = await filterTranscriptsByCwd(allTranscripts, args.repoRoot);\n\n  if (matches.length === 0) {\n    return {\n      ok: false,\n      error:\n        `could not auto-resolve transcript under ${projectsDir}; ` +\n        `no session matches cwd ${args.repoRoot}. ` +\n        `Pass --session <id> or <transcript-path>.`,\n    };\n  }\n\n  // Sort by mtime desc and pick the newest.\n  matches.sort((a, b) => b.mtime - a.mtime);\n  return { ok: true, path: matches[0]!.path };\n}\n\ninterface TranscriptEntry {\n  path: string;\n  mtime: number;\n}\n\nasync function collectTranscripts(\n  projectsDir: string,\n): Promise<TranscriptEntry[]> {\n  const out: TranscriptEntry[] = [];\n  let topLevel: string[];\n  try {\n    topLevel = await readdir(projectsDir);\n  } catch {\n    return out;\n  }\n  for (const name of topLevel) {\n    const projectDir = join(projectsDir, name);\n    let entries: string[];\n    try {\n      entries = await readdir(projectDir);\n    } catch {\n      continue;\n    }\n    for (const entry of entries) {\n      if (!entry.endsWith(\".jsonl\")) continue;\n      const full = join(projectDir, entry);\n      try {\n        const st = await stat(full);\n        if (st.isFile()) {\n          out.push({ path: full, mtime: st.mtimeMs });\n        }\n      } catch {\n        // Transient read error, skip.\n      }\n    }\n  }\n  return out;\n}\n\n/**\n * Keep only transcripts whose first session record mentions a `cwd` that\n * matches `repoRoot` (exact string match). We also match on the Claude\n * Code project-hash heuristic: the per-project dir name is usually the\n * absolute repo path with `/` replaced by `-`. Falling back to the hash\n * heuristic means we still resolve sanely when the JSONL format changes.\n */\nasync function filterTranscriptsByCwd(\n  transcripts: TranscriptEntry[],\n  repoRoot: string,\n): Promise<TranscriptEntry[]> {\n  const dirHash = `-${repoRoot.replace(/^\\/+/, \"\").replace(/\\//g, \"-\")}`;\n\n  const byDirName = transcripts.filter((t) => {\n    const parent = basename(join(t.path, \"..\"));\n    return parent === dirHash || parent.endsWith(dirHash);\n  });\n  if (byDirName.length > 0) return byDirName;\n\n  // Fallback: peek into each JSONL for a `\"cwd\":\"<repoRoot>\"` needle.\n  const needle = `\"cwd\":\"${repoRoot}\"`;\n  const hits: TranscriptEntry[] = [];\n  for (const t of transcripts) {\n    try {\n      const head = await readHead(t.path, 4096);\n      if (head.includes(needle)) hits.push(t);\n    } catch {\n      continue;\n    }\n  }\n  return hits;\n}\n\nasync function readHead(path: string, bytes: number): Promise<string> {\n  // Small files — just read the whole thing. We only call this on .jsonl\n  // files, which can be large, so cap at `bytes` via slicing.\n  const content = await readFile(path, \"utf8\");\n  return content.length > bytes ? content.slice(0, bytes) : content;\n}\n\n// ─── Snapshot / delta ─────────────────────────────────────────────────────\n\ninterface PageSnapshotEntry {\n  slug: string;\n  /** SHA-256 of file bytes — cheap, stable, avoids relying on mtime. */\n  hash: string;\n  /** `true` when the frontmatter has `archived_at` set. */\n  archived: boolean;\n}\n\ntype PageSnapshot = Map<string, PageSnapshotEntry>;\n\nasync function snapshotPages(pagesDir: string): Promise<PageSnapshot> {\n  const out: PageSnapshot = new Map();\n  if (!existsSync(pagesDir)) return out;\n\n  let entries: string[];\n  try {\n    entries = await readdir(pagesDir);\n  } catch {\n    return out;\n  }\n  for (const entry of entries) {\n    if (!entry.endsWith(\".md\")) continue;\n    const slug = entry.slice(0, -3);\n    const full = join(pagesDir, entry);\n    try {\n      const st = statSync(full);\n      if (!st.isFile()) continue;\n      const content = await readFile(full, \"utf8\");\n      const hash = createHash(\"sha256\").update(content).digest(\"hex\");\n      const fm = parseFrontmatter(content);\n      out.set(slug, {\n        slug,\n        hash,\n        archived: fm.archived_at !== null,\n      });\n    } catch {\n      continue;\n    }\n  }\n  return out;\n}\n\ninterface SnapshotDelta {\n  created: number;\n  updated: number;\n  archived: number;\n}\n\nfunction diffSnapshots(\n  before: PageSnapshot,\n  after: PageSnapshot,\n): SnapshotDelta {\n  let created = 0;\n  let updated = 0;\n  let archived = 0;\n\n  for (const [slug, entry] of after) {\n    const prev = before.get(slug);\n    if (prev === undefined) {\n      created += 1;\n      continue;\n    }\n    if (prev.hash !== entry.hash) {\n      // An edit that flips a page from active → archived counts as\n      // \"archived\", not \"updated\" — the archive is the semantically\n      // interesting thing.\n      if (!prev.archived && entry.archived) {\n        archived += 1;\n      } else {\n        updated += 1;\n      }\n    }\n  }\n  // Note: we deliberately don't track deleted pages. The writer prompt\n  // tells agents to archive (via frontmatter), not delete — a page that\n  // disappears entirely is a protocol violation worth surfacing, but not\n  // by silently counting it in the summary.\n\n  return { created, updated, archived };\n}\n\n// ─── Formatting ───────────────────────────────────────────────────────────\n\nfunction formatSummary(\n  result: AgentResult,\n  delta: SnapshotDelta,\n  logPath: string,\n  repoRoot: string,\n): string {\n  const rel = relative(repoRoot, logPath);\n  const cost = `$${result.cost.toFixed(3)}`;\n  const { created, updated, archived } = delta;\n\n  if (created === 0 && updated === 0 && archived === 0) {\n    return (\n      `[capture] no new knowledge met the notability bar (0 pages written), ` +\n      `cost: ${cost}, turns: ${result.turns} (transcript: ${rel})`\n    );\n  }\n\n  return (\n    `[done] ${updated} page${updated === 1 ? \"\" : \"s\"} updated, ` +\n    `${created} created, ` +\n    `${archived} archived, ` +\n    `cost: ${cost}, turns: ${result.turns} (transcript: ${rel})`\n  );\n}\n\nfunction formatTimestamp(d: Date): string {\n  const pad = (n: number): string => n.toString().padStart(2, \"0\");\n  return (\n    `${d.getFullYear()}${pad(d.getMonth() + 1)}${pad(d.getDate())}-` +\n    `${pad(d.getHours())}${pad(d.getMinutes())}${pad(d.getSeconds())}`\n  );\n}\n\nfunction closeStream(stream: WriteStream): Promise<void> {\n  return new Promise((resolve) => {\n    stream.end(() => resolve());\n  });\n}\n","import yaml from \"js-yaml\";\n\nexport interface Frontmatter {\n  title?: string;\n  topics: string[];\n  files: string[];\n  archived_at: number | null;\n  superseded_by: string | null;\n  supersedes: string | null;\n  /**\n   * The body of the file with frontmatter removed, for FTS5 and H1 fallback.\n   * Always populated even when the file has no frontmatter.\n   */\n  body: string;\n}\n\n/**\n * Pull YAML frontmatter off the top of a markdown file and coerce the\n * relevant fields. Unknown fields are tolerated silently — the wiki should\n * accept fields we don't understand yet without spewing warnings at the\n * user (future slices might consume them).\n *\n * Failure modes:\n *   - No frontmatter at all → `{ topics: [], files: [], ..., body: raw }`.\n *     This is legal; a heading + prose is a valid page.\n *   - Malformed YAML → warning to stderr, treated as \"no frontmatter\". We\n *     choose not to throw so a single bad file doesn't tank a reindex.\n *\n * Note on `archived_at`: authors write this as a YAML date (`2026-04-15`),\n * which `js-yaml` parses to a JS `Date`. We also tolerate ISO-8601 strings\n * and raw numbers. Everything else gets dropped (treated as \"not\n * archived\"). Storing epoch seconds keeps `--since`/`--stale`/`archived`\n * arithmetic trivial at query time.\n */\nexport function parseFrontmatter(raw: string): Frontmatter {\n  const empty: Frontmatter = {\n    topics: [],\n    files: [],\n    archived_at: null,\n    superseded_by: null,\n    supersedes: null,\n    body: raw,\n  };\n\n  // Frontmatter fence MUST start on line 1 — a `---` partway through the\n  // document is just a horizontal rule. Be strict about the opening delim\n  // so we don't accidentally strip section headers.\n  if (!raw.startsWith(\"---\")) {\n    return empty;\n  }\n\n  // Tolerate either Unix or Windows line endings. We read the first line\n  // explicitly to confirm it's only `---` (no trailing content).\n  const match = raw.match(/^---\\r?\\n([\\s\\S]*?)\\r?\\n---\\r?\\n?([\\s\\S]*)$/);\n  if (match === null) {\n    return empty;\n  }\n\n  const yamlBody = match[1] ?? \"\";\n  const body = match[2] ?? \"\";\n\n  let parsed: unknown;\n  try {\n    parsed = yaml.load(yamlBody);\n  } catch (err: unknown) {\n    const message = err instanceof Error ? err.message : String(err);\n    process.stderr.write(`almanac: malformed frontmatter (${message})\\n`);\n    return empty;\n  }\n\n  if (parsed === null || parsed === undefined) {\n    return { ...empty, body };\n  }\n  if (typeof parsed !== \"object\" || Array.isArray(parsed)) {\n    // Someone wrote a YAML scalar or list as the document root — not a\n    // mapping, so no fields for us to extract. Treat as empty but keep the\n    // post-fence body so FTS5 still gets content.\n    return { ...empty, body };\n  }\n\n  const obj = parsed as Record<string, unknown>;\n\n  return {\n    title: coerceString(obj.title),\n    topics: coerceStringArray(obj.topics),\n    files: coerceStringArray(obj.files),\n    archived_at: coerceEpochSeconds(obj.archived_at),\n    superseded_by: coerceString(obj.superseded_by) ?? null,\n    supersedes: coerceString(obj.supersedes) ?? null,\n    body,\n  };\n}\n\n/**\n * H1 fallback for title when frontmatter has none.\n *\n * Only considers the first 40 lines of the body — any real wiki page has\n * its H1 near the top. NOTE: `String.prototype.split(sep, limit)` still\n * splits the whole string internally and then truncates; it's not an\n * early-bail iteration. For the multi-megabyte files we might see in\n * practice this is still cheap (one regex pass, no allocation per-line\n * beyond the 40 we keep), so we favor the clearer code over hand-rolled\n * line iteration.\n */\nexport function firstH1(body: string): string | undefined {\n  const lines = body.split(/\\r?\\n/, 40);\n  for (const line of lines) {\n    const m = line.match(/^#\\s+(.+?)\\s*#*\\s*$/);\n    if (m !== null) {\n      return m[1];\n    }\n  }\n  return undefined;\n}\n\nfunction coerceString(v: unknown): string | undefined {\n  if (typeof v === \"string\" && v.trim().length > 0) return v.trim();\n  return undefined;\n}\n\nfunction coerceStringArray(v: unknown): string[] {\n  if (!Array.isArray(v)) return [];\n  const out: string[] = [];\n  for (const item of v) {\n    if (typeof item === \"string\" && item.trim().length > 0) {\n      out.push(item.trim());\n    }\n  }\n  return out;\n}\n\n/**\n * Coerce a frontmatter `archived_at` value (YAML Date, ISO string, or raw\n * epoch number) into epoch seconds. Returns `null` for anything we can't\n * make sense of — pages with an unrecognizable `archived_at` are treated as\n * active rather than silently marked archived, which is the safer default.\n */\nfunction coerceEpochSeconds(v: unknown): number | null {\n  if (v instanceof Date) {\n    return Math.floor(v.getTime() / 1000);\n  }\n  if (typeof v === \"number\" && Number.isFinite(v)) {\n    return Math.floor(v);\n  }\n  if (typeof v === \"string\" && v.trim().length > 0) {\n    const t = Date.parse(v.trim());\n    if (!Number.isNaN(t)) {\n      return Math.floor(t / 1000);\n    }\n  }\n  return null;\n}\n","import { existsSync } from \"node:fs\";\nimport { mkdir, readFile, rename, writeFile } from \"node:fs/promises\";\nimport { homedir } from \"node:os\";\nimport path from \"node:path\";\nimport { fileURLToPath } from \"node:url\";\n\n/**\n * `almanac hook install|uninstall|status` — wires the bundled\n * `hooks/almanac-capture.sh` into `~/.claude/settings.json` as a\n * `SessionEnd` hook.\n *\n * Design notes:\n *\n * - **Idempotent.** `install` twice leaves one entry, not two. We match by\n *   `command` string equality — if the user replaces our absolute path\n *   with a symlink pointing at the same script, we'll treat it as foreign.\n *   That's acceptable; the `status` output shows the path we'd use, so the\n *   user can reconcile manually.\n *\n * - **Refuse foreign entries.** If `SessionEnd` is already populated with\n *   a command we don't recognize, we print the existing value and exit\n *   non-zero. Claude Code lets users wire their own hooks (notifications,\n *   git autocommit scripts, etc.) and silently replacing them would be\n *   rude.\n *\n * - **Atomic write.** `settings.json` is small but heavily touched by\n *   Claude Code. Writing via tmp-file + rename avoids corrupting the file\n *   if we crash mid-write.\n *\n * - **Non-interactive.** No prompts, no confirmations. The caller is\n *   already making an intentional choice by running `almanac hook\n *   install`.\n */\n\nexport interface HookCommandOptions {\n  /**\n   * Override the hook script path. Production code leaves this undefined\n   * and we resolve the bundled `hooks/almanac-capture.sh`. Tests pass a\n   * fixture path to avoid depending on the runtime-install layout.\n   */\n  hookScriptPath?: string;\n  /**\n   * Override `~/.claude/settings.json`. Tests sandbox this to a tmpdir;\n   * production code leaves it undefined.\n   */\n  settingsPath?: string;\n}\n\nexport interface HookCommandResult {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\nconst HOOK_TIMEOUT_SECONDS = 10;\n\ninterface SessionEndEntry {\n  type: \"command\";\n  command: string;\n  timeout?: number;\n}\n\n/**\n * Claude Code's `settings.json` is a free-form JSON object; we only care\n * about the `hooks.SessionEnd` array. Preserve everything else verbatim so\n * we don't drop user settings when we write the file back.\n */\ntype SettingsJson = Record<string, unknown> & {\n  hooks?: Record<string, SessionEndEntry[] | undefined>;\n};\n\nexport async function runHookInstall(\n  options: HookCommandOptions = {},\n): Promise<HookCommandResult> {\n  const script = resolveHookScriptPath(options);\n  if (!script.ok) {\n    return { stdout: \"\", stderr: `almanac: ${script.error}\\n`, exitCode: 1 };\n  }\n\n  const settingsPath = resolveSettingsPath(options);\n  const settings = await readSettings(settingsPath);\n  const existing = (settings.hooks?.SessionEnd ?? []).slice();\n\n  // Find any existing entry with our exact command. If found, the install\n  // is a no-op (idempotent). If SessionEnd has OTHER commands alongside\n  // ours, leave them alone — the user might be composing multiple hooks.\n  const ourEntries = existing.filter((e) => e.command === script.path);\n  const foreignEntries = existing.filter((e) => e.command !== script.path);\n\n  // If the sole existing entry looks like ours-but-on-a-different-path\n  // (e.g. an old install from a different node_modules), replace it so we\n  // don't double-fire on session end. Heuristic: command ends with\n  // `almanac-capture.sh`. We accept this specific rename; unrelated\n  // commands still block.\n  const stale = foreignEntries.filter((e) =>\n    e.command.endsWith(\"almanac-capture.sh\"),\n  );\n  const unrelated = foreignEntries.filter(\n    (e) => !e.command.endsWith(\"almanac-capture.sh\"),\n  );\n\n  if (unrelated.length > 0) {\n    const existingStr = unrelated.map((e) => `  - ${e.command}`).join(\"\\n\");\n    return {\n      stdout: \"\",\n      stderr:\n        `almanac: SessionEnd hook already has a foreign entry:\\n${existingStr}\\n` +\n        `Remove it manually from ${settingsPath} if you want almanac to manage the hook.\\n`,\n      exitCode: 1,\n    };\n  }\n\n  if (ourEntries.length > 0 && stale.length === 0) {\n    return {\n      stdout: `almanac: SessionEnd hook already installed at ${script.path}\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  // Compose the new SessionEnd array: keep our one entry (fresh), drop any\n  // stale almanac entries.\n  const newEntries: SessionEndEntry[] = [\n    {\n      type: \"command\",\n      command: script.path,\n      timeout: HOOK_TIMEOUT_SECONDS,\n    },\n  ];\n\n  settings.hooks = { ...(settings.hooks ?? {}), SessionEnd: newEntries };\n  await writeSettings(settingsPath, settings);\n\n  return {\n    stdout:\n      `almanac: SessionEnd hook installed\\n` +\n      `  script: ${script.path}\\n` +\n      `  settings: ${settingsPath}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\nexport async function runHookUninstall(\n  options: HookCommandOptions = {},\n): Promise<HookCommandResult> {\n  const settingsPath = resolveSettingsPath(options);\n\n  if (!existsSync(settingsPath)) {\n    return {\n      stdout: `almanac: SessionEnd hook not installed (no settings file)\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  const settings = await readSettings(settingsPath);\n  const existing = (settings.hooks?.SessionEnd ?? []).slice();\n\n  // Remove ONLY our entries — anything else stays. We treat any entry with\n  // a command ending in `almanac-capture.sh` as ours (handles the case\n  // where the bundled path moved between `npm i` locations).\n  const kept = existing.filter((e) => !e.command.endsWith(\"almanac-capture.sh\"));\n  const removed = existing.length - kept.length;\n\n  if (removed === 0) {\n    return {\n      stdout: `almanac: SessionEnd hook not installed\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  if (settings.hooks !== undefined) {\n    if (kept.length === 0) {\n      // Empty SessionEnd array confuses some linters; drop the key when\n      // nothing's left.\n      const { SessionEnd: _dropped, ...rest } = settings.hooks;\n      void _dropped;\n      settings.hooks = rest;\n    } else {\n      settings.hooks = { ...settings.hooks, SessionEnd: kept };\n    }\n\n    // If `hooks` itself is now empty (user had only our SessionEnd entry\n    // and no other hook categories), drop the `hooks` key entirely so\n    // uninstall leaves the settings file in the same shape it would be\n    // in had we never run install. An empty `\"hooks\": {}` is an obvious\n    // breadcrumb in commit diffs.\n    if (Object.keys(settings.hooks).length === 0) {\n      delete settings.hooks;\n    }\n  }\n\n  await writeSettings(settingsPath, settings);\n\n  return {\n    stdout: `almanac: SessionEnd hook removed\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\nexport async function runHookStatus(\n  options: HookCommandOptions = {},\n): Promise<HookCommandResult> {\n  const script = resolveHookScriptPath(options);\n  const settingsPath = resolveSettingsPath(options);\n\n  if (!existsSync(settingsPath)) {\n    return {\n      stdout:\n        `SessionEnd hook: not installed\\n` +\n        `settings: ${settingsPath} (does not exist)\\n` +\n        (script.ok ? `script would be: ${script.path}\\n` : \"\"),\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  const settings = await readSettings(settingsPath);\n  const existing = settings.hooks?.SessionEnd ?? [];\n  const ours = existing.find((e) => e.command.endsWith(\"almanac-capture.sh\"));\n\n  if (ours === undefined) {\n    const foreign = existing\n      .map((e) => `  - ${e.command}`)\n      .join(\"\\n\");\n    return {\n      stdout:\n        `SessionEnd hook: not installed\\n` +\n        `settings: ${settingsPath}\\n` +\n        (existing.length > 0\n          ? `(${existing.length} foreign entr${existing.length === 1 ? \"y\" : \"ies\"} present:\\n${foreign})\\n`\n          : \"\") +\n        (script.ok ? `script would be: ${script.path}\\n` : \"\"),\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  return {\n    stdout:\n      `SessionEnd hook: installed\\n` +\n      `script: ${ours.command}\\n` +\n      `settings: ${settingsPath}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\n// ─── Helpers ─────────────────────────────────────────────────────────────\n\nfunction resolveSettingsPath(options: HookCommandOptions): string {\n  if (options.settingsPath !== undefined) return options.settingsPath;\n  return path.join(homedir(), \".claude\", \"settings.json\");\n}\n\ntype ScriptResolution =\n  | { ok: true; path: string }\n  | { ok: false; error: string };\n\n/**\n * Locate the bundled `hooks/almanac-capture.sh`. Mirrors\n * `resolvePromptsDir` from `src/agent/prompts.ts`: two plausible layouts\n * (installed dist vs. source dev), probe each.\n */\nfunction resolveHookScriptPath(options: HookCommandOptions): ScriptResolution {\n  if (options.hookScriptPath !== undefined) {\n    return { ok: true, path: options.hookScriptPath };\n  }\n\n  const here = path.dirname(fileURLToPath(import.meta.url));\n\n  const candidates = [\n    // Bundled: `.../codealmanac/dist/codealmanac.js` → `../hooks/…`\n    path.resolve(here, \"..\", \"hooks\", \"almanac-capture.sh\"),\n    // Source: `.../codealmanac/src/commands/hook.ts` → `../../hooks/…`\n    path.resolve(here, \"..\", \"..\", \"hooks\", \"almanac-capture.sh\"),\n    // Defensive nested fallback.\n    path.resolve(here, \"..\", \"..\", \"..\", \"hooks\", \"almanac-capture.sh\"),\n  ];\n\n  for (const candidate of candidates) {\n    if (existsSync(candidate)) {\n      return { ok: true, path: candidate };\n    }\n  }\n\n  return {\n    ok: false,\n    error:\n      `could not locate hooks/almanac-capture.sh. Tried:\\n` +\n      candidates.map((c) => `  - ${c}`).join(\"\\n\"),\n  };\n}\n\nasync function readSettings(settingsPath: string): Promise<SettingsJson> {\n  if (!existsSync(settingsPath)) return {};\n  try {\n    const raw = await readFile(settingsPath, \"utf8\");\n    if (raw.trim().length === 0) return {};\n    const parsed = JSON.parse(raw) as unknown;\n    if (parsed === null || typeof parsed !== \"object\") return {};\n    return parsed as SettingsJson;\n  } catch (err: unknown) {\n    const msg = err instanceof Error ? err.message : String(err);\n    throw new Error(`failed to read ${settingsPath}: ${msg}`);\n  }\n}\n\nasync function writeSettings(\n  settingsPath: string,\n  settings: SettingsJson,\n): Promise<void> {\n  const dir = path.dirname(settingsPath);\n  await mkdir(dir, { recursive: true });\n\n  // Atomic write: JSON.stringify → tmp file → rename. `rename` within the\n  // same filesystem is atomic on POSIX; Claude Code never sees a partial\n  // file. Formatted with 2-space indent to match the existing settings.\n  const tmp = `${settingsPath}.almanac-tmp-${process.pid}`;\n  const body = `${JSON.stringify(settings, null, 2)}\\n`;\n  await writeFile(tmp, body, \"utf8\");\n  await rename(tmp, settingsPath);\n}\n","import { existsSync } from \"node:fs\";\nimport { readFile } from \"node:fs/promises\";\nimport { basename, join } from \"node:path\";\n\nimport fg from \"fast-glob\";\nimport type Database from \"better-sqlite3\";\n\nimport { parseDuration } from \"../indexer/duration.js\";\nimport { ensureFreshIndex } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\nimport { findEntry } from \"../registry/index.js\";\nimport { toKebabCase } from \"../slug.js\";\nimport { subtreeInDb } from \"../topics/dag.js\";\n\n/**\n * `almanac health` — flag problems in the wiki.\n *\n * Eight independent categories, each checked against the current index\n * and filesystem. Categories never throw each other off; one failing\n * is not a reason to skip the others.\n *\n * Scoping:\n *   - `--topic <slug>` narrows every page-scoped category to pages\n *     tagged with that topic OR any descendant topic (DAG traversal).\n *     Topic-level categories (`empty_topics`) are narrowed to the\n *     subtree itself.\n *   - `--stdin` reads page slugs from stdin and limits page-scoped\n *     categories to that set.\n *\n * Output:\n *   - default: human-readable, grouped by category with counts.\n *   - `--json`: one big object, shape = `HealthReport`.\n */\n\nexport interface HealthReport {\n  orphans: { slug: string }[];\n  stale: { slug: string; days_since_update: number }[];\n  dead_refs: { slug: string; path: string }[];\n  broken_links: { source_slug: string; target_slug: string }[];\n  broken_xwiki: { source_slug: string; target_wiki: string; target_slug: string }[];\n  empty_topics: { slug: string }[];\n  empty_pages: { slug: string }[];\n  slug_collisions: { slug: string; paths: string[] }[];\n}\n\nexport interface HealthOptions {\n  cwd: string;\n  wiki?: string;\n  topic?: string;\n  stale?: string;\n  stdin?: boolean;\n  stdinInput?: string;\n  json?: boolean;\n}\n\nexport interface HealthCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * Default `--stale` window. 90 days matches the spec. Users can tune\n * with `--stale <duration>` using the shared parser.\n */\nconst DEFAULT_STALE_SECONDS = 90 * 24 * 60 * 60;\n\nexport async function runHealth(\n  options: HealthOptions,\n): Promise<HealthCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  await ensureFreshIndex({ repoRoot });\n\n  const almanacDir = join(repoRoot, \".almanac\");\n  const pagesDir = join(almanacDir, \"pages\");\n  const db = openIndex(join(almanacDir, \"index.db\"));\n\n  try {\n    const staleSeconds = options.stale !== undefined\n      ? parseDuration(options.stale)\n      : DEFAULT_STALE_SECONDS;\n\n    const scope = resolveScope(db, options);\n\n    const report: HealthReport = {\n      orphans: findOrphans(db, scope),\n      stale: findStale(db, scope, staleSeconds),\n      dead_refs: await findDeadRefs(db, scope, repoRoot),\n      broken_links: findBrokenLinks(db, scope),\n      broken_xwiki: await findBrokenXwiki(db, scope),\n      empty_topics: findEmptyTopics(db, scope),\n      empty_pages: await findEmptyPages(db, scope, pagesDir),\n      slug_collisions: await findSlugCollisions(pagesDir),\n    };\n\n    if (options.json === true) {\n      return {\n        stdout: `${JSON.stringify(report, null, 2)}\\n`,\n        stderr: \"\",\n        exitCode: 0,\n      };\n    }\n\n    return {\n      stdout: formatReport(report),\n      stderr: \"\",\n      exitCode: 0,\n    };\n  } finally {\n    db.close();\n  }\n}\n\ninterface HealthScope {\n  /** When non-null, restrict page-scoped checks to these slugs. */\n  pages: Set<string> | null;\n  /** When non-null, restrict topic-scoped checks to these slugs. */\n  topics: Set<string> | null;\n}\n\n/**\n * Compute the active page/topic scope from `--topic` and `--stdin`\n * flags. Both null = no restriction (report everything).\n */\nfunction resolveScope(db: Database.Database, options: HealthOptions): HealthScope {\n  let pages: Set<string> | null = null;\n  let topics: Set<string> | null = null;\n\n  if (options.topic !== undefined) {\n    const rootSlug = toKebabCase(options.topic);\n    if (rootSlug.length > 0) {\n      const subtree = subtreeInDb(db, rootSlug);\n      topics = new Set(subtree);\n      const placeholders = subtree.map(() => \"?\").join(\", \");\n      const rows = db\n        .prepare<unknown[], { page_slug: string }>(\n          `SELECT DISTINCT page_slug FROM page_topics\n           WHERE topic_slug IN (${placeholders})`,\n        )\n        .all(...subtree);\n      pages = new Set(rows.map((r) => r.page_slug));\n    }\n  }\n\n  if (options.stdin === true && options.stdinInput !== undefined) {\n    const stdinPages = new Set<string>();\n    for (const line of options.stdinInput.split(/\\r?\\n/)) {\n      const s = line.trim();\n      if (s.length > 0) stdinPages.add(s);\n    }\n    // Intersect with any existing topic-scoped set.\n    if (pages === null) pages = stdinPages;\n    else {\n      const out = new Set<string>();\n      for (const s of stdinPages) if (pages.has(s)) out.add(s);\n      pages = out;\n    }\n  }\n\n  return { pages, topics };\n}\n\nfunction inPageScope(scope: HealthScope, slug: string): boolean {\n  if (scope.pages === null) return true;\n  return scope.pages.has(slug);\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// individual checks\n// ─────────────────────────────────────────────────────────────────────\n\n/**\n * Pages with zero `topics:`. Archived pages are exempt — the spec\n * excludes them from search by default and they're inherently\n * \"retired\", not \"abandoned\".\n */\nfunction findOrphans(\n  db: Database.Database,\n  scope: HealthScope,\n): { slug: string }[] {\n  const rows = db\n    .prepare<[], { slug: string }>(\n      `SELECT p.slug FROM pages p\n       WHERE p.archived_at IS NULL\n         AND NOT EXISTS (\n           SELECT 1 FROM page_topics pt WHERE pt.page_slug = p.slug\n         )\n       ORDER BY p.slug`,\n    )\n    .all();\n  return rows.filter((r) => inPageScope(scope, r.slug));\n}\n\n/**\n * Active pages whose `updated_at` is older than `staleSeconds`. We\n * report `days_since_update` rather than a raw timestamp because the\n * spec's example output (\"old-architecture (124 days)\") shows that.\n */\nfunction findStale(\n  db: Database.Database,\n  scope: HealthScope,\n  staleSeconds: number,\n): { slug: string; days_since_update: number }[] {\n  const now = Math.floor(Date.now() / 1000);\n  const threshold = now - staleSeconds;\n  const rows = db\n    .prepare<[number], { slug: string; updated_at: number }>(\n      `SELECT slug, updated_at FROM pages\n       WHERE archived_at IS NULL AND updated_at < ?\n       ORDER BY updated_at ASC`,\n    )\n    .all(threshold);\n  return rows\n    .filter((r) => inPageScope(scope, r.slug))\n    .map((r) => ({\n      slug: r.slug,\n      days_since_update: Math.floor((now - r.updated_at) / (60 * 60 * 24)),\n    }));\n}\n\n/**\n * `file_refs` whose target paths no longer exist on disk. We `stat`\n * each referenced path, relative to the repo root, and report misses.\n *\n * Only checks active pages — archived pages are allowed to reference\n * files that have since been deleted (that's often why they were\n * archived in the first place).\n *\n * We stat the `original_path` (author's casing) rather than the\n * lowercased `path` — on case-sensitive filesystems like Linux, stat\n * of a lowercased alias of `src/Dockerfile` returns ENOENT even\n * though the file exists. macOS and Windows are case-insensitive so\n * either form resolves there; using the original consistently means\n * the code behaves identically on every host.\n */\nasync function findDeadRefs(\n  db: Database.Database,\n  scope: HealthScope,\n  repoRoot: string,\n): Promise<{ slug: string; path: string }[]> {\n  const rows = db\n    .prepare<\n      [],\n      { slug: string; path: string; original_path: string; is_dir: number }\n    >(\n      `SELECT p.slug, r.path, r.original_path, r.is_dir\n       FROM file_refs r\n       JOIN pages p ON p.slug = r.page_slug\n       WHERE p.archived_at IS NULL\n       ORDER BY p.slug, r.path`,\n    )\n    .all();\n  const out: { slug: string; path: string }[] = [];\n  for (const r of rows) {\n    if (!inPageScope(scope, r.slug)) continue;\n    const abs = join(repoRoot, r.original_path);\n    if (!existsSync(abs)) {\n      // Surface the author's casing in the report — matches what's in\n      // the user's frontmatter/wikilink, which is what they'll search\n      // for when fixing the miss.\n      out.push({ slug: r.slug, path: r.original_path });\n    }\n  }\n  return out;\n}\n\n/**\n * Wikilinks whose target slug has no row in `pages`. Every other\n * page-scoped check filters archived source pages out; this one and\n * `findBrokenXwiki` follow the same rule so the report doesn't flag\n * broken links from pages that have been retired.\n */\nfunction findBrokenLinks(\n  db: Database.Database,\n  scope: HealthScope,\n): { source_slug: string; target_slug: string }[] {\n  const rows = db\n    .prepare<[], { source_slug: string; target_slug: string }>(\n      `SELECT w.source_slug, w.target_slug\n       FROM wikilinks w\n       JOIN pages src ON src.slug = w.source_slug\n       LEFT JOIN pages tgt ON tgt.slug = w.target_slug\n       WHERE tgt.slug IS NULL AND src.archived_at IS NULL\n       ORDER BY w.source_slug, w.target_slug`,\n    )\n    .all();\n  return rows.filter((r) => inPageScope(scope, r.source_slug));\n}\n\n/**\n * Cross-wiki links whose target wiki isn't registered OR whose path\n * is unreachable. Per the plan we stop at \"wiki unregistered or path\n * missing\" — walking into the other wiki's `index.db` to check the\n * slug exists is explicitly out of scope for slice 3 (documented in\n * the plan). A follow-up slice can deepen this.\n */\nasync function findBrokenXwiki(\n  db: Database.Database,\n  scope: HealthScope,\n): Promise<{ source_slug: string; target_wiki: string; target_slug: string }[]> {\n  const rows = db\n    .prepare<\n      [],\n      { source_slug: string; target_wiki: string; target_slug: string }\n    >(\n      // Same archived-source filter as `findBrokenLinks`. Retired pages\n      // shouldn't spam the report with links to wikis that may have\n      // been intentionally retired too.\n      `SELECT x.source_slug, x.target_wiki, x.target_slug\n       FROM cross_wiki_links x\n       JOIN pages src ON src.slug = x.source_slug\n       WHERE src.archived_at IS NULL\n       ORDER BY x.source_slug, x.target_wiki, x.target_slug`,\n    )\n    .all();\n  const out: { source_slug: string; target_wiki: string; target_slug: string }[] = [];\n  // Cache the registry lookup so we only resolve each wiki once.\n  const reachableCache = new Map<string, boolean>();\n  for (const r of rows) {\n    if (!inPageScope(scope, r.source_slug)) continue;\n    let ok = reachableCache.get(r.target_wiki);\n    if (ok === undefined) {\n      const entry = await findEntry({ name: r.target_wiki });\n      ok = entry !== null && existsSync(join(entry.path, \".almanac\"));\n      reachableCache.set(r.target_wiki, ok);\n    }\n    if (!ok) {\n      out.push({\n        source_slug: r.source_slug,\n        target_wiki: r.target_wiki,\n        target_slug: r.target_slug,\n      });\n    }\n  }\n  return out;\n}\n\n/** Topics with zero pages. */\nfunction findEmptyTopics(\n  db: Database.Database,\n  scope: HealthScope,\n): { slug: string }[] {\n  const rows = db\n    .prepare<[], { slug: string }>(\n      `SELECT t.slug FROM topics t\n       WHERE NOT EXISTS (\n         SELECT 1 FROM page_topics pt WHERE pt.topic_slug = t.slug\n       )\n       ORDER BY t.slug`,\n    )\n    .all();\n  if (scope.topics === null) return rows;\n  return rows.filter((r) => scope.topics!.has(r.slug));\n}\n\n/**\n * Pages whose body is effectively empty — only frontmatter, maybe a\n * heading, no prose. \"Empty\" = after dropping frontmatter and heading\n * lines, the remaining non-blank non-whitespace content is < 40\n * characters. This matches the test from the plan: \"a page with only\n * frontmatter + heading is empty; with a paragraph it's not.\"\n *\n * Archived pages are exempt — deliberately minimal archive stubs\n * shouldn't be flagged.\n */\nasync function findEmptyPages(\n  db: Database.Database,\n  scope: HealthScope,\n  pagesDir: string,\n): Promise<{ slug: string }[]> {\n  const rows = db\n    .prepare<[], { slug: string; file_path: string }>(\n      `SELECT slug, file_path FROM pages\n       WHERE archived_at IS NULL\n       ORDER BY slug`,\n    )\n    .all();\n  const out: { slug: string }[] = [];\n  for (const r of rows) {\n    if (!inPageScope(scope, r.slug)) continue;\n    let raw: string;\n    try {\n      raw = await readFile(r.file_path, \"utf8\");\n    } catch {\n      continue;\n    }\n    // Strip frontmatter if present.\n    const m = raw.match(/^---\\r?\\n[\\s\\S]*?\\r?\\n---\\r?\\n?([\\s\\S]*)$/);\n    const body = m !== null ? (m[1] ?? \"\") : raw;\n    // \"Empty\" = after dropping frontmatter, heading lines, and blank\n    // lines, nothing non-trivial remains. A single-line wikilink or\n    // one-sentence paragraph counts as content; a page with only a\n    // heading (or a heading + whitespace) does not.\n    //\n    // `pagesDir` is accepted for parity with future content-resolution\n    // checks (e.g., resolving includes); referenced so lint doesn't\n    // complain about an unused parameter.\n    void pagesDir;\n    const hasSubstance = body\n      .split(/\\r?\\n/)\n      .some((l) => {\n        const t = l.trim();\n        if (t.length === 0) return false;\n        if (t.startsWith(\"#\")) return false;\n        return true;\n      });\n    if (!hasSubstance) {\n      out.push({ slug: r.slug });\n    }\n  }\n  return out;\n}\n\n/**\n * Walk `.almanac/pages/` and group filenames by their kebab-cased\n * slug. Any slug with >1 filename is a collision. We rescan rather\n * than reading a persisted table — indexing surfaces collisions only\n * as warnings, so a dedicated rescan gives us a definitive answer\n * without adding a new table.\n */\nasync function findSlugCollisions(\n  pagesDir: string,\n): Promise<{ slug: string; paths: string[] }[]> {\n  if (!existsSync(pagesDir)) return [];\n  const files = await fg(\"**/*.md\", {\n    cwd: pagesDir,\n    absolute: false,\n    onlyFiles: true,\n    caseSensitiveMatch: true,\n  });\n  const bySlug = new Map<string, string[]>();\n  for (const rel of files) {\n    const slug = toKebabCase(basename(rel, \".md\"));\n    if (slug.length === 0) continue;\n    const list = bySlug.get(slug) ?? [];\n    list.push(rel);\n    bySlug.set(slug, list);\n  }\n  const out: { slug: string; paths: string[] }[] = [];\n  for (const [slug, paths] of bySlug.entries()) {\n    if (paths.length > 1) {\n      out.push({ slug, paths: paths.sort() });\n    }\n  }\n  out.sort((a, b) => a.slug.localeCompare(b.slug));\n  return out;\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// pretty-print\n// ─────────────────────────────────────────────────────────────────────\n\nfunction formatReport(r: HealthReport): string {\n  const sections: string[] = [];\n  sections.push(\n    section(\n      \"orphans\",\n      r.orphans.length,\n      r.orphans.map((o) => `  ${o.slug}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"stale\",\n      r.stale.length,\n      r.stale.map((s) => `  ${s.slug}     (${s.days_since_update} days)`),\n    ),\n  );\n  sections.push(\n    section(\n      \"dead-refs\",\n      r.dead_refs.length,\n      r.dead_refs.map((d) => `  ${d.slug}  references ${d.path} (missing)`),\n    ),\n  );\n  sections.push(\n    section(\n      \"broken-links\",\n      r.broken_links.length,\n      r.broken_links.map(\n        (b) => `  ${b.source_slug} → ${b.target_slug} (target does not exist)`,\n      ),\n    ),\n  );\n  sections.push(\n    section(\n      \"broken-xwiki\",\n      r.broken_xwiki.length,\n      r.broken_xwiki.map(\n        (b) =>\n          `  ${b.source_slug} → ${b.target_wiki}:${b.target_slug} (wiki unregistered or unreachable)`,\n      ),\n    ),\n  );\n  sections.push(\n    section(\n      \"empty-topics\",\n      r.empty_topics.length,\n      r.empty_topics.map((e) => `  ${e.slug}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"empty-pages\",\n      r.empty_pages.length,\n      r.empty_pages.map((e) => `  ${e.slug}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"slug-collisions\",\n      r.slug_collisions.length,\n      r.slug_collisions.map((c) => `  ${c.slug}: ${c.paths.join(\", \")}`),\n    ),\n  );\n  return `${sections.join(\"\\n\\n\")}\\n`;\n}\n\nfunction section(label: string, count: number, lines: string[]): string {\n  if (count === 0) return `${label} (0): (ok)`;\n  return `${label} (${count}):\\n${lines.join(\"\\n\")}`;\n}\n","/**\n * Parse a compact duration string of the form `<N><unit>` into seconds.\n *\n * Accepted units (from the spec, `--since` / `--stale`):\n *   - `m` — minutes\n *   - `h` — hours\n *   - `d` — days\n *   - `w` — weeks\n *\n * Examples: `2w` → 1209600, `30d` → 2592000, `12h` → 43200.\n *\n * Anything else throws — the CLI surfaces the error with the usual\n * `almanac: <message>` prefix, which is clearer than silently treating\n * `2weeks` or `30 days` as zero.\n */\nexport function parseDuration(input: string): number {\n  const trimmed = input.trim();\n  const m = trimmed.match(/^(\\d+)([mhdw])$/);\n  if (m === null) {\n    throw new Error(\n      `invalid duration \"${input}\" (expected Nw, Nd, Nh, or Nm — e.g. 2w, 30d)`,\n    );\n  }\n  const n = Number.parseInt(m[1] ?? \"0\", 10);\n  const unit = m[2];\n  switch (unit) {\n    case \"m\":\n      return n * 60;\n    case \"h\":\n      return n * 60 * 60;\n    case \"d\":\n      return n * 60 * 60 * 24;\n    case \"w\":\n      return n * 60 * 60 * 24 * 7;\n    default:\n      // Unreachable — regex pins the unit — but satisfies exhaustiveness.\n      throw new Error(`invalid duration unit \"${unit ?? \"\"}\"`);\n  }\n}\n","import { createHash } from \"node:crypto\";\nimport { existsSync, statSync } from \"node:fs\";\nimport { readFile, utimes } from \"node:fs/promises\";\nimport { basename, join, relative } from \"node:path\";\n\nimport fg from \"fast-glob\";\nimport type Database from \"better-sqlite3\";\n\nimport { toKebabCase } from \"../slug.js\";\nimport { loadTopicsFile, titleCase } from \"../topics/yaml.js\";\nimport { firstH1, parseFrontmatter } from \"./frontmatter.js\";\nimport {\n  normalizePath,\n  normalizePathPreservingCase,\n  looksLikeDir,\n} from \"./paths.js\";\nimport { openIndex } from \"./schema.js\";\nimport { extractWikilinks } from \"./wikilinks.js\";\n\n/**\n * Filename relative to the `.almanac/` dir where the topic DAG + metadata\n * lives. The indexer loads it on every reindex; the topics commands\n * mutate it atomically. Keep this in sync with `src/topics/paths.ts`'s\n * `topicsYamlPath` — duplicated here only so the indexer doesn't import\n * a second \"where is it\" helper.\n */\nconst TOPICS_YAML_FILENAME = \"topics.yaml\";\n\nexport interface IndexContext {\n  /** Absolute path to the repo root (the dir containing `.almanac/`). */\n  repoRoot: string;\n}\n\nexport interface IndexResult {\n  /** Pages parsed or re-parsed during this run. Zero when the DB was already up to date. */\n  changed: number;\n  /** Pages present in the DB before this run but missing from disk. */\n  removed: number;\n  /**\n   * Pages on disk at the end of this run — i.e. files that made it all the\n   * way through to the index. Skipped files (slug collisions, unreadable,\n   * un-sluggable filenames) are NOT counted here. Use `filesSeen` for the\n   * raw count of `.md` files encountered on disk.\n   *\n   * Alias retained for backwards-compat with existing tests/consumers; new\n   * code should prefer `pagesIndexed` for clarity.\n   */\n  total: number;\n  /** Pages that made it into the index. Same number as `total`. */\n  pagesIndexed: number;\n  /**\n   * Count of `.md` files found under `pages/` before any filtering. Always\n   * `>= pagesIndexed`; the difference is `filesSkipped`.\n   */\n  filesSeen: number;\n  /**\n   * Files dropped before making it into the index — slug collisions,\n   * un-sluggable filenames, or filesystem races (deleted/unreadable mid-run).\n   * Covered by stderr warnings when non-zero.\n   */\n  filesSkipped: number;\n}\n\n// Glob is relative to `pagesDir` (which is `.almanac/pages/`), so this is\n// just \"every .md at any depth\" — not `pages/**/*.md`, because we've\n// already `cd`'d into `pages/` logically.\nconst PAGES_GLOB = \"**/*.md\";\n\n/**\n * The \"front door\" for query commands. Runs the indexer only if the DB is\n * missing or at least one page is newer than it. Meant to be cheap — the\n * common case is \"nothing changed, mtime check returns fast, we're done\".\n *\n * The spec is explicit: \"Reindex is implicit and invisible. If the user\n * didn't didn't explicitly run `reindex`, they shouldn't see reindex\n * output. Silent by default.\" So this function never writes to stdout;\n * warnings (slug collisions, bad frontmatter) still go to stderr.\n */\nexport async function ensureFreshIndex(ctx: IndexContext): Promise<IndexResult> {\n  const almanacDir = join(ctx.repoRoot, \".almanac\");\n  const dbPath = join(almanacDir, \"index.db\");\n  const pagesDir = join(almanacDir, \"pages\");\n\n  if (!existsSync(pagesDir)) {\n    // No pages dir = nothing to index. Open/create the DB so downstream\n    // queries can run against an empty schema rather than crashing on a\n    // missing file.\n    const db = openIndex(dbPath);\n    db.close();\n    return emptyResult();\n  }\n\n  if (\n    !existsSync(dbPath) ||\n    pagesNewerThan(pagesDir, dbPath) ||\n    topicsYamlNewerThan(almanacDir, dbPath)\n  ) {\n    return runIndexer(ctx);\n  }\n  return emptyResult();\n}\n\nfunction emptyResult(): IndexResult {\n  return {\n    changed: 0,\n    removed: 0,\n    total: 0,\n    pagesIndexed: 0,\n    filesSeen: 0,\n    filesSkipped: 0,\n  };\n}\n\n/**\n * Force a full reindex. Identical to `ensureFreshIndex` except it runs\n * the indexer unconditionally. Exposed for `almanac reindex`.\n */\nexport async function runIndexer(ctx: IndexContext): Promise<IndexResult> {\n  const almanacDir = join(ctx.repoRoot, \".almanac\");\n  const dbPath = join(almanacDir, \"index.db\");\n  const pagesDir = join(almanacDir, \"pages\");\n\n  const db = openIndex(dbPath);\n  let result: IndexResult;\n  try {\n    result = await indexPagesInto(db, pagesDir);\n    // After pages are indexed, reconcile the topics table against\n    // `.almanac/topics.yaml` (if present). `indexPagesInto` has already\n    // lazily inserted rows for every topic slug mentioned in page\n    // frontmatter with a title-cased title; `applyTopicsYaml` now\n    // promotes the declared title/description and rewrites parent edges\n    // for those topics that live in the file.\n    await applyTopicsYaml(db, join(almanacDir, TOPICS_YAML_FILENAME));\n  } finally {\n    db.close();\n  }\n\n  // Bump the DB mtime to \"now\" after a successful reindex (even a no-op\n  // one). Otherwise, a page file with a future mtime (clock skew,\n  // `git checkout` preserving source mtimes) would trigger `ensureFreshIndex`\n  // on every query: the freshness check sees `page.mtime > db.mtime`,\n  // reindex runs, finds no content-hash changes, and the DB mtime stays\n  // stale — locking us into a reindex-on-every-query loop. Touching the\n  // DB mtime makes the comparison monotonic.\n  try {\n    const now = new Date();\n    await utimes(dbPath, now, now);\n  } catch {\n    // Touching mtime is a freshness optimization; failures here are\n    // non-fatal and the reindex result is still correct.\n  }\n  return result;\n}\n\ninterface ExistingRow {\n  slug: string;\n  content_hash: string;\n  file_path: string;\n}\n\nasync function indexPagesInto(\n  db: Database.Database,\n  pagesDir: string,\n): Promise<IndexResult> {\n  const files = await fg(PAGES_GLOB, {\n    cwd: pagesDir,\n    absolute: false,\n    onlyFiles: true,\n    caseSensitiveMatch: true,\n  });\n\n  // Load the current state of the index into memory so we can diff against\n  // what's on disk. This is cheap even at 10k pages (one INTEGER + two\n  // short strings per row).\n  const existingRows = db\n    .prepare<[], ExistingRow>(\"SELECT slug, content_hash, file_path FROM pages\")\n    .all();\n  const existingBySlug = new Map<string, ExistingRow>();\n  for (const row of existingRows) existingBySlug.set(row.slug, row);\n\n  // First pass: decide what to do with each file on disk. We record the\n  // intent here so the transaction below can run synchronously — mixing\n  // async file reads into a better-sqlite3 transaction doesn't work\n  // (transactions are sync).\n  const planned: Array<{\n    slug: string;\n    title: string;\n    filePath: string;\n    fullPath: string;\n    contentHash: string;\n    updatedAt: number;\n    archivedAt: number | null;\n    supersededBy: string | null;\n    topics: string[];\n    frontmatterFiles: string[];\n    wikilinks: ReturnType<typeof extractWikilinks>;\n    content: string;\n  }> = [];\n  const seenSlugs = new Set<string>();\n  let filesSkipped = 0;\n\n  for (const rel of files) {\n    const fullPath = join(pagesDir, rel);\n    const base = basename(rel, \".md\");\n    const slug = toKebabCase(base);\n    if (slug.length === 0) {\n      process.stderr.write(\n        `almanac: skipping \"${rel}\" — filename has no slug-able characters\\n`,\n      );\n      filesSkipped++;\n      continue;\n    }\n    if (slug !== base) {\n      // Filename isn't already canonical kebab-case. Warn, but still\n      // index under the canonical slug. `almanac health` (slice 3) will\n      // surface these as a proper report.\n      process.stderr.write(\n        `almanac: warning — \"${rel}\" is not canonical; indexed as slug \"${slug}\"\\n`,\n      );\n    }\n    if (seenSlugs.has(slug)) {\n      // Two files slugify to the same slug. Keep the first, skip the\n      // rest — health will flag this properly in slice 3.\n      process.stderr.write(\n        `almanac: warning — slug \"${slug}\" collides with an earlier file; skipping \"${rel}\"\\n`,\n      );\n      filesSkipped++;\n      continue;\n    }\n\n    // `fast-glob` gave us the list in one shot, but by the time we stat\n    // and read each file it can have been deleted, renamed, or swapped\n    // (editors that save via rename-swap expose this briefly). A single\n    // such race shouldn't tank the whole reindex — matches the malformed-\n    // YAML behavior (\"one bad file doesn't stop the others\"). We narrow\n    // to ENOENT/EACCES so genuine I/O failures (EIO, EMFILE, etc.) still\n    // surface.\n    let st: ReturnType<typeof statSync>;\n    let raw: string;\n    try {\n      st = statSync(fullPath);\n      raw = await readFile(fullPath, \"utf8\");\n    } catch (err: unknown) {\n      if (\n        err instanceof Error &&\n        \"code\" in err &&\n        (err.code === \"ENOENT\" || err.code === \"EACCES\")\n      ) {\n        process.stderr.write(\n          `almanac: skipping \"${rel}\" — ${err.message}\\n`,\n        );\n        filesSkipped++;\n        continue;\n      }\n      throw err;\n    }\n\n    seenSlugs.add(slug);\n    const updatedAt = Math.floor(st.mtimeMs / 1000);\n\n    // Content-hash skip: if the hash matches what's in the DB and the\n    // file path hasn't moved, we can leave this page's rows alone. This\n    // is the fast-path for \"user ran a query; one page was touched\".\n    const contentHash = hashContent(raw);\n    const existing = existingBySlug.get(slug);\n    if (\n      existing !== undefined &&\n      existing.content_hash === contentHash &&\n      existing.file_path === fullPath\n    ) {\n      continue;\n    }\n\n    const fm = parseFrontmatter(raw);\n    const title = fm.title ?? firstH1(fm.body) ?? base;\n    const links = extractWikilinks(fm.body);\n\n    planned.push({\n      slug,\n      title,\n      filePath: rel,\n      fullPath,\n      contentHash,\n      updatedAt,\n      archivedAt: fm.archived_at,\n      supersededBy: fm.superseded_by,\n      topics: fm.topics,\n      frontmatterFiles: fm.files,\n      wikilinks: links,\n      content: fm.body,\n    });\n  }\n\n  // Compute deletions: anything in the DB whose slug isn't on disk\n  // anymore (or whose file slugifies to a different slug now).\n  const toDelete: string[] = [];\n  for (const slug of existingBySlug.keys()) {\n    if (!seenSlugs.has(slug)) toDelete.push(slug);\n  }\n\n  const deleteByPage = db.prepare<[string]>(\"DELETE FROM pages WHERE slug = ?\");\n  const deleteFtsByPage = db.prepare<[string]>(\n    \"DELETE FROM fts_pages WHERE slug = ?\",\n  );\n\n  const replacePage = db.prepare<\n    [string, string, string, string, number, number | null, string | null]\n  >(\n    `INSERT INTO pages (slug, title, file_path, content_hash, updated_at, archived_at, superseded_by)\n     VALUES (?, ?, ?, ?, ?, ?, ?)\n     ON CONFLICT(slug) DO UPDATE SET\n       title         = excluded.title,\n       file_path     = excluded.file_path,\n       content_hash  = excluded.content_hash,\n       updated_at    = excluded.updated_at,\n       archived_at   = excluded.archived_at,\n       superseded_by = excluded.superseded_by`,\n  );\n\n  const deletePageTopics = db.prepare<[string]>(\n    \"DELETE FROM page_topics WHERE page_slug = ?\",\n  );\n  const insertPageTopic = db.prepare<[string, string]>(\n    \"INSERT OR IGNORE INTO page_topics (page_slug, topic_slug) VALUES (?, ?)\",\n  );\n  // Seed ad-hoc topics with a title-cased default. If the topic is\n  // later declared in `.almanac/topics.yaml`, `applyTopicsYaml` will\n  // promote the title/description to whatever the file says. We set the\n  // title here (rather than leaving NULL) so `topics list` and\n  // `health --topic` have a display name even before a user writes to\n  // topics.yaml.\n  const insertTopic = db.prepare<[string, string]>(\n    \"INSERT OR IGNORE INTO topics (slug, title) VALUES (?, ?)\",\n  );\n\n  const deleteFileRefs = db.prepare<[string]>(\n    \"DELETE FROM file_refs WHERE page_slug = ?\",\n  );\n  const insertFileRef = db.prepare<[string, string, string, number]>(\n    \"INSERT OR IGNORE INTO file_refs (page_slug, path, original_path, is_dir) VALUES (?, ?, ?, ?)\",\n  );\n\n  const deleteWikilinks = db.prepare<[string]>(\n    \"DELETE FROM wikilinks WHERE source_slug = ?\",\n  );\n  const insertWikilink = db.prepare<[string, string]>(\n    \"INSERT OR IGNORE INTO wikilinks (source_slug, target_slug) VALUES (?, ?)\",\n  );\n\n  const deleteXwiki = db.prepare<[string]>(\n    \"DELETE FROM cross_wiki_links WHERE source_slug = ?\",\n  );\n  const insertXwiki = db.prepare<[string, string, string]>(\n    \"INSERT OR IGNORE INTO cross_wiki_links (source_slug, target_wiki, target_slug) VALUES (?, ?, ?)\",\n  );\n\n  const insertFts = db.prepare<[string, string, string]>(\n    \"INSERT INTO fts_pages (slug, title, content) VALUES (?, ?, ?)\",\n  );\n\n  const apply = db.transaction(() => {\n    for (const slug of toDelete) {\n      // `fts_pages` is an FTS5 virtual table — FK cascades do NOT propagate\n      // into it, so we must delete FTS rows explicitly before relying on\n      // `DELETE FROM pages` to cascade-clean the four real tables\n      // (page_topics, file_refs, wikilinks, cross_wiki_links). If this\n      // explicit delete ever gets removed, orphaned FTS rows will show up\n      // as phantom search hits pointing at non-existent slugs.\n      deleteFtsByPage.run(slug);\n      deleteByPage.run(slug); // CASCADE cleans page_topics, file_refs, wikilinks, cross_wiki_links\n    }\n\n    for (const p of planned) {\n      // page_topics/file_refs/wikilinks/cross_wiki_links all cascade on\n      // delete, so the cleanest \"replace\" story is: delete-then-insert\n      // the per-page rows under the same transaction. Doing it this way\n      // (rather than `ON CONFLICT DO UPDATE` per row) keeps the logic\n      // uniform and makes \"remove a topic from frontmatter\" work.\n      deletePageTopics.run(p.slug);\n      deleteFileRefs.run(p.slug);\n      deleteWikilinks.run(p.slug);\n      deleteXwiki.run(p.slug);\n      // Same virtual-table reason as the deletion branch above — FTS5\n      // rows do not cascade, so clean them by hand before reinserting.\n      deleteFtsByPage.run(p.slug);\n\n      replacePage.run(\n        p.slug,\n        p.title,\n        p.fullPath,\n        p.contentHash,\n        p.updatedAt,\n        p.archivedAt,\n        p.supersededBy,\n      );\n\n      for (const topic of p.topics) {\n        const topicSlug = toKebabCase(topic);\n        if (topicSlug.length === 0) continue;\n        insertTopic.run(topicSlug, titleCase(topicSlug));\n        insertPageTopic.run(p.slug, topicSlug);\n      }\n\n      // Frontmatter `files:` — normalize each entry, inferring directness\n      // from its trailing slash. Authors who write `src/payments` (no\n      // trailing slash) are asserting a file; this matches how `[[...]]`\n      // classifies the same string. We store both the lowercased form\n      // (for `--mentions` GLOB queries) and the casing-preserving form\n      // (for dead-ref `existsSync` on case-sensitive filesystems).\n      for (const raw of p.frontmatterFiles) {\n        const isDir = looksLikeDir(raw);\n        const path = normalizePath(raw, isDir);\n        const originalPath = normalizePathPreservingCase(raw, isDir);\n        if (path.length === 0) continue;\n        insertFileRef.run(p.slug, path, originalPath, isDir ? 1 : 0);\n      }\n\n      // Inline `[[...]]` extracted from body.\n      for (const ref of p.wikilinks) {\n        switch (ref.kind) {\n          case \"page\":\n            insertWikilink.run(p.slug, ref.target);\n            break;\n          case \"file\":\n            insertFileRef.run(p.slug, ref.path, ref.originalPath, 0);\n            break;\n          case \"folder\":\n            insertFileRef.run(p.slug, ref.path, ref.originalPath, 1);\n            break;\n          case \"xwiki\":\n            insertXwiki.run(p.slug, ref.wiki, ref.target);\n            break;\n        }\n      }\n\n      insertFts.run(p.slug, p.title, p.content);\n    }\n  });\n  apply();\n\n  // `relative` keeps lint happy about unused imports; total is just the\n  // count of .md files we saw on this pass.\n  void relative;\n  const pagesIndexed = seenSlugs.size;\n  return {\n    changed: planned.length,\n    removed: toDelete.length,\n    total: pagesIndexed,\n    pagesIndexed,\n    filesSeen: files.length,\n    filesSkipped,\n  };\n}\n\n/**\n * Return true if any `pages/**\\/*.md` has an mtime strictly greater than\n * the index DB's mtime. We walk with `fast-glob` rather than shell out to\n * `find` for portability.\n *\n * This is the \"should we reindex?\" check. It's intentionally cheap —\n * `fast-glob` with `stats: true` gives us mtimes without a second `stat`\n * round-trip.\n */\nfunction pagesNewerThan(pagesDir: string, dbPath: string): boolean {\n  let dbMtime: number;\n  try {\n    dbMtime = statSync(dbPath).mtimeMs;\n  } catch {\n    return true;\n  }\n\n  // Synchronous walk — `fg.sync` is fine at this scale and keeps the\n  // decision path simple (we don't need to await inside every CLI entry).\n  const entries = fg.sync(PAGES_GLOB, {\n    cwd: pagesDir,\n    absolute: true,\n    onlyFiles: true,\n    stats: true,\n  }) as Array<{ path: string; stats?: { mtimeMs: number } }>;\n\n  for (const entry of entries) {\n    const mtime = entry.stats?.mtimeMs;\n    if (mtime !== undefined && mtime > dbMtime) return true;\n  }\n  return false;\n}\n\nfunction hashContent(raw: string): string {\n  return createHash(\"sha256\").update(raw).digest(\"hex\");\n}\n\n/**\n * Return true if `topics.yaml` has an mtime strictly greater than the\n * index DB's mtime. This is the topics-side mirror of `pagesNewerThan`\n * — mutations to `topics.yaml` (title/description/parents) aren't\n * visible from any page mtime, so we need a separate freshness hook\n * for the file itself.\n *\n * Missing `topics.yaml` → false. Absence is legal and means \"no topic\n * metadata, only whatever pages declare\". A missing file doesn't\n * invalidate the existing index.\n */\nfunction topicsYamlNewerThan(almanacDir: string, dbPath: string): boolean {\n  const path = join(almanacDir, \"topics.yaml\");\n  if (!existsSync(path)) return false;\n  let dbMtime: number;\n  try {\n    dbMtime = statSync(dbPath).mtimeMs;\n  } catch {\n    return true;\n  }\n  try {\n    const st = statSync(path);\n    return st.mtimeMs > dbMtime;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Apply the contents of `.almanac/topics.yaml` to SQLite.\n *\n * Called at the tail of every reindex. For each entry in the file we\n * upsert a row into `topics` (with title + description) and rewrite\n * that topic's edges in `topic_parents`. Topics that were ad-hoc-only\n * before (mentioned in page frontmatter, never `almanac topics\n * create`d) get their display name promoted to whatever is in the\n * file.\n *\n * Importantly, we do NOT delete `topics` rows that live only in page\n * frontmatter — those are legal, per the spec (\"any slug mentioned in\n * pages' `topics:` frontmatter gets a row, even if not in\n * topics.yaml\"). We also do NOT clear `topic_parents` wholesale; we\n * rewrite edges for each declared topic but leave untouched rows for\n * ad-hoc topics (which by definition have no declared parents).\n *\n * Missing file = no-op. This is the \"no topic metadata yet\" state and\n * callers shouldn't have to paper over it.\n */\nasync function applyTopicsYaml(\n  db: Database.Database,\n  topicsYamlPath: string,\n): Promise<void> {\n  if (!existsSync(topicsYamlPath)) return;\n  let file;\n  try {\n    file = await loadTopicsFile(topicsYamlPath);\n  } catch (err: unknown) {\n    const message = err instanceof Error ? err.message : String(err);\n    process.stderr.write(`almanac: ${message}\\n`);\n    return;\n  }\n\n  const upsertTopic = db.prepare<[string, string, string | null]>(\n    `INSERT INTO topics (slug, title, description) VALUES (?, ?, ?)\n     ON CONFLICT(slug) DO UPDATE SET\n       title = excluded.title,\n       description = excluded.description`,\n  );\n  const clearParents = db.prepare<[string]>(\n    \"DELETE FROM topic_parents WHERE child_slug = ?\",\n  );\n  const insertParent = db.prepare<[string, string]>(\n    \"INSERT OR IGNORE INTO topic_parents (child_slug, parent_slug) VALUES (?, ?)\",\n  );\n\n  // Collect every slug we consider \"declared\" — in topics.yaml or\n  // referenced by any page_topics row. Anything outside this set is\n  // stale (e.g., a topic that used to be in the file before a rename\n  // or delete, or an ad-hoc slug whose only page just got untagged).\n  // Those get removed so `empty-topics` doesn't falsely flag them.\n  const declared = new Set<string>();\n  for (const t of file.topics) declared.add(t.slug);\n  const adHoc = db\n    .prepare<[], { topic_slug: string }>(\n      \"SELECT DISTINCT topic_slug FROM page_topics\",\n    )\n    .all();\n  for (const r of adHoc) declared.add(r.topic_slug);\n\n  const apply = db.transaction(() => {\n    for (const t of file.topics) {\n      upsertTopic.run(t.slug, t.title, t.description);\n      clearParents.run(t.slug);\n      for (const parent of t.parents) {\n        if (parent === t.slug) continue;\n        insertParent.run(t.slug, parent);\n      }\n    }\n\n    // Prune stale topic rows + any edges attached to them. We do this\n    // last so the upserts above have already promoted declared slugs.\n    const existing = db\n      .prepare<[], { slug: string }>(\"SELECT slug FROM topics\")\n      .all();\n    const deleteTopic = db.prepare<[string]>(\"DELETE FROM topics WHERE slug = ?\");\n    const deleteEdgesByChild = db.prepare<[string]>(\n      \"DELETE FROM topic_parents WHERE child_slug = ?\",\n    );\n    const deleteEdgesByParent = db.prepare<[string]>(\n      \"DELETE FROM topic_parents WHERE parent_slug = ?\",\n    );\n    for (const r of existing) {\n      if (declared.has(r.slug)) continue;\n      deleteEdgesByChild.run(r.slug);\n      deleteEdgesByParent.run(r.slug);\n      deleteTopic.run(r.slug);\n    }\n  });\n  apply();\n}\n","import { existsSync } from \"node:fs\";\nimport { mkdir, readFile, rename, writeFile } from \"node:fs/promises\";\nimport { dirname } from \"node:path\";\n\nimport yaml from \"js-yaml\";\n\nimport { toKebabCase } from \"../slug.js\";\n\n/**\n * One entry in `.almanac/topics.yaml` — the source of truth for topic\n * metadata (title, description, DAG parents). Pages are still the source\n * of truth for which pages belong to which topics; this file only holds\n * the topic-level attributes.\n *\n * `slug` is the canonical kebab-case key used everywhere downstream\n * (SQLite `topics.slug`, page frontmatter `topics:` entries, wikilink\n * targets). `title` is the human-readable name the user typed at create\n * time. `description` is a free-form one-liner (or null when unset).\n * `parents` is the DAG edge list — kept as an array of slugs rather than\n * a nested structure so round-tripping stays boring and a user eyeballing\n * the file can see the full graph.\n */\nexport interface TopicEntry {\n  slug: string;\n  title: string;\n  description: string | null;\n  parents: string[];\n}\n\nexport interface TopicsFile {\n  topics: TopicEntry[];\n}\n\n/**\n * Load `.almanac/topics.yaml` into a `TopicsFile`. A missing file is not\n * an error — it's the first-run state, which we treat as \"no topic\n * metadata, only whatever the pages declare in frontmatter\". Malformed\n * YAML IS an error; we surface it rather than silently clobbering the\n * user's committed source of truth.\n *\n * The return shape is always normalized — callers don't have to guard\n * for missing `topics` key, wrong types, or absent `parents` arrays.\n */\nexport async function loadTopicsFile(path: string): Promise<TopicsFile> {\n  if (!existsSync(path)) {\n    return { topics: [] };\n  }\n  let raw: string;\n  try {\n    raw = await readFile(path, \"utf8\");\n  } catch (err: unknown) {\n    if (isNodeError(err) && err.code === \"ENOENT\") {\n      return { topics: [] };\n    }\n    throw err;\n  }\n\n  const trimmed = raw.trim();\n  if (trimmed.length === 0) {\n    return { topics: [] };\n  }\n\n  let parsed: unknown;\n  try {\n    parsed = yaml.load(raw);\n  } catch (err: unknown) {\n    const message = err instanceof Error ? err.message : String(err);\n    throw new Error(`topics.yaml at ${path} is not valid YAML: ${message}`);\n  }\n\n  if (parsed === null || parsed === undefined) {\n    return { topics: [] };\n  }\n\n  if (typeof parsed !== \"object\" || Array.isArray(parsed)) {\n    throw new Error(`topics.yaml at ${path} must be a mapping`);\n  }\n\n  const obj = parsed as Record<string, unknown>;\n  const rawTopics = obj.topics;\n  if (rawTopics === undefined || rawTopics === null) {\n    return { topics: [] };\n  }\n  if (!Array.isArray(rawTopics)) {\n    throw new Error(`topics.yaml at ${path} — \"topics\" must be a list`);\n  }\n\n  const topics: TopicEntry[] = [];\n  for (const item of rawTopics) {\n    if (typeof item !== \"object\" || item === null || Array.isArray(item)) {\n      continue;\n    }\n    const entry = item as Record<string, unknown>;\n    const slugRaw = entry.slug;\n    if (typeof slugRaw !== \"string\" || slugRaw.trim().length === 0) continue;\n    const slug = toKebabCase(slugRaw);\n    if (slug.length === 0) continue;\n    const title =\n      typeof entry.title === \"string\" && entry.title.trim().length > 0\n        ? entry.title.trim()\n        : titleCase(slug);\n    const description =\n      typeof entry.description === \"string\" &&\n      entry.description.trim().length > 0\n        ? entry.description.trim()\n        : null;\n    const parents: string[] = [];\n    if (Array.isArray(entry.parents)) {\n      for (const p of entry.parents) {\n        if (typeof p === \"string\" && p.trim().length > 0) {\n          const ps = toKebabCase(p);\n          if (ps.length > 0 && ps !== slug && !parents.includes(ps)) {\n            parents.push(ps);\n          }\n        }\n      }\n    }\n    topics.push({ slug, title, description, parents });\n  }\n\n  return { topics };\n}\n\n/**\n * Write a `TopicsFile` atomically — tmp file + rename, same pattern as\n * the registry. A half-written topics.yaml would corrupt the user's\n * committed source of truth, so we never write in place.\n *\n * Ordering: topics are sorted by slug for stable diffs. Parents within\n * each entry stay in the order the caller passed them (semantically an\n * ordered list — topics.yaml is the place a user can visibly reason\n * about \"primary parent first\", even though SQLite treats them as a\n * set).\n *\n * We emit a leading comment so first-time readers know the file is\n * edited by the CLI and what its role is.\n */\nexport async function writeTopicsFile(\n  path: string,\n  file: TopicsFile,\n): Promise<void> {\n  const sorted = [...file.topics].sort((a, b) => a.slug.localeCompare(b.slug));\n  const doc = {\n    topics: sorted.map((t) => {\n      // Emit all four keys in a stable order: slug, title, description,\n      // parents. description is emitted as `null` in YAML when unset so\n      // the schema stays consistent across entries (js-yaml renders the\n      // literal word `null`, not the `~` shorthand).\n      return {\n        slug: t.slug,\n        title: t.title,\n        description: t.description,\n        parents: t.parents,\n      };\n    }),\n  };\n\n  const header =\n    `# .almanac/topics.yaml — source of truth for topic metadata.\\n` +\n    `# Managed by \\`almanac topics\\` commands. User-added comments\\n` +\n    `# between entries will be stripped on the next write (js-yaml\\n` +\n    `# doesn't round-trip comments). Edit at your own risk — or use the\\n` +\n    `# CLI (\\`almanac topics create|link|describe|rename|delete\\`)\\n` +\n    `# which preserves the structure correctly.\\n`;\n  const body = yaml.dump(doc, {\n    lineWidth: 100,\n    noRefs: true,\n    sortKeys: false,\n  });\n  const content = `${header}${body}`;\n  const tmpPath = `${path}.tmp`;\n  // mkdir parent in case `.almanac/` vanished (shouldn't, but cheap insurance)\n  const parent = dirname(path);\n  if (!existsSync(parent)) {\n    await mkdir(parent, { recursive: true });\n  }\n  await writeFile(tmpPath, content, \"utf8\");\n  await rename(tmpPath, path);\n}\n\n/**\n * Look up a topic by slug. Returns `null` when the slug is absent —\n * callers distinguish \"declared in topics.yaml\" from \"ad-hoc (only\n * appears in page frontmatter)\" based on this.\n */\nexport function findTopic(file: TopicsFile, slug: string): TopicEntry | null {\n  for (const t of file.topics) {\n    if (t.slug === slug) return t;\n  }\n  return null;\n}\n\n/**\n * Ensure a topic entry exists. If missing, inserts a minimal entry with\n * title-cased title and null description. Returns the (possibly new)\n * entry. Used by `tag`, `topics create` (with `--parent auto-creating`),\n * and `topics link` (auto-creating child/parent on demand).\n */\nexport function ensureTopic(file: TopicsFile, slug: string): TopicEntry {\n  const existing = findTopic(file, slug);\n  if (existing !== null) return existing;\n  const entry: TopicEntry = {\n    slug,\n    title: titleCase(slug),\n    description: null,\n    parents: [],\n  };\n  file.topics.push(entry);\n  return entry;\n}\n\n/**\n * Convert a slug back to a human-ish title: `auth-flow` → `Auth Flow`.\n * Used as the fallback title when the caller didn't provide one\n * (auto-creation paths, ad-hoc slugs coming from page frontmatter).\n */\nexport function titleCase(slug: string): string {\n  if (slug.length === 0) return slug;\n  return slug\n    .split(\"-\")\n    .filter((s) => s.length > 0)\n    .map((s) => `${s[0]?.toUpperCase() ?? \"\"}${s.slice(1)}`)\n    .join(\" \");\n}\n\nfunction isNodeError(err: unknown): err is NodeJS.ErrnoException {\n  return err instanceof Error && \"code\" in err;\n}\n","/**\n * Path normalization for the file/folder references stored in `file_refs`\n * and for the query input passed to `--mentions`.\n *\n * The same function runs over both sides so a value written at index time\n * and a value looked up at query time compare byte-for-byte. If this ever\n * drifts between writers and readers, `--mentions` starts silently missing\n * matches — apply one canonicalization, not two.\n *\n * Rules (from the spec, Correctness):\n *   - Lowercase (macOS filesystems are case-insensitive, so the wiki treats\n *     `Src/Checkout/` and `src/checkout/` as the same path)\n *   - Forward slashes only (never backslashes from Windows-authored content)\n *   - No leading `./`\n *   - Collapse redundant slashes (`src//checkout/` → `src/checkout/`)\n *   - Trailing `/` iff the caller says it's a directory\n *\n * The `isDir` flag is a signal carried alongside the path — we don't infer\n * it from the raw string here, because frontmatter `files:` entries and the\n * inline `[[...]]` classifier both decide directness themselves and pass\n * the answer in. Having one place decide and one place normalize keeps the\n * directory inference rule testable in isolation.\n */\nexport function normalizePath(raw: string, isDir: boolean): string {\n  const normalized = normalizeShape(raw, isDir);\n  return normalized.toLowerCase();\n}\n\n/**\n * Normalize shape without lowercasing — preserves the author's casing.\n * Used to store `original_path` in `file_refs` so dead-ref checks on\n * case-sensitive filesystems (Linux, `git` checkouts with core.ignorecase\n * false) stat the actual path on disk rather than a lowercased alias.\n *\n * Everything else about the result is identical to `normalizePath`:\n * forward slashes, no `./`, no duplicate slashes, trailing `/` iff\n * `isDir`. The ONLY difference is the final `.toLowerCase()` is skipped.\n */\nexport function normalizePathPreservingCase(raw: string, isDir: boolean): string {\n  return normalizeShape(raw, isDir);\n}\n\nfunction normalizeShape(raw: string, isDir: boolean): string {\n  let s = raw.trim();\n\n  // Windows-style backslashes → forward slashes. We never want to store\n  // backslashes; a path authored on Windows and checked in should match\n  // the same path authored on macOS.\n  s = s.replace(/\\\\+/g, \"/\");\n\n  // Drop a leading `./` — it's syntactic noise and authors inconsistently\n  // include it. `./src/checkout/` and `src/checkout/` must hash equal.\n  while (s.startsWith(\"./\")) s = s.slice(2);\n\n  // Collapse any run of slashes to a single slash. This also normalizes\n  // `src//checkout/` and accidental doubled slashes from string concat.\n  s = s.replace(/\\/+/g, \"/\");\n\n  // Strip any trailing slashes before re-applying the directory marker —\n  // this way we don't care if the caller fed us `src/checkout` or\n  // `src/checkout/` as a directory; we impose our own rule.\n  s = s.replace(/\\/+$/, \"\");\n\n  if (isDir) {\n    // Directories ALWAYS end with a trailing slash. This is what lets the\n    // GLOB queries distinguish `src/checkout/` (the directory) from\n    // `src/checkout` (a file with no extension) without ambiguity.\n    return `${s}/`;\n  }\n  return s;\n}\n\n/**\n * Infer `isDir` from the raw string the author wrote. Only used at the\n * point of parsing frontmatter `files:` entries and inline `[[...]]`\n * references — everywhere else, `isDir` is already known from context.\n *\n * Rule: trailing `/` (after backslash normalization) means directory.\n */\nexport function looksLikeDir(raw: string): boolean {\n  const s = raw.trim().replace(/\\\\+/g, \"/\");\n  return s.endsWith(\"/\");\n}\n","import Database from \"better-sqlite3\";\n\n/**\n * Schema DDL, applied on every open. All statements are `CREATE ... IF NOT\n * EXISTS` so this is idempotent — handy when the file already exists but\n * was written by an older version, and tolerable because the schema is\n * append-only (new tables don't collide).\n *\n * Departures from the raw spec, explained:\n *   - `page_topics.topic_slug` has no FK to `topics(slug)`. Topics are\n *     created lazily when a page declares them; a strict FK would force us\n *     to upsert topic rows before the page rows, which doesn't buy us\n *     anything in slice 2 and locks us out of slice 3's \"no explicit topic\n *     registration needed\" behavior.\n *   - `wikilinks.target_slug` / `cross_wiki_links.target_slug` also have\n *     no FK — these can be intentionally broken (unwritten target page),\n *     and `almanac health` will surface them in slice 3.\n *\n * `file_refs` carries TWO forms of each path:\n *   - `path`          — normalized + lowercased, used for GLOB/equality\n *                       queries (`--mentions`). Stable across casing\n *                       choices on macOS/Windows.\n *   - `original_path` — as-written (normalized slashes, no `./`, trailing\n *                       `/` for dirs), preserving the author's casing.\n *                       Used for filesystem stats (dead-refs on\n *                       case-sensitive filesystems like Linux) and for\n *                       user-facing display (`almanac info`).\n *\n * See also: `SCHEMA_VERSION` below and the migration logic in `openIndex`.\n */\nconst SCHEMA_DDL = `\nCREATE TABLE IF NOT EXISTS pages (\n  slug          TEXT PRIMARY KEY,\n  title         TEXT,\n  file_path     TEXT NOT NULL,\n  content_hash  TEXT NOT NULL,\n  updated_at    INTEGER NOT NULL,\n  archived_at   INTEGER,\n  superseded_by TEXT\n);\n\nCREATE TABLE IF NOT EXISTS topics (\n  slug        TEXT PRIMARY KEY,\n  title       TEXT,\n  description TEXT\n);\n\nCREATE TABLE IF NOT EXISTS page_topics (\n  page_slug  TEXT NOT NULL REFERENCES pages(slug) ON DELETE CASCADE,\n  topic_slug TEXT NOT NULL,\n  PRIMARY KEY (page_slug, topic_slug)\n);\n\nCREATE TABLE IF NOT EXISTS topic_parents (\n  child_slug  TEXT NOT NULL,\n  parent_slug TEXT NOT NULL,\n  PRIMARY KEY (child_slug, parent_slug),\n  CHECK (child_slug != parent_slug)\n);\n\nCREATE TABLE IF NOT EXISTS file_refs (\n  page_slug     TEXT NOT NULL REFERENCES pages(slug) ON DELETE CASCADE,\n  path          TEXT NOT NULL,\n  original_path TEXT NOT NULL,\n  is_dir        INTEGER NOT NULL,\n  PRIMARY KEY (page_slug, path)\n);\nCREATE INDEX IF NOT EXISTS idx_file_refs_path ON file_refs(path);\n\nCREATE TABLE IF NOT EXISTS wikilinks (\n  source_slug TEXT NOT NULL REFERENCES pages(slug) ON DELETE CASCADE,\n  target_slug TEXT NOT NULL,\n  PRIMARY KEY (source_slug, target_slug)\n);\n\nCREATE TABLE IF NOT EXISTS cross_wiki_links (\n  source_slug TEXT NOT NULL REFERENCES pages(slug) ON DELETE CASCADE,\n  target_wiki TEXT NOT NULL,\n  target_slug TEXT NOT NULL,\n  PRIMARY KEY (source_slug, target_wiki, target_slug)\n);\n\n-- NOTE: virtual FTS5 table — ON DELETE CASCADE from pages does NOT apply.\n-- The indexer must explicitly DELETE FROM fts_pages whenever it removes\n-- or replaces a page row, or we leak orphaned FTS rows.\nCREATE VIRTUAL TABLE IF NOT EXISTS fts_pages USING fts5(slug, title, content);\n`;\n\n/**\n * Bump this whenever the schema changes in a backwards-incompatible way.\n * On open we compare the stored `user_version` against this constant; if\n * it's lower, we drop the affected tables so the next `runIndexer` can\n * rebuild them. Full reindex is cheap (everything lives on disk as\n * markdown), so \"drop + recreate\" is simpler than ALTER TABLE migrations.\n *\n * Version history:\n *   1 — initial slice-2 schema\n *   2 — slice-3-review: added `file_refs.original_path`\n */\nconst SCHEMA_VERSION = 2;\n\n/**\n * Open `index.db` and apply the schema. Foreign keys are off by default in\n * SQLite; we turn them on per-connection so the ON DELETE CASCADE on\n * `pages` actually fires when we delete stale rows during incremental\n * reindex.\n *\n * We don't wrap this open in a transaction — `CREATE ... IF NOT EXISTS` is\n * safe to run repeatedly and the FTS5 virtual-table creation is already\n * atomic.\n *\n * Migration: if the DB was created by an older schema (`user_version` <\n * `SCHEMA_VERSION`), we drop the tables whose shape changed and let the\n * CREATE IF NOT EXISTS below rebuild them. The next `runIndexer` repopulates\n * from the filesystem — cheap and avoids the ALTER TABLE dance.\n */\nexport function openIndex(dbPath: string): Database.Database {\n  const db = new Database(dbPath);\n  // WAL journal mode is persistent — once set, it's recorded in the DB\n  // header and survives close/open cycles. Check first and only switch if\n  // we're not already there; this avoids a redundant pragma write on every\n  // query command.\n  const mode = db.pragma(\"journal_mode\", { simple: true });\n  if (typeof mode !== \"string\" || mode.toLowerCase() !== \"wal\") {\n    db.pragma(\"journal_mode = WAL\");\n  }\n  db.pragma(\"foreign_keys = ON\");\n\n  const rawVersion = db.pragma(\"user_version\", { simple: true });\n  const currentVersion = typeof rawVersion === \"number\" ? rawVersion : 0;\n  if (currentVersion < SCHEMA_VERSION) {\n    // Drop tables whose shape changed. `file_refs` got `original_path`\n    // as of v2; easiest to drop it entirely so CREATE IF NOT EXISTS\n    // runs with the new definition. Pages/topics/links are untouched.\n    db.exec(\"DROP TABLE IF EXISTS file_refs\");\n    // The indexer's fast-path skips pages whose content_hash matches,\n    // which means a migration-dropped `file_refs` wouldn't get\n    // repopulated until a page changed. Clear the hash column so the\n    // next reindex treats every page as changed and rebuilds its\n    // file_refs/wikilinks/cross-wiki rows. Table may not exist yet on\n    // a brand-new DB, so swallow errors.\n    try {\n      db.exec(\"UPDATE pages SET content_hash = ''\");\n    } catch {\n      // pages table didn't exist yet; the upcoming CREATE IF NOT EXISTS\n      // takes care of a fresh install.\n    }\n    db.pragma(`user_version = ${SCHEMA_VERSION}`);\n  }\n\n  db.exec(SCHEMA_DDL);\n  return db;\n}\n","import { toKebabCase } from \"../slug.js\";\nimport {\n  looksLikeDir,\n  normalizePath,\n  normalizePathPreservingCase,\n} from \"./paths.js\";\n\n/**\n * One parsed `[[...]]` reference from a page body. Classification is\n * deterministic and content-based — see `classifyWikilink` below.\n *\n * Callers dispatch on `kind`:\n *   - `page`    → row in `wikilinks`\n *   - `file`    → row in `file_refs` with `is_dir = 0`\n *   - `folder`  → row in `file_refs` with `is_dir = 1`\n *   - `xwiki`   → row in `cross_wiki_links`\n *\n * File/folder refs carry TWO forms of the path:\n *   - `path`         — lowercased (for `--mentions` lookups)\n *   - `originalPath` — as-written (for filesystem stats on case-sensitive\n *                      systems and for user-facing display)\n */\nexport type WikilinkRef =\n  | { kind: \"page\"; target: string }\n  | { kind: \"file\"; path: string; originalPath: string }\n  | { kind: \"folder\"; path: string; originalPath: string }\n  | { kind: \"xwiki\"; wiki: string; target: string };\n\n/**\n * Rules from the spec (\"Classification rules\"), applied in order:\n *\n *   1. Contains `:` before any `/`  → cross-wiki reference (`wiki:slug`)\n *   2. Contains `/`                  → file or folder reference\n *          - Trailing `/` = folder\n *          - Otherwise    = file\n *   3. Otherwise                     → page slug wikilink\n *\n * Edge cases the test suite pins down:\n *   - `[[a:b/c]]`      → xwiki (colon is before the slash, rule 1 wins)\n *   - `[[src/a:b]]`    → file (slash is before the colon, rule 2 wins)\n *   - `[[./x]]`        → the leading `./` is stripped by `normalizePath`,\n *                        so this lands in `file_refs` as `x`. A bare `./x`\n *                        with no inner slash would classify as a file.\n *   - `[[foo|display]]`→ Obsidian-style display text is stripped; we key\n *                        on the target only. A future slice could surface\n *                        display text in `almanac info`.\n */\nexport function classifyWikilink(raw: string): WikilinkRef | null {\n  // Strip Obsidian-style `|display` suffix — we don't index display text\n  // in slice 2, but we want the classifier to see the real target.\n  const pipe = raw.indexOf(\"|\");\n  let body = pipe === -1 ? raw : raw.slice(0, pipe);\n  body = body.trim();\n  if (body.length === 0) return null;\n\n  const firstColon = body.indexOf(\":\");\n  const firstSlash = body.indexOf(\"/\");\n\n  // Rule 1: cross-wiki, `wiki:slug`. Only if the colon comes before any\n  // slash — otherwise `src/urls.ts:42` (hypothetical) would wrongly\n  // classify as xwiki.\n  if (firstColon !== -1 && (firstSlash === -1 || firstColon < firstSlash)) {\n    const wiki = body.slice(0, firstColon).trim();\n    const target = body.slice(firstColon + 1).trim();\n    if (wiki.length === 0 || target.length === 0) return null;\n    return { kind: \"xwiki\", wiki, target };\n  }\n\n  // Rule 2: file or folder. The `/` may be anywhere including trailing.\n  if (firstSlash !== -1) {\n    const isDir = looksLikeDir(body);\n    const path = normalizePath(body, isDir);\n    const originalPath = normalizePathPreservingCase(body, isDir);\n    if (path.length === 0) return null;\n    return isDir\n      ? { kind: \"folder\", path, originalPath }\n      : { kind: \"file\", path, originalPath };\n  }\n\n  // Rule 3: page slug wikilink. Authors might write `Checkout Flow` or\n  // `Checkout_Flow` by accident — slugify defensively so backlinks still\n  // resolve in those cases.\n  const target = toKebabCase(body);\n  if (target.length === 0) return null;\n  return { kind: \"page\", target };\n}\n\n/**\n * Walk a markdown body and pull every `[[...]]` reference. We scan the\n * whole body rather than try to skip code blocks — the spec is explicit:\n * \"Prose outside `[[...]]` is just prose. No backtick-path heuristics, no\n * false positives from code blocks or log output.\" A `[[foo]]` inside a\n * fenced code block is still a wikilink. Authors who genuinely need a\n * literal `[[x]]` in code can escape one of the brackets.\n */\nexport function extractWikilinks(body: string): WikilinkRef[] {\n  const out: WikilinkRef[] = [];\n  const re = /\\[\\[([^\\]\\n]+)\\]\\]/g;\n  let m: RegExpExecArray | null;\n  while ((m = re.exec(body)) !== null) {\n    const ref = classifyWikilink(m[1] ?? \"\");\n    if (ref !== null) out.push(ref);\n  }\n  return out;\n}\n","import { existsSync } from \"node:fs\";\nimport { join } from \"node:path\";\n\nimport { findNearestAlmanacDir } from \"../paths.js\";\nimport { findEntry } from \"../registry/index.js\";\n\n/**\n * Figure out which repo root a query command should run against.\n *\n * Two modes, in order of precedence:\n *   1. `--wiki <name>`  — look it up in the global registry. Fails\n *      explicitly if the name isn't registered or its path has gone\n *      missing (unmounted drive, deleted repo). No silent fallback, which\n *      would hide the real problem from the user.\n *   2. default — walk up from `cwd` like git does. Fails if we're not\n *      inside a `.almanac/` repo.\n *\n * Returns the absolute path to the repo root (the directory containing\n * `.almanac/`).\n *\n * NOTE (spec contract, not yet implemented): when `--all` lands in a\n * future slice, it must silently skip wikis whose paths have gone\n * unreachable — the asymmetry with `--wiki <name>` is deliberate.\n * Explicit lookup is loud about failures (user named a specific wiki);\n * bulk `--all` is quiet (user asked \"whatever's available\"). Don't\n * unify the error behavior when adding `--all`.\n */\nexport async function resolveWikiRoot(params: {\n  cwd: string;\n  wiki?: string;\n}): Promise<string> {\n  if (params.wiki !== undefined) {\n    const entry = await findEntry({ name: params.wiki });\n    if (entry === null) {\n      throw new Error(`no registered wiki named \"${params.wiki}\"`);\n    }\n    if (!existsSync(join(entry.path, \".almanac\"))) {\n      throw new Error(\n        `wiki \"${params.wiki}\" path is unreachable (${entry.path})`,\n      );\n    }\n    return entry.path;\n  }\n\n  const nearest = findNearestAlmanacDir(params.cwd);\n  if (nearest === null) {\n    throw new Error(\n      \"no .almanac/ found in this directory or any parent; run `almanac init` first\",\n    );\n  }\n  return nearest;\n}\n","import type Database from \"better-sqlite3\";\n\nimport type { TopicsFile } from \"./yaml.js\";\n\n/**\n * Depth cap for all recursive traversals of the topics DAG. Belt and\n * suspenders alongside the `CHECK (child_slug != parent_slug)` on the\n * `topic_parents` table — even if a cycle somehow slipped into the data\n * (hand-edited `topics.yaml`, past bug), the CTE can't runaway.\n *\n * 32 is chosen as \"deeper than any real human-authored taxonomy will\n * ever go\". A 32-level topic hierarchy is absurd; anything hitting this\n * cap is almost certainly a cycle.\n */\nexport const DAG_DEPTH_CAP = 32;\n\n/**\n * Given a `topics.yaml` in memory, compute the set of ancestors of a\n * given slug (not including the slug itself). Used by `topics link`\n * to check whether a proposed edge would create a cycle.\n *\n * Running off the in-memory file lets `link` validate BEFORE touching\n * either the DB or the YAML, so a refusal doesn't leave half the state\n * mutated. Depth-capped with the same constant as the SQLite CTE.\n */\nexport function ancestorsInFile(\n  file: TopicsFile,\n  slug: string,\n): Set<string> {\n  // Build a child → parents map once.\n  const parentsOf = new Map<string, string[]>();\n  for (const t of file.topics) {\n    parentsOf.set(t.slug, t.parents);\n  }\n  const ancestors = new Set<string>();\n  // BFS, depth-capped. We stop descending when we've hit the cap or\n  // revisit an already-seen node (self-loop defense).\n  let frontier: string[] = parentsOf.get(slug) ?? [];\n  let depth = 0;\n  while (frontier.length > 0 && depth < DAG_DEPTH_CAP) {\n    const next: string[] = [];\n    for (const node of frontier) {\n      if (ancestors.has(node)) continue;\n      ancestors.add(node);\n      const ps = parentsOf.get(node);\n      if (ps !== undefined) next.push(...ps);\n    }\n    frontier = next;\n    depth += 1;\n  }\n  return ancestors;\n}\n\n/**\n * Return all descendants of a given topic slug via the SQLite\n * `topic_parents` table. Depth-capped at `DAG_DEPTH_CAP`.\n *\n * Used by `topics show --descendants` to expand a topic's page list\n * through its subtopics. The query is a canonical recursive CTE; we\n * `UNION` (not `UNION ALL`) so cycles in the data don't spin forever.\n */\nexport function descendantsInDb(\n  db: Database.Database,\n  slug: string,\n): string[] {\n  const rows = db\n    .prepare<[string, number], { slug: string }>(\n      `WITH RECURSIVE desc(slug, depth) AS (\n         SELECT child_slug, 1 FROM topic_parents WHERE parent_slug = ?\n         UNION\n         SELECT tp.child_slug, d.depth + 1\n         FROM topic_parents tp\n         JOIN desc d ON tp.parent_slug = d.slug\n         WHERE d.depth < ?\n       )\n       SELECT DISTINCT slug FROM desc ORDER BY slug`,\n    )\n    .all(slug, DAG_DEPTH_CAP)\n    .map((r) => r.slug);\n  return rows;\n}\n\n/**\n * Return the subtree rooted at `slug` (the slug itself + all\n * descendants). Convenience wrapper used by `health --topic` to scope\n * reports through the DAG.\n */\nexport function subtreeInDb(db: Database.Database, slug: string): string[] {\n  return [slug, ...descendantsInDb(db, slug)];\n}\n","import { join } from \"node:path\";\n\nimport type Database from \"better-sqlite3\";\n\nimport { ensureFreshIndex } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\n\nexport interface InfoOptions {\n  cwd: string;\n  slug?: string;\n  stdin?: boolean;\n  stdinInput?: string;\n  json?: boolean;\n  wiki?: string;\n}\n\nexport interface InfoRecord {\n  slug: string;\n  title: string | null;\n  file_path: string;\n  updated_at: number;\n  archived_at: number | null;\n  superseded_by: string | null;\n  supersedes: string[]; // pages that declare superseded_by = this slug\n  topics: string[];\n  file_refs: Array<{ path: string; is_dir: boolean }>;\n  wikilinks_out: string[];\n  wikilinks_in: string[];\n  cross_wiki_links: Array<{ wiki: string; target: string }>;\n}\n\nexport interface InfoCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * `almanac info <slug>` — structured view of one page.\n *\n * Human-readable output groups the fields into labeled sections; `--json`\n * emits the raw record. Bulk mode (`--stdin`) defaults to JSON output\n * (array of records) because interleaved human-readable blobs are hard to\n * parse downstream.\n *\n * Backlinks (`wikilinks_in`) are computed per call — there's no\n * materialized reverse index in slice 2, which keeps indexing simple and\n * the query is trivial at the size of a normal wiki.\n */\nexport async function runInfo(\n  options: InfoOptions,\n): Promise<InfoCommandOutput> {\n  const repoRoot = await resolveWikiRoot({\n    cwd: options.cwd,\n    wiki: options.wiki,\n  });\n  await ensureFreshIndex({ repoRoot });\n\n  const dbPath = join(repoRoot, \".almanac\", \"index.db\");\n  const db = openIndex(dbPath);\n\n  try {\n    const slugs = collectSlugs(options);\n    if (slugs.length === 0) {\n      return {\n        stdout: \"\",\n        stderr: \"almanac: info requires a slug (or --stdin)\\n\",\n        exitCode: 1,\n      };\n    }\n\n    const records: InfoRecord[] = [];\n    const missing: string[] = [];\n    for (const slug of slugs) {\n      const rec = fetchInfo(db, slug);\n      if (rec === null) {\n        missing.push(slug);\n        continue;\n      }\n      records.push(rec);\n    }\n\n    const bulk = options.stdin === true;\n    const jsonOut = options.json === true || bulk;\n\n    // JSON shape rule (consumers depend on this being predictable):\n    //   --stdin        → always array of records (even for a single slug)\n    //   positional     → always a single object (never an array)\n    // The previous implementation accidentally reshaped \"positional with\n    // zero records\" as an array and positional with one record as an\n    // object, which made downstream callers have to sniff the shape.\n    // Now: `info --stdin` gives you a list to iterate; `info <slug>` gives\n    // you one record to dot-access.\n    let stdout: string;\n    if (jsonOut) {\n      if (bulk) {\n        stdout = `${JSON.stringify(records, null, 2)}\\n`;\n      } else {\n        // Positional mode: we already short-circuited on empty slugs,\n        // and a missing page is in `missing[]` — so `records` is either\n        // length 1 (found) or length 0 (missing). For length 0 we emit\n        // `null` so the shape is still object-ish, not an empty array.\n        const only = records[0] ?? null;\n        stdout = `${JSON.stringify(only, null, 2)}\\n`;\n      }\n    } else {\n      stdout = records.map(formatHumanReadable).join(\"\\n\");\n    }\n\n    const stderr = missing\n      .map((s) => `almanac: no such page \"${s}\"\\n`)\n      .join(\"\");\n    return {\n      stdout,\n      stderr,\n      exitCode: missing.length > 0 ? 1 : 0,\n    };\n  } finally {\n    db.close();\n  }\n}\n\nfunction fetchInfo(db: Database.Database, slug: string): InfoRecord | null {\n  const pageRow = db\n    .prepare<\n      [string],\n      {\n        slug: string;\n        title: string | null;\n        file_path: string;\n        updated_at: number;\n        archived_at: number | null;\n        superseded_by: string | null;\n      }\n    >(\n      \"SELECT slug, title, file_path, updated_at, archived_at, superseded_by FROM pages WHERE slug = ?\",\n    )\n    .get(slug);\n  if (pageRow === undefined) return null;\n\n  const topics = db\n    .prepare<[string], { topic_slug: string }>(\n      \"SELECT topic_slug FROM page_topics WHERE page_slug = ? ORDER BY topic_slug\",\n    )\n    .all(slug)\n    .map((r) => r.topic_slug);\n\n  const refs = db\n    .prepare<[string], { original_path: string; is_dir: number }>(\n      // Display the author's casing (`original_path`), not the\n      // lowercased lookup form. The lowercased `path` column is the\n      // query key for `--mentions`; it's not a user-facing string.\n      \"SELECT original_path, is_dir FROM file_refs WHERE page_slug = ? ORDER BY original_path\",\n    )\n    .all(slug)\n    .map((r) => ({ path: r.original_path, is_dir: r.is_dir === 1 }));\n\n  const linksOut = db\n    .prepare<[string], { target_slug: string }>(\n      \"SELECT target_slug FROM wikilinks WHERE source_slug = ? ORDER BY target_slug\",\n    )\n    .all(slug)\n    .map((r) => r.target_slug);\n\n  const linksIn = db\n    .prepare<[string], { source_slug: string }>(\n      \"SELECT source_slug FROM wikilinks WHERE target_slug = ? ORDER BY source_slug\",\n    )\n    .all(slug)\n    .map((r) => r.source_slug);\n\n  const xwiki = db\n    .prepare<[string], { target_wiki: string; target_slug: string }>(\n      \"SELECT target_wiki, target_slug FROM cross_wiki_links WHERE source_slug = ? ORDER BY target_wiki, target_slug\",\n    )\n    .all(slug)\n    .map((r) => ({ wiki: r.target_wiki, target: r.target_slug }));\n\n  // \"Pages that say `supersedes: <me>`\" — the reverse side of this\n  // page's `superseded_by` field. We read this from `pages` rather than\n  // a dedicated column because the spec (deliberately) doesn't index\n  // `supersedes:` as its own table — the relationship is already implicit\n  // in whoever points at us.\n  const supersedesRows = db\n    .prepare<[string], { slug: string }>(\n      \"SELECT slug FROM pages WHERE superseded_by = ? ORDER BY slug\",\n    )\n    .all(slug)\n    .map((r) => r.slug);\n\n  return {\n    slug: pageRow.slug,\n    title: pageRow.title,\n    file_path: pageRow.file_path,\n    updated_at: pageRow.updated_at,\n    archived_at: pageRow.archived_at,\n    superseded_by: pageRow.superseded_by,\n    supersedes: supersedesRows,\n    topics,\n    file_refs: refs,\n    wikilinks_out: linksOut,\n    wikilinks_in: linksIn,\n    cross_wiki_links: xwiki,\n  };\n}\n\nfunction collectSlugs(options: InfoOptions): string[] {\n  if (options.stdin === true && options.stdinInput !== undefined) {\n    return options.stdinInput\n      .split(/\\r?\\n/)\n      .map((s) => s.trim())\n      .filter((s) => s.length > 0);\n  }\n  if (options.slug !== undefined && options.slug.length > 0) {\n    return [options.slug];\n  }\n  return [];\n}\n\nfunction formatHumanReadable(rec: InfoRecord): string {\n  const lines: string[] = [];\n  lines.push(`slug:          ${rec.slug}`);\n  lines.push(`title:         ${rec.title ?? \"—\"}`);\n  lines.push(`file:          ${rec.file_path}`);\n  lines.push(`updated_at:    ${new Date(rec.updated_at * 1000).toISOString()}`);\n  if (rec.archived_at !== null) {\n    lines.push(\n      `archived_at:   ${new Date(rec.archived_at * 1000).toISOString()}`,\n    );\n  }\n  if (rec.superseded_by !== null) {\n    lines.push(`superseded_by: ${rec.superseded_by}`);\n  }\n  if (rec.supersedes.length > 0) {\n    lines.push(`supersedes:    ${rec.supersedes.join(\", \")}`);\n  }\n  lines.push(`topics:        ${rec.topics.length > 0 ? rec.topics.join(\", \") : \"—\"}`);\n  lines.push(\"file_refs:\");\n  if (rec.file_refs.length === 0) {\n    lines.push(\"  —\");\n  } else {\n    for (const r of rec.file_refs) {\n      lines.push(`  ${r.path}${r.is_dir ? \"  (dir)\" : \"\"}`);\n    }\n  }\n  lines.push(\"wikilinks_out:\");\n  if (rec.wikilinks_out.length === 0) lines.push(\"  —\");\n  else for (const t of rec.wikilinks_out) lines.push(`  ${t}`);\n  lines.push(\"wikilinks_in:\");\n  if (rec.wikilinks_in.length === 0) lines.push(\"  —\");\n  else for (const s of rec.wikilinks_in) lines.push(`  ${s}`);\n  if (rec.cross_wiki_links.length > 0) {\n    lines.push(\"cross_wiki_links:\");\n    for (const x of rec.cross_wiki_links) {\n      lines.push(`  ${x.wiki}:${x.target}`);\n    }\n  }\n  return `${lines.join(\"\\n\")}\\n`;\n}\n","import { existsSync } from \"node:fs\";\n\nimport {\n  dropEntry,\n  readRegistry,\n  type RegistryEntry,\n} from \"../registry/index.js\";\n\nexport interface ListOptions {\n  json?: boolean;\n  drop?: string;\n}\n\nexport interface ListCommandOutput {\n  stdout: string;\n  exitCode: number;\n}\n\n/**\n * `almanac list` — the global discovery surface. Three modes:\n *\n *  - default: pretty table of reachable wikis\n *  - `--json`: structured output (reachable wikis only, by default)\n *  - `--drop <name>`: explicit removal, then exits\n *\n * **Unreachable paths are silently skipped in the default output**, but\n * never auto-dropped. This is the registry hygiene rule from the design —\n * branch switches, unmounted drives, and VM-offline repos should not cost\n * the user a registration. Only `--drop` removes entries.\n */\nexport async function listWikis(\n  options: ListOptions,\n): Promise<ListCommandOutput> {\n  if (options.drop !== undefined) {\n    return handleDrop(options.drop);\n  }\n\n  const entries = await readRegistry();\n  const reachable = entries.filter((e) => isReachable(e));\n\n  if (options.json === true) {\n    return { stdout: `${JSON.stringify(reachable, null, 2)}\\n`, exitCode: 0 };\n  }\n\n  return { stdout: formatPretty(reachable), exitCode: 0 };\n}\n\nasync function handleDrop(name: string): Promise<ListCommandOutput> {\n  const removed = await dropEntry(name);\n  if (removed === null) {\n    return {\n      stdout: `no registry entry named \"${name}\"\\n`,\n      exitCode: 1,\n    };\n  }\n  return {\n    stdout: `removed \"${removed.name}\" (${removed.path})\\n`,\n    exitCode: 0,\n  };\n}\n\n/**\n * A registry path is \"reachable\" if something still exists at that path.\n * We use `existsSync` rather than `stat` — we don't care whether the path\n * is a directory or has a `.almanac/` inside; we only hide it from default\n * output when the path itself is gone (e.g., repo deleted, drive\n * unmounted).\n */\nfunction isReachable(entry: RegistryEntry): boolean {\n  if (entry.path.length === 0) return false;\n  return existsSync(entry.path);\n}\n\n/**\n * Human-readable listing. Empty state prints a gentle hint rather than a\n * blank screen, and entries render in registration order (chronological,\n * since `addEntry` appends).\n */\nfunction formatPretty(entries: RegistryEntry[]): string {\n  if (entries.length === 0) {\n    return \"no wikis registered. run `almanac init` in a repo to create one.\\n\";\n  }\n\n  // Column-width the name for alignment; cap at 30 so absurd names don't\n  // stretch the whole table.\n  const nameWidth = Math.min(\n    30,\n    entries.reduce((w, e) => Math.max(w, e.name.length), 0),\n  );\n\n  const lines: string[] = [];\n  for (const entry of entries) {\n    const name = entry.name.padEnd(nameWidth);\n    const desc = entry.description.length > 0 ? entry.description : \"—\";\n    lines.push(`${name}  ${desc}`);\n    lines.push(`${\" \".repeat(nameWidth)}  ${entry.path}`);\n  }\n  return `${lines.join(\"\\n\")}\\n`;\n}\n","import { join } from \"node:path\";\n\nimport { ensureFreshIndex } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\n\nexport interface PathOptions {\n  cwd: string;\n  slug?: string;\n  stdin?: boolean;\n  stdinInput?: string;\n  wiki?: string;\n}\n\nexport interface PathCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * `almanac path <slug>` — slug → absolute file path.\n *\n * Pure scripting helper. With `--stdin` it maps each line of input to its\n * resolved path; unresolvable slugs go to stderr with a non-zero exit\n * while the resolvable ones still print on stdout.\n */\nexport async function runPath(\n  options: PathOptions,\n): Promise<PathCommandOutput> {\n  const repoRoot = await resolveWikiRoot({\n    cwd: options.cwd,\n    wiki: options.wiki,\n  });\n  await ensureFreshIndex({ repoRoot });\n\n  const dbPath = join(repoRoot, \".almanac\", \"index.db\");\n  const db = openIndex(dbPath);\n\n  try {\n    const slugs = collectSlugs(options);\n    if (slugs.length === 0) {\n      return {\n        stdout: \"\",\n        stderr: \"almanac: path requires a slug (or --stdin)\\n\",\n        exitCode: 1,\n      };\n    }\n\n    const stmt = db.prepare<[string], { file_path: string }>(\n      \"SELECT file_path FROM pages WHERE slug = ?\",\n    );\n    const resolved: string[] = [];\n    const missing: string[] = [];\n    for (const slug of slugs) {\n      const row = stmt.get(slug);\n      if (row === undefined) {\n        missing.push(slug);\n        continue;\n      }\n      resolved.push(row.file_path);\n    }\n\n    const stdout = resolved.length > 0 ? `${resolved.join(\"\\n\")}\\n` : \"\";\n    const stderr = missing\n      .map((s) => `almanac: no such page \"${s}\"\\n`)\n      .join(\"\");\n    return {\n      stdout,\n      stderr,\n      exitCode: missing.length > 0 ? 1 : 0,\n    };\n  } finally {\n    db.close();\n  }\n}\n\nfunction collectSlugs(options: PathOptions): string[] {\n  if (options.stdin === true && options.stdinInput !== undefined) {\n    return options.stdinInput\n      .split(/\\r?\\n/)\n      .map((s) => s.trim())\n      .filter((s) => s.length > 0);\n  }\n  if (options.slug !== undefined && options.slug.length > 0) {\n    return [options.slug];\n  }\n  return [];\n}\n","import { runIndexer, type IndexResult } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\n\nexport interface ReindexOptions {\n  cwd: string;\n  wiki?: string;\n}\n\nexport interface ReindexCommandOutput {\n  result: IndexResult;\n  stdout: string;\n  exitCode: number;\n}\n\n/**\n * `almanac reindex` — force a full rebuild.\n *\n * Unlike the implicit reindex every query command triggers, this one\n * prints a summary line so the user gets feedback for an explicitly\n * requested action. The summary is terse on purpose (one line, three\n * numbers) — verbose progress reporting would fight the design rule that\n * the CLI stays quiet by default.\n */\nexport async function runReindex(\n  options: ReindexOptions,\n): Promise<ReindexCommandOutput> {\n  const repoRoot = await resolveWikiRoot({\n    cwd: options.cwd,\n    wiki: options.wiki,\n  });\n  const result = await runIndexer({ repoRoot });\n  // Summary wording: \"reindexed: N pages (K updated, R removed)\". When\n  // some files were on disk but never made it into the index\n  // (slug collisions, ENOENT races, un-sluggable filenames), tack on a\n  // `; S skipped` suffix so the user notices. The per-file reason was\n  // already written to stderr at indexing time.\n  const skipSuffix =\n    result.filesSkipped > 0 ? `; ${result.filesSkipped} skipped` : \"\";\n  const stdout = `reindexed: ${result.pagesIndexed} page${result.pagesIndexed === 1 ? \"\" : \"s\"} (${result.changed} updated, ${result.removed} removed${skipSuffix})\\n`;\n  return { result, stdout, exitCode: 0 };\n}\n","import { join } from \"node:path\";\n\nimport type Database from \"better-sqlite3\";\n\nimport { parseDuration } from \"../indexer/duration.js\";\nimport { ensureFreshIndex } from \"../indexer/index.js\";\nimport { looksLikeDir, normalizePath } from \"../indexer/paths.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\n\nexport interface SearchOptions {\n  cwd: string;\n  query?: string;\n  topics: string[];\n  mentions?: string;\n  since?: string;\n  stale?: string;\n  orphan?: boolean;\n  includeArchive?: boolean;\n  archived?: boolean;\n  wiki?: string;\n  json?: boolean;\n  limit?: number;\n}\n\nexport interface SearchResult {\n  slug: string;\n  title: string | null;\n  updated_at: number;\n  archived_at: number | null;\n  superseded_by: string | null;\n  topics: string[];\n}\n\nexport interface SearchCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * `almanac search` — the core query surface.\n *\n * Filters compose with AND logic. The implementation is deliberately\n * pedestrian: build a list of clauses + params, join them with `AND`,\n * intersect topic filters by requiring one subquery per `--topic`. No\n * clever query-planner tricks needed for the sizes we handle (<10k pages).\n *\n * All output ordering is stable: `updated_at DESC, slug ASC`. FTS5 rank\n * is layered on top when the user passed a text query — we ORDER BY rank\n * first, then fall through to the default.\n */\nexport async function runSearch(\n  options: SearchOptions,\n): Promise<SearchCommandOutput> {\n  const repoRoot = await resolveWikiRoot({\n    cwd: options.cwd,\n    wiki: options.wiki,\n  });\n  await ensureFreshIndex({ repoRoot });\n\n  const dbPath = join(repoRoot, \".almanac\", \"index.db\");\n  const db = openIndex(dbPath);\n\n  try {\n    const rows = executeQuery(db, options);\n    const limited =\n      options.limit !== undefined && options.limit >= 0\n        ? rows.slice(0, options.limit)\n        : rows;\n\n    const stdout = formatResults(limited, options);\n    const stderr = buildStderr(limited, options);\n    return { stdout, stderr, exitCode: 0 };\n  } finally {\n    db.close();\n  }\n}\n\ninterface PageRow {\n  slug: string;\n  title: string | null;\n  updated_at: number;\n  archived_at: number | null;\n  superseded_by: string | null;\n}\n\nfunction executeQuery(\n  db: Database.Database,\n  options: SearchOptions,\n): SearchResult[] {\n  const whereClauses: string[] = [];\n  const params: (string | number)[] = [];\n\n  // Archive scope. Three modes, mutually exclusive in practice:\n  //   - default            → active only\n  //   - --include-archive  → active + archived\n  //   - --archived         → archived only\n  // `--archived` wins over `--include-archive` when both are passed —\n  // being explicit about \"only archived\" is strictly narrower than\n  // \"include archived\", so intersecting them yields \"only archived\".\n  if (options.archived === true) {\n    whereClauses.push(\"p.archived_at IS NOT NULL\");\n  } else if (options.includeArchive !== true) {\n    whereClauses.push(\"p.archived_at IS NULL\");\n  }\n\n  // --topic foo --topic bar → page must have BOTH. We add one EXISTS\n  // subquery per topic rather than grouping, which keeps param order\n  // simple and the plan readable.\n  for (const rawTopic of options.topics) {\n    const topicSlug = slugForTopic(rawTopic);\n    if (topicSlug.length === 0) continue;\n    whereClauses.push(\n      \"EXISTS (SELECT 1 FROM page_topics pt WHERE pt.page_slug = p.slug AND pt.topic_slug = ?)\",\n    );\n    params.push(topicSlug);\n  }\n\n  // --mentions: look for a file_refs row on this page that either\n  // matches exactly, OR is a containing folder (is_dir=1 and the query\n  // path starts with the row's path), OR the row itself lives inside\n  // the queried folder. See spec → \"Graph querying → Query examples\".\n  //\n  // We deliberately avoid GLOB on the RHS of the comparison with stored\n  // `r.path`, because stored paths can legitimately contain GLOB\n  // metacharacters — Next.js dynamic routes like `src/[id]/page.tsx`\n  // store a literal `[id]`, and `[abc]` is a SQL GLOB character class.\n  // Concatenating `r.path || '*'` into a GLOB pattern would make\n  // `src/[id]/page.tsx*` match `src/i/page.tsx` (spurious hit on the\n  // character class).\n  //\n  // Instead we enumerate the prefix folders in JS and use parameterized\n  // equality. For `src/checkout/handler.ts` the prefixes are\n  // `['src/', 'src/checkout/']`; any file_refs row with is_dir=1 and\n  // a path in that list is a containing folder of the queried file.\n  // This also lets SQLite use `idx_file_refs_path` as an equality\n  // probe rather than a range scan.\n  if (options.mentions !== undefined && options.mentions.length > 0) {\n    const isDir = looksLikeDir(options.mentions);\n    const norm = normalizePath(options.mentions, isDir);\n    if (isDir) {\n      // Query is a folder. Match: the exact folder, OR any file/sub-\n      // folder whose path starts with the folder prefix. The prefix\n      // match is the one place we still need GLOB — but we escape any\n      // wildcard metacharacters in `norm` first so a user-supplied\n      // `src/[id]/` query is treated as a literal. Note: the query\n      // path comes from the caller, not from stored data, but a user\n      // typing `--mentions src/[id]/` should get the literal folder,\n      // not a character class.\n      const escaped = escapeGlobMeta(norm);\n      whereClauses.push(\n        `EXISTS (\n           SELECT 1 FROM file_refs r\n           WHERE r.page_slug = p.slug\n             AND (r.path = ? OR r.path GLOB ?)\n         )`,\n      );\n      params.push(norm, `${escaped}*`);\n    } else {\n      // Query is a file. Match: the exact file, OR any folder whose\n      // path is a prefix of this file. Build the prefix list in JS and\n      // probe file_refs with equality — no GLOB on stored values.\n      const prefixes = parentFolderPrefixes(norm);\n      if (prefixes.length === 0) {\n        whereClauses.push(\n          `EXISTS (\n             SELECT 1 FROM file_refs r\n             WHERE r.page_slug = p.slug AND r.path = ?\n           )`,\n        );\n        params.push(norm);\n      } else {\n        const placeholders = prefixes.map(() => \"?\").join(\", \");\n        whereClauses.push(\n          `EXISTS (\n             SELECT 1 FROM file_refs r\n             WHERE r.page_slug = p.slug\n               AND (\n                 r.path = ?\n                 OR (r.is_dir = 1 AND r.path IN (${placeholders}))\n               )\n           )`,\n        );\n        params.push(norm, ...prefixes);\n      }\n    }\n  }\n\n  const now = Math.floor(Date.now() / 1000);\n\n  if (options.since !== undefined) {\n    const seconds = parseDuration(options.since);\n    whereClauses.push(\"p.updated_at >= ?\");\n    params.push(now - seconds);\n  }\n\n  if (options.stale !== undefined) {\n    const seconds = parseDuration(options.stale);\n    whereClauses.push(\"p.updated_at < ?\");\n    params.push(now - seconds);\n  }\n\n  if (options.orphan === true) {\n    whereClauses.push(\n      \"NOT EXISTS (SELECT 1 FROM page_topics pt WHERE pt.page_slug = p.slug)\",\n    );\n  }\n\n  // FTS5 text query. When a text query is supplied we JOIN against\n  // `fts_pages` so we can ORDER BY its `rank` column — lower (more\n  // negative) ranks are better matches. Without a query we skip the\n  // join entirely.\n  let sql: string;\n  if (options.query !== undefined && options.query.trim().length > 0) {\n    const ftsExpr = buildFtsQuery(options.query);\n    sql = `\n      SELECT p.slug, p.title, p.updated_at, p.archived_at, p.superseded_by\n      FROM pages p\n      JOIN fts_pages f ON f.slug = p.slug\n      WHERE fts_pages MATCH ?\n        ${whereClauses.length > 0 ? `AND ${whereClauses.join(\" AND \")}` : \"\"}\n      ORDER BY f.rank ASC, p.updated_at DESC, p.slug ASC\n    `;\n    // MATCH param goes first (it's the first `?` in the compiled SQL).\n    params.unshift(ftsExpr);\n  } else {\n    sql = buildSql(whereClauses);\n  }\n\n  const rows = db.prepare<unknown[], PageRow>(sql).all(...params);\n\n  // Attach topics in a second pass — simpler than a correlated\n  // `GROUP_CONCAT`, and the output rows are small enough that N+1 on a\n  // single prepared statement is fine.\n  const topicStmt = db.prepare<[string], { topic_slug: string }>(\n    \"SELECT topic_slug FROM page_topics WHERE page_slug = ? ORDER BY topic_slug\",\n  );\n  const out: SearchResult[] = rows.map((row) => ({\n    slug: row.slug,\n    title: row.title,\n    updated_at: row.updated_at,\n    archived_at: row.archived_at,\n    superseded_by: row.superseded_by,\n    topics: topicStmt.all(row.slug).map((t) => t.topic_slug),\n  }));\n\n  return out;\n}\n\nfunction buildSql(whereClauses: string[]): string {\n  const where =\n    whereClauses.length > 0 ? `WHERE ${whereClauses.join(\" AND \")}` : \"\";\n  return `\n    SELECT p.slug, p.title, p.updated_at, p.archived_at, p.superseded_by\n    FROM pages p\n    ${where}\n    ORDER BY p.updated_at DESC, p.slug ASC\n  `;\n}\n\n/**\n * Turn a user query into an FTS5 MATCH expression. FTS5's default\n * grammar gets unhappy with punctuation (hyphens, colons, slashes), so\n * we tokenize into alphanumeric runs and emit a conjunction of prefixed\n * tokens. Each token is suffixed with `*` so \"stri\" matches \"stripe\".\n *\n * Quoted input (`\"stripe webhook\"`) is treated as an FTS5 phrase query\n * — tokens must appear contiguously in that order. This matches shell\n * conventions where quoting something means \"match it literally\". We\n * strip the surrounding quotes, collapse inner punctuation to spaces,\n * and re-wrap in quotes for FTS5's phrase syntax. Any embedded `\"` in\n * the user input is dropped (FTS5 phrase syntax has no escape).\n *\n * Anything that tokenizes to empty (e.g. pure punctuation) falls back\n * to an empty MATCH, which yields no rows — which is the right answer.\n */\nfunction buildFtsQuery(raw: string): string {\n  const trimmed = raw.trim();\n  if (\n    trimmed.length >= 2 &&\n    trimmed.startsWith(\"\\\"\") &&\n    trimmed.endsWith(\"\\\"\")\n  ) {\n    // Phrase mode. Strip outer quotes, lowercase, collapse non-alnum\n    // runs to a single space, trim. Any surviving inner `\"` are\n    // removed since FTS5 phrase syntax has no escape mechanism.\n    const inner = trimmed\n      .slice(1, -1)\n      .toLowerCase()\n      .replace(/[^a-z0-9]+/g, \" \")\n      .trim();\n    if (inner.length === 0) return \"\\\"\\\"\";\n    return `\"${inner}\"`;\n  }\n  const tokens = trimmed\n    .toLowerCase()\n    .split(/[^a-z0-9]+/)\n    .filter((t) => t.length > 0);\n  if (tokens.length === 0) return \"\\\"\\\"\";\n  return tokens.map((t) => `${t}*`).join(\" AND \");\n}\n\nfunction slugForTopic(raw: string): string {\n  return raw\n    .toLowerCase()\n    .replace(/[^a-z0-9]+/g, \"-\")\n    .replace(/^-+|-+$/g, \"\");\n}\n\n/**\n * For a normalized file path like `src/checkout/handler.ts`, enumerate\n * every containing folder in the form those folders are stored (trailing\n * slash): `['src/', 'src/checkout/']`. Empty for paths with no folder\n * separator (e.g. `README.md`) — a top-level file has no parent folder\n * recorded in `file_refs`.\n *\n * Used by the `--mentions <file>` path to let us probe `file_refs` with\n * equality instead of GLOB, sidestepping wildcard-escape bugs entirely.\n */\nfunction parentFolderPrefixes(filePath: string): string[] {\n  const out: string[] = [];\n  let cursor = 0;\n  while (true) {\n    const next = filePath.indexOf(\"/\", cursor);\n    if (next === -1) break;\n    // Slice includes the slash — matches how directories are stored.\n    out.push(filePath.slice(0, next + 1));\n    cursor = next + 1;\n  }\n  return out;\n}\n\n/**\n * Escape SQLite GLOB metacharacters (`*`, `?`, `[`) by wrapping each in\n * a single-character class. SQLite GLOB has no backslash-escape, so the\n * idiomatic trick is `[*]` → literal `*`, `[?]` → literal `?`, `[[]` →\n * literal `[`. `]` doesn't need escaping outside a class.\n *\n * We only need this on the *query* side — stored paths aren't\n * concatenated into GLOB patterns anymore (see --mentions handling).\n * But a user-typed `--mentions src/[id]/` should still match a stored\n * `src/[id]/` literally, not as a character class over `i` or `d`.\n */\nfunction escapeGlobMeta(s: string): string {\n  return s.replace(/[\\*\\?\\[]/g, (ch) => `[${ch}]`);\n}\n\nfunction formatResults(\n  rows: SearchResult[],\n  options: SearchOptions,\n): string {\n  if (options.json === true) {\n    return `${JSON.stringify(rows, null, 2)}\\n`;\n  }\n  // Default output: one slug per line. Empty result = empty output (not\n  // \"no results found\") — makes piping into xargs / subsequent commands\n  // degrade gracefully.\n  if (rows.length === 0) return \"\";\n  return `${rows.map((r) => r.slug).join(\"\\n\")}\\n`;\n}\n\nfunction buildStderr(rows: SearchResult[], options: SearchOptions): string {\n  // Spec: \"print warns if >50 when not --json\". The warning goes to\n  // stderr so it doesn't corrupt pipelines that filter stdout.\n  if (options.json === true) return \"\";\n  if (options.limit !== undefined) return \"\";\n  if (rows.length > 50) {\n    return `almanac: ${rows.length} results — consider --limit or a narrower query\\n`;\n  }\n  return \"\";\n}\n","import { readFile } from \"node:fs/promises\";\nimport { join } from \"node:path\";\n\nimport { ensureFreshIndex } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\n\nexport interface ShowOptions {\n  cwd: string;\n  slug?: string;\n  stdin?: boolean;\n  stdinInput?: string; // injected by the CLI when --stdin is set; tests can pass directly\n  wiki?: string;\n}\n\nexport interface ShowCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * `almanac show <slug>` — cat the markdown file for a page.\n *\n * This is the one command that is allowed to read page file contents;\n * everything else operates on the index (per the spec's design\n * principles).\n *\n * Output shapes:\n *   - positional slug → raw markdown on stdout, unchanged (the cat case)\n *   - `--stdin`       → JSON Lines: one `{slug, content}` object per\n *                       successfully-read page, terminated by `\\n`. JSON\n *                       Lines is parseable, unlike the old `\\n---\\n`\n *                       separator which collided with YAML frontmatter\n *                       delimiters in the page bodies themselves.\n *\n * Unresolvable slugs go to stderr with a non-zero exit; we still print\n * whatever we could resolve on stdout so bulk runs don't have to fail\n * atomically.\n */\nexport async function runShow(\n  options: ShowOptions,\n): Promise<ShowCommandOutput> {\n  const repoRoot = await resolveWikiRoot({\n    cwd: options.cwd,\n    wiki: options.wiki,\n  });\n  await ensureFreshIndex({ repoRoot });\n\n  const dbPath = join(repoRoot, \".almanac\", \"index.db\");\n  const db = openIndex(dbPath);\n\n  try {\n    const slugs = collectSlugs(options);\n    if (slugs.length === 0) {\n      return {\n        stdout: \"\",\n        stderr: \"almanac: show requires a slug (or --stdin)\\n\",\n        exitCode: 1,\n      };\n    }\n\n    const stmt = db.prepare<[string], { file_path: string }>(\n      \"SELECT file_path FROM pages WHERE slug = ?\",\n    );\n\n    const records: Array<{ slug: string; content: string }> = [];\n    const missing: string[] = [];\n    for (const slug of slugs) {\n      const row = stmt.get(slug);\n      if (row === undefined) {\n        missing.push(slug);\n        continue;\n      }\n      try {\n        records.push({ slug, content: await readFile(row.file_path, \"utf8\") });\n      } catch (err: unknown) {\n        const message = err instanceof Error ? err.message : String(err);\n        missing.push(`${slug} (${message})`);\n      }\n    }\n\n    const bulk = options.stdin === true;\n    let stdout: string;\n    if (bulk) {\n      // JSON Lines: one object per line, trailing newline on the last.\n      // Consumers can split on `\\n` and `JSON.parse` each line.\n      stdout = records\n        .map((r) => JSON.stringify(r))\n        .join(\"\\n\");\n      if (stdout.length > 0) stdout += \"\\n\";\n    } else {\n      // Positional single-slug: just emit the raw markdown. No\n      // separator, no wrapping — this is the \"cat\" case.\n      stdout = records.map((r) => r.content).join(\"\");\n    }\n    const stderr = missing\n      .map((s) => `almanac: no such page \"${s}\"\\n`)\n      .join(\"\");\n    return {\n      stdout,\n      stderr,\n      exitCode: missing.length > 0 ? 1 : 0,\n    };\n  } finally {\n    db.close();\n  }\n}\n\nfunction collectSlugs(options: ShowOptions): string[] {\n  if (options.stdin === true && options.stdinInput !== undefined) {\n    return options.stdinInput\n      .split(/\\r?\\n/)\n      .map((s) => s.trim())\n      .filter((s) => s.length > 0);\n  }\n  if (options.slug !== undefined && options.slug.length > 0) {\n    return [options.slug];\n  }\n  return [];\n}\n","import { readFile, rename, writeFile } from \"node:fs/promises\";\n\nimport yaml from \"js-yaml\";\n\n/**\n * Rewrite the `topics:` field in a markdown file's YAML frontmatter.\n *\n * The absolute requirement is **body byte-preservation**. Tag/untag/\n * rename commands touch only the frontmatter; everything after the\n * closing `---` must be byte-identical to the input (same line endings,\n * same trailing whitespace, same final-newline-or-not). We lean on a\n * precise split rather than re-serializing the whole file so any\n * incidental bytes in the body (literal `\\r\\n`, unusual trailing\n * whitespace, triple-hyphen rulers) are left alone.\n *\n * For the frontmatter itself we do a **surgical rewrite of the `topics:`\n * field only** — not a full YAML roundtrip. Reasons:\n *   - `js-yaml` normalizes quoting, re-orders keys alphabetically by\n *     default, and can drop comments. Any of those would surprise a user\n *     who hand-edited their own frontmatter and expects their formatting\n *     preserved byte-for-byte.\n *   - We only care about one field. Replacing just that field lets the\n *     rest of the YAML survive verbatim.\n *\n * The strategy:\n *   1. Find the exact span of the `topics:` key (whether flow\n *      `topics: [a, b]` or block `topics:\\n  - a\\n  - b\\n`) using a\n *      small line scanner.\n *   2. Compute the new topics list from the caller's transform.\n *   3. Replace the span with a freshly-emitted `topics: [a, b, c]` line\n *      (flow style — compact, readable, and what most authors write).\n *   4. If no `topics:` key exists and the new list is non-empty, append\n *      a line to the end of the frontmatter block.\n *   5. If `topics:` exists but the new list is empty, drop the line\n *      entirely rather than leaving `topics: []` around.\n *\n * The transform function gets the current deduplicated topic list and\n * returns the new list. Returning an empty array means \"remove the\n * `topics:` key entirely\".\n */\n\nexport interface RewriteResult {\n  /** The page's topics before the rewrite (possibly empty). */\n  before: string[];\n  /** The page's topics after the rewrite (possibly empty). */\n  after: string[];\n  /** True iff the file content actually changed. */\n  changed: boolean;\n}\n\n/**\n * Read `filePath`, compute the new topics via `transform`, and\n * atomically rewrite if the result differs.\n *\n * Atomic per file: write to `<path>.tmp` then rename, same pattern as\n * the registry and topics.yaml writers. A half-written page would\n * corrupt committed user content, so this is non-negotiable.\n */\nexport async function rewritePageTopics(\n  filePath: string,\n  transform: (current: string[]) => string[],\n): Promise<RewriteResult> {\n  const raw = await readFile(filePath, \"utf8\");\n  const { before, after, output, changed } = applyTopicsTransform(\n    raw,\n    transform,\n  );\n  if (changed) {\n    const tmp = `${filePath}.tmp`;\n    await writeFile(tmp, output, \"utf8\");\n    await rename(tmp, filePath);\n  }\n  return { before, after, changed };\n}\n\ninterface TransformApplied {\n  before: string[];\n  after: string[];\n  output: string;\n  changed: boolean;\n}\n\n/**\n * Pure-string version of `rewritePageTopics`. Useful for tests and for\n * the few places (rename, delete) where we loop many files and want to\n * short-circuit no-op writes cheaply.\n */\nexport function applyTopicsTransform(\n  raw: string,\n  transform: (current: string[]) => string[],\n): TransformApplied {\n  const parsed = splitFrontmatter(raw);\n  if (parsed === null) {\n    // No frontmatter at all. Tagging a topic on such a page means\n    // creating a frontmatter block. We keep the body untouched and\n    // prepend `---\\ntopics: [...]\\n---\\n\\n`. If the transform yields\n    // an empty list, this is a no-op. Line endings: default to LF for a\n    // brand-new frontmatter — we can't infer intent from a file that\n    // doesn't have frontmatter yet, and LF is the committed default in\n    // most modern repos.\n    const next = dedupeSlugs(transform([]));\n    if (next.length === 0) {\n      return { before: [], after: [], output: raw, changed: false };\n    }\n    const fm = `---\\ntopics: ${flowList(next)}\\n---\\n\\n`;\n    return {\n      before: [],\n      after: next,\n      output: `${fm}${raw}`,\n      changed: true,\n    };\n  }\n\n  const { opener, fmLines, closer, body, eol } = parsed;\n  const { before, existingRange } = readTopicsFromLines(fmLines);\n  const beforeDeduped = dedupeSlugs(before);\n  const after = dedupeSlugs(transform(beforeDeduped));\n\n  if (arraysEqual(beforeDeduped, after)) {\n    return { before: beforeDeduped, after, output: raw, changed: false };\n  }\n\n  let nextFmLines: string[];\n  if (existingRange === null) {\n    // No `topics:` key currently present. Add one (only if non-empty).\n    if (after.length === 0) {\n      return { before: beforeDeduped, after, output: raw, changed: false };\n    }\n    nextFmLines = [...fmLines, `topics: ${flowList(after)}`];\n  } else {\n    const replacement =\n      after.length === 0 ? null : `topics: ${flowList(after)}`;\n    // Interleaved comments/blank lines from a block-style list are\n    // re-emitted BELOW the new flow-style `topics:` line so the\n    // author's commentary sticks around. Flow/scalar inputs produce an\n    // empty `preserved` array, so this collapses to the old behavior\n    // for the common case. When we fully delete the key (empty after)\n    // the preserved lines go too — without a `topics:` key to anchor\n    // them to, trailing \"# below the topics list\" comments become\n    // orphans that no longer mean what they said.\n    const preservedTail =\n      replacement === null ? [] : existingRange.preserved;\n    nextFmLines = [\n      ...fmLines.slice(0, existingRange.start),\n      ...(replacement === null ? [] : [replacement]),\n      ...preservedTail,\n      ...fmLines.slice(existingRange.end),\n    ];\n  }\n\n  // Rejoin with the same line ending the input frontmatter used so a\n  // CRLF-authored file comes out CRLF end-to-end. `splitFrontmatter`\n  // sniffed the dominant separator for us.\n  const fmBlock =\n    nextFmLines.length === 0 ? \"\" : `${nextFmLines.join(eol)}${eol}`;\n  const output = `${opener}${fmBlock}${closer}${body}`;\n  return {\n    before: beforeDeduped,\n    after,\n    output,\n    changed: true,\n  };\n}\n\ninterface SplitFrontmatter {\n  /** The opening `---\\n` or `---\\r\\n`. */\n  opener: string;\n  /** Frontmatter lines (no line-ending character included). */\n  fmLines: string[];\n  /** The closing `---\\n` (or `---\\r\\n`, possibly without trailing newline if EOF). */\n  closer: string;\n  /** Everything after the closing fence, byte-for-byte. */\n  body: string;\n  /**\n   * Dominant line ending inside the frontmatter block. CRLF-authored\n   * files stay CRLF on write; LF stays LF. We sniff once at split time\n   * so rewriting doesn't have to re-inspect every line.\n   */\n  eol: \"\\n\" | \"\\r\\n\";\n}\n\n/**\n * Split a file into (opener, frontmatter lines, closer, body). The\n * regex mirrors `parseFrontmatter` in `indexer/frontmatter.ts` so the\n * indexer and the rewriter agree on what \"has frontmatter\" means.\n *\n * Returns `null` when the file doesn't start with a `---` fence or\n * lacks a matching closer — both cases are legal (a page with only\n * body content) and the caller treats them as \"no frontmatter to\n * rewrite\".\n */\nfunction splitFrontmatter(raw: string): SplitFrontmatter | null {\n  if (!raw.startsWith(\"---\")) return null;\n  // Match the exact opener (with its line ending) so we can preserve\n  // it byte-for-byte.\n  const openerMatch = raw.match(/^---(\\r?\\n)/);\n  if (openerMatch === null) return null;\n  const opener = `---${openerMatch[1] ?? \"\\n\"}`;\n  const rest = raw.slice(opener.length);\n  // Find the closing `---` that begins at the start of a line. We\n  // also handle the edge case where the closer sits at position 0 of\n  // `rest` (frontmatter was empty).\n  let fenceIdx: number;\n  if (rest.startsWith(\"---\")) {\n    fenceIdx = 0;\n  } else {\n    const m = rest.match(/\\r?\\n---(\\r?\\n|$)/);\n    if (m === null || m.index === undefined) return null;\n    // `m.index` points at the `\\r?\\n` before `---`; skip that newline\n    // so fenceIdx lands exactly on the `-`.\n    const leadingNewlineLen = (m[0] ?? \"\").startsWith(\"\\r\\n\") ? 2 : 1;\n    fenceIdx = m.index + leadingNewlineLen;\n  }\n  const fmBlock = rest.slice(0, fenceIdx);\n  // Determine the closer's full span, including its trailing newline if any.\n  const afterDashes = rest.slice(fenceIdx + 3);\n  let closerTail = \"\";\n  if (afterDashes.startsWith(\"\\r\\n\")) {\n    closerTail = \"\\r\\n\";\n  } else if (afterDashes.startsWith(\"\\n\")) {\n    closerTail = \"\\n\";\n  }\n  const closer = `---${closerTail}`;\n  const body = afterDashes.slice(closerTail.length);\n  const fmLines =\n    fmBlock.length === 0 ? [] : fmBlock.replace(/\\r?\\n$/, \"\").split(/\\r?\\n/);\n  // Sniff the frontmatter's dominant line ending. We look at the\n  // opener first (most reliable signal — it's always present and\n  // always has an ending). Fall back to checking the fmBlock for any\n  // `\\r\\n` runs so a frontmatter with a single-line opener and\n  // multi-line body still gets classified right.\n  const eol: \"\\n\" | \"\\r\\n\" =\n    opener.endsWith(\"\\r\\n\") || /\\r\\n/.test(fmBlock) ? \"\\r\\n\" : \"\\n\";\n  return { opener, fmLines, closer, body, eol };\n}\n\ninterface ExistingRange {\n  /** Index in `fmLines` of the `topics:` key line (inclusive). */\n  start: number;\n  /** Index in `fmLines` one past the last line belonging to this key. */\n  end: number;\n  /**\n   * Lines inside `[start+1, end)` that aren't `- entry` lines — i.e.\n   * interleaved comments and blank lines a user wrote between entries.\n   * We preserve these verbatim when rewriting block-style lists to\n   * flow; otherwise a `tag` on a commented list would silently drop\n   * the commentary. Empty for flow/scalar shapes.\n   */\n  preserved: string[];\n}\n\n/**\n * Find `topics:` in a frontmatter-lines array and read the values.\n *\n * Handles three YAML shapes authors commonly write:\n *   - `topics: [a, b, c]`       (flow sequence, one line)\n *   - `topics:` followed by block entries like `  - a` (block sequence)\n *   - `topics: a` (a single scalar — treated as one element)\n *\n * Also handles the empty case `topics:` with nothing after it, and the\n * \"no topics key\" case (returns `existingRange: null`).\n *\n * This is NOT a general YAML parser — it's intentionally scoped to the\n * one key we mutate, because using `js-yaml` for a round-trip would\n * lose comments and re-quote strings the user picked a specific way.\n */\nfunction readTopicsFromLines(fmLines: string[]): {\n  before: string[];\n  existingRange: ExistingRange | null;\n} {\n  const keyLineIdx = findTopKey(fmLines, \"topics\");\n  if (keyLineIdx === -1) {\n    return { before: [], existingRange: null };\n  }\n  const keyLine = fmLines[keyLineIdx] ?? \"\";\n  const colonIdx = keyLine.indexOf(\":\");\n  // Everything to the right of the first colon, trimmed.\n  const after = keyLine.slice(colonIdx + 1).trim();\n  // Strip trailing `# ...` line-comment from a flow value so we don't\n  // parse comments as list contents. (A block list's sub-items have\n  // their own comments stripped in the block branch below.)\n  const afterNoComment = stripTrailingComment(after);\n\n  if (afterNoComment.length === 0) {\n    // Block sequence style: collect subsequent `- item` lines. Between\n    // entries a user may have written:\n    //   - interleaved `# comment` lines\n    //   - blank lines\n    // We must NOT break the scan on those — doing so would drop every\n    // entry after the first comment/blank when we rewrite (silent data\n    // loss: the original bug that triggered this fix). We skip them in\n    // the scan and stash them in `preserved` so the replacement step\n    // can re-emit them verbatim BETWEEN the new flow-style line and\n    // the rest of the frontmatter.\n    //\n    // Edge: comments/blanks that appear BEFORE the first `- entry` or\n    // AFTER the last `- entry` count as part of the block too — pulling\n    // them out keeps the author's commentary near the list it belongs\n    // to. We cap the scan when we hit a real non-entry line (e.g. the\n    // next top-level key), leaving everything from that line onward\n    // outside the range.\n    const values: string[] = [];\n    const preserved: string[] = [];\n    // Provisional scan cursor. `endIdx` only advances when we've seen\n    // something we're sure belongs to this block (an entry line), so\n    // trailing whitespace/comments that don't precede another entry\n    // stay OUTSIDE the range and aren't shuffled on rewrite.\n    let i = keyLineIdx + 1;\n    let endIdx = i;\n    // `pendingNonEntries` holds comments/blanks we've seen since the\n    // last confirmed entry. They're committed to `preserved` only\n    // when a subsequent `- entry` proves they live mid-list.\n    let pendingNonEntries: string[] = [];\n    while (i < fmLines.length) {\n      const line = fmLines[i] ?? \"\";\n      const trimmed = line.trim();\n      if (trimmed.length === 0 || trimmed.startsWith(\"#\")) {\n        pendingNonEntries.push(line);\n        i += 1;\n        continue;\n      }\n      const m = line.match(/^\\s*-\\s+(.*)$/);\n      if (m === null) break;\n      // Promote any pending comments/blanks — they're between entries\n      // (or before the first entry within the block).\n      if (pendingNonEntries.length > 0) {\n        preserved.push(...pendingNonEntries);\n        pendingNonEntries = [];\n      }\n      const raw = stripTrailingComment((m[1] ?? \"\").trim());\n      const parsed = parseScalar(raw);\n      if (parsed.length > 0) values.push(parsed);\n      i += 1;\n      endIdx = i;\n    }\n    return {\n      before: values,\n      existingRange: { start: keyLineIdx, end: endIdx, preserved },\n    };\n  }\n\n  // Flow / scalar shape on one line. Let js-yaml handle the value-parsing\n  // (quoting, escapes, etc.) for the RHS only.\n  let parsed: unknown;\n  try {\n    parsed = yaml.load(afterNoComment);\n  } catch {\n    parsed = null;\n  }\n  const values: string[] = [];\n  if (Array.isArray(parsed)) {\n    for (const v of parsed) {\n      if (typeof v === \"string\" && v.trim().length > 0) {\n        values.push(v.trim());\n      }\n    }\n  } else if (typeof parsed === \"string\" && parsed.trim().length > 0) {\n    values.push(parsed.trim());\n  }\n  return {\n    before: values,\n    existingRange: { start: keyLineIdx, end: keyLineIdx + 1, preserved: [] },\n  };\n}\n\n/**\n * Find a top-level key line. \"Top-level\" means no leading whitespace —\n * we don't walk into nested mappings. The indexer's frontmatter parser\n * only reads top-level keys too, so this matches.\n */\nfunction findTopKey(fmLines: string[], key: string): number {\n  const re = new RegExp(`^${escapeRegex(key)}\\\\s*:`);\n  for (let i = 0; i < fmLines.length; i += 1) {\n    if (re.test(fmLines[i] ?? \"\")) return i;\n  }\n  return -1;\n}\n\nfunction escapeRegex(s: string): string {\n  return s.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n}\n\nfunction stripTrailingComment(s: string): string {\n  // Only strip `#` outside of quotes. For the shapes we handle —\n  // slug-like kebab-case topics — quoted strings with `#` are rare, but\n  // be defensive.\n  let inSingle = false;\n  let inDouble = false;\n  for (let i = 0; i < s.length; i += 1) {\n    const ch = s[i];\n    if (ch === \"'\" && !inDouble) inSingle = !inSingle;\n    else if (ch === '\"' && !inSingle) inDouble = !inDouble;\n    else if (ch === \"#\" && !inSingle && !inDouble) {\n      return s.slice(0, i).trimEnd();\n    }\n  }\n  return s;\n}\n\n/**\n * Strip YAML quoting from a scalar. Block-sequence items might be\n * written as `- 'foo'` or `- \"foo\"` or bare `- foo`; we accept all\n * three and return the plain string.\n */\nfunction parseScalar(s: string): string {\n  if (s.length === 0) return s;\n  if (s.length >= 2 && s[0] === '\"' && s[s.length - 1] === '\"') {\n    return s.slice(1, -1);\n  }\n  if (s.length >= 2 && s[0] === \"'\" && s[s.length - 1] === \"'\") {\n    return s.slice(1, -1);\n  }\n  return s;\n}\n\n/**\n * Emit a flow-style YAML sequence like `[auth, jwt, security]`. We use\n * flow because it's the shape most authors write by hand and stays on\n * one line, which keeps diffs tight. Values are quoted only when\n * necessary — plain kebab-case slugs never need quoting.\n */\nfunction flowList(items: string[]): string {\n  return `[${items.map((t) => formatScalar(t)).join(\", \")}]`;\n}\n\nfunction formatScalar(s: string): string {\n  // If it's a bare kebab/alnum slug, no quotes. Otherwise fall back to\n  // js-yaml for correct escaping. We check against a conservative\n  // pattern — anything outside it gets YAML-quoted.\n  if (/^[a-z0-9][a-z0-9-]*$/.test(s)) return s;\n  return yaml\n    .dump(s, { flowLevel: 0, lineWidth: Number.MAX_SAFE_INTEGER })\n    .trimEnd();\n}\n\nfunction dedupeSlugs(list: string[]): string[] {\n  const seen = new Set<string>();\n  const out: string[] = [];\n  for (const raw of list) {\n    const s = raw.trim();\n    if (s.length === 0) continue;\n    if (seen.has(s)) continue;\n    seen.add(s);\n    out.push(s);\n  }\n  return out;\n}\n\nfunction arraysEqual(a: string[], b: string[]): boolean {\n  if (a.length !== b.length) return false;\n  for (let i = 0; i < a.length; i += 1) {\n    if (a[i] !== b[i]) return false;\n  }\n  return true;\n}\n","import { join } from \"node:path\";\n\n/**\n * `.almanac/topics.yaml` inside a given repo root. Single helper so no\n * caller has to remember where the file lives.\n */\nexport function topicsYamlPath(repoRoot: string): string {\n  return join(repoRoot, \".almanac\", \"topics.yaml\");\n}\n\n/**\n * `.almanac/index.db` inside a given repo root. Mirrors `topicsYamlPath`\n * so the topics commands don't have to import from scattered places.\n */\nexport function indexDbPath(repoRoot: string): string {\n  return join(repoRoot, \".almanac\", \"index.db\");\n}\n","import { ensureFreshIndex, runIndexer } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\nimport { toKebabCase } from \"../slug.js\";\nimport { rewritePageTopics } from \"../topics/frontmatterRewrite.js\";\nimport { indexDbPath, topicsYamlPath } from \"../topics/paths.js\";\nimport {\n  ensureTopic,\n  loadTopicsFile,\n  writeTopicsFile,\n} from \"../topics/yaml.js\";\n\n/**\n * `almanac tag <page> <topic>...` and `almanac untag <page> <topic>`.\n *\n * These are the page-side of the topics system — `topics ...` manages\n * the DAG and metadata; `tag`/`untag` wires concrete pages into\n * topics. Both commands mutate page frontmatter atomically per file\n * and leave body bytes untouched.\n *\n * Auto-creation policy: if a topic passed to `tag` doesn't yet exist\n * in `topics.yaml`, we create a minimal entry for it (title-cased\n * title, no description, no parents). This matches the spec: \"Ensure\n * topic exists in topics.yaml; if not, create a minimal entry.\" We\n * don't silently create topics on `untag` — you can only untag\n * something that was already a topic.\n */\n\nexport interface TagCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\nexport interface TagOptions {\n  cwd: string;\n  wiki?: string;\n  page?: string;\n  topics: string[];\n  stdin?: boolean;\n  stdinInput?: string;\n}\n\nexport interface UntagOptions {\n  cwd: string;\n  wiki?: string;\n  page: string;\n  topic: string;\n}\n\nexport async function runTag(options: TagOptions): Promise<TagCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n\n  const topics = options.topics\n    .map((t) => toKebabCase(t))\n    .filter((t) => t.length > 0);\n  if (topics.length === 0) {\n    return {\n      stdout: \"\",\n      stderr: \"almanac: tag requires at least one topic\\n\",\n      exitCode: 1,\n    };\n  }\n\n  // Bulk mode reads slugs from stdin; single mode uses the positional.\n  const pages: string[] = [];\n  if (options.stdin === true) {\n    if (options.stdinInput === undefined) {\n      return {\n        stdout: \"\",\n        stderr: \"almanac: tag --stdin called without stdin input\\n\",\n        exitCode: 1,\n      };\n    }\n    for (const line of options.stdinInput.split(/\\r?\\n/)) {\n      const s = line.trim();\n      if (s.length > 0) pages.push(s);\n    }\n  } else if (options.page !== undefined && options.page.length > 0) {\n    pages.push(options.page);\n  } else {\n    return {\n      stdout: \"\",\n      stderr: \"almanac: tag requires a page slug (or --stdin)\\n\",\n      exitCode: 1,\n    };\n  }\n\n  // Resolve slugs to file paths from the DB. A stale index is fine for\n  // `tag` — we just need to find each page's file; `ensureFreshIndex`\n  // runs first so the common path is consistent.\n  await ensureFreshIndex({ repoRoot });\n  const db = openIndex(indexDbPath(repoRoot));\n\n  // Validate every requested page exists BEFORE touching topics.yaml.\n  // Previously we auto-created topics first, which meant\n  // `almanac tag does-not-exist brand-new` left `brand-new` in\n  // topics.yaml as a state leak even though the tag itself errored. We\n  // resolve rows up front, then short-circuit with an error (and no\n  // mutations) if none of the pages are valid.\n  const stmt = db.prepare<[string], { file_path: string }>(\n    \"SELECT file_path FROM pages WHERE slug = ?\",\n  );\n  const resolved: { page: string; filePath: string }[] = [];\n  const missing: string[] = [];\n  try {\n    for (const page of pages) {\n      const row = stmt.get(toKebabCase(page));\n      if (row === undefined) {\n        missing.push(page);\n      } else {\n        resolved.push({ page, filePath: row.file_path });\n      }\n    }\n  } finally {\n    db.close();\n  }\n\n  // Hard-fail when NO page resolved. We deliberately don't mutate\n  // topics.yaml on this path — the user's intent (tag page X) is\n  // inarguably unsatisfiable, so we shouldn't leave breadcrumbs.\n  //\n  // In bulk mode (`--stdin`) some pages might resolve and others\n  // won't; keeping the original partial-progress behavior for that case\n  // (topics get created, resolved pages get tagged, `missing` are\n  // reported on stderr with exitCode 1). The state leak only matters\n  // when NOTHING succeeds, and that's the case we're fixing.\n  if (resolved.length === 0) {\n    const stderr = missing.map((p) => `almanac: no such page \"${p}\"\\n`).join(\"\");\n    return {\n      stdout: \"\",\n      stderr,\n      exitCode: 1,\n    };\n  }\n\n  // Auto-create missing topics in topics.yaml. Safe to do now — we have\n  // at least one page that will actually end up tagged with them.\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n  let fileChanged = false;\n  for (const t of topics) {\n    // ensureTopic mutates the file; we check presence beforehand so\n    // we only write when something actually changes (skip a redundant\n    // atomic rewrite + mtime bump).\n    const before = file.topics.length;\n    ensureTopic(file, t);\n    if (file.topics.length > before) fileChanged = true;\n  }\n  if (fileChanged) {\n    await writeTopicsFile(yamlPath, file);\n  }\n\n  const summary: string[] = [];\n  let taggedPages = 0;\n  for (const { page, filePath } of resolved) {\n    const result = await rewritePageTopics(filePath, (current) => {\n      // Preserve existing order; append new topics in the order\n      // the caller supplied them. `applyTopicsTransform` will\n      // dedupe for us, but we skip redundant work here too.\n      const out = [...current];\n      for (const t of topics) if (!current.includes(t)) out.push(t);\n      return out;\n    });\n    if (result.changed) {\n      taggedPages += 1;\n      // Only surface the NEWLY ADDED topics — not the full request.\n      // Reporting every requested topic (including ones the page\n      // already had) reads like false positives in commit diffs.\n      const added = result.after.filter((t) => !result.before.includes(t));\n      summary.push(`tagged ${page}: ${added.join(\", \")}`);\n    } else {\n      summary.push(\n        `no change ${page} (already tagged with ${topics.join(\", \")})`,\n      );\n    }\n  }\n\n  if (taggedPages > 0 || fileChanged) {\n    // Trigger a reindex so downstream queries see the new rows\n    // immediately. Writes to page files bumped their mtimes; writes to\n    // topics.yaml are caught by `topicsYamlNewerThan`.\n    await runIndexer({ repoRoot });\n  }\n\n  const stderr = missing.map((p) => `almanac: no such page \"${p}\"\\n`).join(\"\");\n  return {\n    stdout: summary.length > 0 ? `${summary.join(\"\\n\")}\\n` : \"\",\n    stderr,\n    exitCode: missing.length > 0 ? 1 : 0,\n  };\n}\n\nexport async function runUntag(\n  options: UntagOptions,\n): Promise<TagCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  const page = toKebabCase(options.page);\n  const topic = toKebabCase(options.topic);\n  if (page.length === 0) {\n    return {\n      stdout: \"\",\n      stderr: \"almanac: untag requires a page slug\\n\",\n      exitCode: 1,\n    };\n  }\n  if (topic.length === 0) {\n    return {\n      stdout: \"\",\n      stderr: \"almanac: untag requires a topic\\n\",\n      exitCode: 1,\n    };\n  }\n\n  await ensureFreshIndex({ repoRoot });\n  const db = openIndex(indexDbPath(repoRoot));\n  let filePath: string;\n  try {\n    const row = db\n      .prepare<[string], { file_path: string }>(\n        \"SELECT file_path FROM pages WHERE slug = ?\",\n      )\n      .get(page);\n    if (row === undefined) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: no such page \"${page}\"\\n`,\n        exitCode: 1,\n      };\n    }\n    filePath = row.file_path;\n  } finally {\n    db.close();\n  }\n\n  const result = await rewritePageTopics(filePath, (current) =>\n    current.filter((t) => t !== topic),\n  );\n  if (result.changed) {\n    await runIndexer({ repoRoot });\n  }\n\n  return {\n    stdout: result.changed\n      ? `untagged ${page}: ${topic}\\n`\n      : `no change ${page} (not tagged with ${topic})\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n","import { readFile } from \"node:fs/promises\";\nimport { join } from \"node:path\";\n\nimport fg from \"fast-glob\";\nimport type Database from \"better-sqlite3\";\n\nimport { ensureFreshIndex, runIndexer } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\nimport { toKebabCase } from \"../slug.js\";\nimport { ancestorsInFile, descendantsInDb } from \"../topics/dag.js\";\nimport {\n  applyTopicsTransform,\n  rewritePageTopics,\n} from \"../topics/frontmatterRewrite.js\";\nimport { indexDbPath, topicsYamlPath } from \"../topics/paths.js\";\nimport {\n  ensureTopic,\n  findTopic,\n  loadTopicsFile,\n  titleCase,\n  writeTopicsFile,\n  type TopicEntry,\n  type TopicsFile,\n} from \"../topics/yaml.js\";\n\n/**\n * All `almanac topics <verb>` logic lives here. The CLI dispatches on\n * `verb` and forwards positionals/flags. One module per top-level\n * command group matches the pattern used by `search`, `info`, etc.\n *\n * Design notes:\n *   - The module is stateless; every entry function takes a `cwd` and\n *     optional `wiki` and is safe to call many times in a test suite.\n *   - Mutations go file → DB: write `.almanac/topics.yaml` atomically,\n *     then trigger a reindex so the DB reflects the new state by the\n *     time the command prints its summary. Reads run after a cheap\n *     `ensureFreshIndex` so they always see the latest committed data.\n *   - The command functions return a `TopicsCommandOutput`; the CLI\n *     layer in `cli.ts` decides how to print. This mirrors the shape of\n *     `runSearch`, `runInfo`, and friends.\n */\n\nexport interface TopicsCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\nexport interface TopicsBaseOptions {\n  cwd: string;\n  wiki?: string;\n  json?: boolean;\n}\n\nexport interface TopicsListOptions extends TopicsBaseOptions {}\n\nexport interface TopicsShowOptions extends TopicsBaseOptions {\n  slug: string;\n  descendants?: boolean;\n}\n\nexport interface TopicsCreateOptions extends TopicsBaseOptions {\n  name: string;\n  parents?: string[];\n}\n\nexport interface TopicsLinkOptions extends TopicsBaseOptions {\n  child: string;\n  parent: string;\n}\n\nexport interface TopicsUnlinkOptions extends TopicsLinkOptions {}\n\nexport interface TopicsRenameOptions extends TopicsBaseOptions {\n  oldSlug: string;\n  newSlug: string;\n}\n\nexport interface TopicsDeleteOptions extends TopicsBaseOptions {\n  slug: string;\n}\n\nexport interface TopicsDescribeOptions extends TopicsBaseOptions {\n  slug: string;\n  description: string;\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// list — `almanac topics`\n// ─────────────────────────────────────────────────────────────────────\n\n/**\n * `almanac topics` (and `almanac topics list`). Prints one line per\n * known topic — from the DB, which already unions topics.yaml with any\n * ad-hoc slugs found in page frontmatter. Page counts come straight\n * from `page_topics`, which the indexer rebuilt on entry.\n */\nexport async function runTopicsList(\n  options: TopicsListOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  await ensureFreshIndex({ repoRoot });\n\n  const db = openIndex(indexDbPath(repoRoot));\n  try {\n    const rows = db\n      .prepare<\n        [],\n        { slug: string; title: string | null; description: string | null; page_count: number }\n      >(\n        // page_count excludes archived pages — matches the policy used\n        // by `topics show` (see `pagesDirectlyTagged`) and by every\n        // page-scoped check in `health`. Pick one rule and apply it\n        // everywhere; a topic with \"5 pages\" in `topics list` and \"3\n        // pages\" in `topics show` is a trust-eroding inconsistency.\n        `SELECT t.slug, t.title, t.description,\n                (SELECT COUNT(*)\n                   FROM page_topics pt\n                   JOIN pages p ON p.slug = pt.page_slug\n                   WHERE pt.topic_slug = t.slug AND p.archived_at IS NULL\n                ) AS page_count\n         FROM topics t\n         ORDER BY t.slug`,\n      )\n      .all();\n\n    if (options.json === true) {\n      return {\n        stdout: `${JSON.stringify(rows, null, 2)}\\n`,\n        stderr: \"\",\n        exitCode: 0,\n      };\n    }\n\n    if (rows.length === 0) {\n      return {\n        stdout:\n          \"no topics. create one with `almanac topics create <name>` or tag a page.\\n\",\n        stderr: \"\",\n        exitCode: 0,\n      };\n    }\n\n    const slugWidth = rows.reduce((w, r) => Math.max(w, r.slug.length), 0);\n    const lines = rows.map((r) => {\n      const slug = r.slug.padEnd(slugWidth);\n      const count = `(${r.page_count} page${r.page_count === 1 ? \"\" : \"s\"})`;\n      return `${slug}  ${count}`;\n    });\n    return { stdout: `${lines.join(\"\\n\")}\\n`, stderr: \"\", exitCode: 0 };\n  } finally {\n    db.close();\n  }\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// show — `almanac topics show <slug>`\n// ─────────────────────────────────────────────────────────────────────\n\nexport interface TopicsShowRecord {\n  slug: string;\n  title: string | null;\n  description: string | null;\n  parents: string[];\n  children: string[];\n  pages: string[];\n  descendants_used?: boolean;\n}\n\n/**\n * `almanac topics show <slug>`. Prints metadata + parents, children,\n * and the page list. `--descendants` widens the page list to include\n * pages tagged with any descendant topic (via the DAG).\n */\nexport async function runTopicsShow(\n  options: TopicsShowOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  await ensureFreshIndex({ repoRoot });\n\n  const slug = toKebabCase(options.slug);\n  if (slug.length === 0) {\n    return {\n      stdout: \"\",\n      stderr: `almanac: empty topic slug\\n`,\n      exitCode: 1,\n    };\n  }\n\n  const db = openIndex(indexDbPath(repoRoot));\n  try {\n    const row = db\n      .prepare<\n        [string],\n        { slug: string; title: string | null; description: string | null }\n      >(\"SELECT slug, title, description FROM topics WHERE slug = ?\")\n      .get(slug);\n    if (row === undefined) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: no such topic \"${slug}\"\\n`,\n        exitCode: 1,\n      };\n    }\n\n    const parents = db\n      .prepare<[string], { parent_slug: string }>(\n        \"SELECT parent_slug FROM topic_parents WHERE child_slug = ? ORDER BY parent_slug\",\n      )\n      .all(slug)\n      .map((r) => r.parent_slug);\n\n    const children = db\n      .prepare<[string], { child_slug: string }>(\n        \"SELECT child_slug FROM topic_parents WHERE parent_slug = ? ORDER BY child_slug\",\n      )\n      .all(slug)\n      .map((r) => r.child_slug);\n\n    const pageSlugs = options.descendants === true\n      ? pagesForSubtree(db, slug)\n      : pagesDirectlyTagged(db, slug);\n\n    const record: TopicsShowRecord = {\n      slug: row.slug,\n      title: row.title,\n      description: row.description,\n      parents,\n      children,\n      pages: pageSlugs,\n      descendants_used: options.descendants === true,\n    };\n\n    if (options.json === true) {\n      return {\n        stdout: `${JSON.stringify(record, null, 2)}\\n`,\n        stderr: \"\",\n        exitCode: 0,\n      };\n    }\n    return { stdout: formatShow(record), stderr: \"\", exitCode: 0 };\n  } finally {\n    db.close();\n  }\n}\n\nfunction pagesDirectlyTagged(db: Database.Database, slug: string): string[] {\n  return db\n    .prepare<[string], { page_slug: string }>(\n      `SELECT pt.page_slug\n       FROM page_topics pt\n       JOIN pages p ON p.slug = pt.page_slug\n       WHERE pt.topic_slug = ? AND p.archived_at IS NULL\n       ORDER BY pt.page_slug`,\n    )\n    .all(slug)\n    .map((r) => r.page_slug);\n}\n\nfunction pagesForSubtree(db: Database.Database, slug: string): string[] {\n  const slugs = [slug, ...descendantsInDb(db, slug)];\n  // Deduplicate + preserve order via a Set — a page can belong to\n  // multiple topics in the subtree and we only want one row per page.\n  const placeholders = slugs.map(() => \"?\").join(\", \");\n  const rows = db\n    .prepare<unknown[], { page_slug: string }>(\n      `SELECT DISTINCT pt.page_slug\n       FROM page_topics pt\n       JOIN pages p ON p.slug = pt.page_slug\n       WHERE pt.topic_slug IN (${placeholders}) AND p.archived_at IS NULL\n       ORDER BY pt.page_slug`,\n    )\n    .all(...slugs);\n  return rows.map((r) => r.page_slug);\n}\n\nfunction formatShow(r: TopicsShowRecord): string {\n  const lines: string[] = [];\n  lines.push(`slug:         ${r.slug}`);\n  lines.push(`title:        ${r.title ?? titleCase(r.slug)}`);\n  lines.push(`description:  ${r.description ?? \"—\"}`);\n  lines.push(\n    `parents:      ${r.parents.length > 0 ? r.parents.join(\", \") : \"—\"}`,\n  );\n  lines.push(\n    `children:     ${r.children.length > 0 ? r.children.join(\", \") : \"—\"}`,\n  );\n  const pagesLabel = r.descendants_used === true ? \"pages (incl. descendants)\" : \"pages\";\n  lines.push(`${pagesLabel}:`);\n  if (r.pages.length === 0) {\n    lines.push(\"  —\");\n  } else {\n    for (const p of r.pages) lines.push(`  ${p}`);\n  }\n  return `${lines.join(\"\\n\")}\\n`;\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// create — `almanac topics create <name> [--parent <slug>]...`\n// ─────────────────────────────────────────────────────────────────────\n\n/**\n * `almanac topics create <name> [--parent <slug>]...`.\n *\n * Policy: `--parent <slug>` MUST refer to an existing topic (created\n * earlier in topics.yaml or indexed from page frontmatter). Auto-\n * creating parents silently would let typos cascade — `create JWT\n * --parent secuirty` would quietly spawn a \"secuirty\" topic. Better to\n * refuse and point the user at `almanac topics create <parent>` first.\n *\n * Already-exists is not an error if no new parents are being added —\n * rerunning the same `create` is a no-op. If new parents are introduced\n * we add them (respecting cycle prevention, just like `link`).\n */\nexport async function runTopicsCreate(\n  options: TopicsCreateOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n\n  const slug = toKebabCase(options.name);\n  if (slug.length === 0) {\n    return {\n      stdout: \"\",\n      stderr: `almanac: topic name \"${options.name}\" has no slug-able characters\\n`,\n      exitCode: 1,\n    };\n  }\n  const title = options.name.trim().length > 0 ? options.name.trim() : titleCase(slug);\n\n  // Reindex first so an ad-hoc `--parent <slug>` created by a\n  // just-written page is visible to `topicExists`. Every other topics\n  // command did this; `create` silently skipped the refresh which meant\n  // a brand-new page's `topics: [newparent]` couldn't be used as a\n  // parent until the next query touched the DB.\n  await ensureFreshIndex({ repoRoot });\n\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n\n  // Hoist the DB open out of the parents loop. We used to open + close\n  // the DB inside `isAdHocTopicInDb` for every parent; opening is\n  // cheap but not free, and the iteration pattern shows up in other\n  // topics commands too.\n  const db = openIndex(indexDbPath(repoRoot));\n  try {\n    // Resolve/validate parents BEFORE mutating the file. All-or-nothing.\n    const requestedParents = (options.parents ?? [])\n      .map((p) => toKebabCase(p))\n      .filter((p) => p.length > 0);\n    for (const p of requestedParents) {\n      if (p === slug) {\n        return {\n          stdout: \"\",\n          stderr: `almanac: topic cannot be its own parent\\n`,\n          exitCode: 1,\n        };\n      }\n      if (!topicExists(file, db, p)) {\n        return {\n          stdout: \"\",\n          stderr: `almanac: parent topic \"${p}\" does not exist; create it first with \\`almanac topics create ${p}\\`\\n`,\n          exitCode: 1,\n        };\n      }\n      if (findTopic(file, p) === null) {\n        // Topic exists only as an ad-hoc DB entry. Promote it into\n        // topics.yaml so it has a proper record. `ensureTopic` is\n        // idempotent so this is safe even if two loop iterations\n        // reference the same ad-hoc parent.\n        ensureTopic(file, p);\n      }\n    }\n\n    const existing = findTopic(file, slug);\n    if (existing === null) {\n      const entry: TopicEntry = {\n        slug,\n        title,\n        description: null,\n        parents: requestedParents,\n      };\n      file.topics.push(entry);\n    } else {\n      // Add any new parents, skipping ones that already exist or would\n      // create a cycle.\n      for (const p of requestedParents) {\n        if (existing.parents.includes(p)) continue;\n        const ancestors = ancestorsInFile(file, p);\n        if (ancestors.has(slug) || p === slug) {\n          return {\n            stdout: \"\",\n            stderr: `almanac: adding \"${p}\" as a parent of \"${slug}\" would create a cycle\\n`,\n            exitCode: 1,\n          };\n        }\n        existing.parents.push(p);\n      }\n      // Promote the user-supplied title only if the existing one was a\n      // title-cased default (i.e., they didn't describe it yet). Don't\n      // clobber a deliberate title silently.\n      if (\n        existing.title === titleCase(existing.slug) &&\n        title !== titleCase(slug) &&\n        title !== existing.title\n      ) {\n        existing.title = title;\n      }\n    }\n\n    await writeTopicsFile(yamlPath, file);\n    await runIndexer({ repoRoot });\n    return {\n      stdout: existing === null\n        ? `created topic \"${slug}\"\\n`\n        : `updated topic \"${slug}\"\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  } finally {\n    db.close();\n  }\n}\n\n/**\n * Is `slug` a known topic anywhere — in `topics.yaml`, or as an ad-hoc\n * slug that a page's frontmatter mentioned and the indexer seeded?\n *\n * Collapses the previous `findTopic(file, s) === null &&\n * !isAdHocTopicInDb(root, s)` duplication into one intent-revealing\n * helper. Takes an open `db` handle so the caller can hoist DB open\n * out of tight loops — every earlier call site created + destroyed a\n * new connection per iteration.\n */\nfunction topicExists(\n  file: TopicsFile,\n  db: Database.Database,\n  slug: string,\n): boolean {\n  if (findTopic(file, slug) !== null) return true;\n  const row = db\n    .prepare<[string], { slug: string }>(\n      \"SELECT slug FROM topics WHERE slug = ?\",\n    )\n    .get(slug);\n  return row !== undefined;\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// link / unlink\n// ─────────────────────────────────────────────────────────────────────\n\n/**\n * `almanac topics link <child> <parent>`. Adds a DAG edge after\n * checking that it wouldn't close a cycle. Both topics must exist.\n */\nexport async function runTopicsLink(\n  options: TopicsLinkOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  const child = toKebabCase(options.child);\n  const parent = toKebabCase(options.parent);\n  if (child.length === 0 || parent.length === 0) {\n    return { stdout: \"\", stderr: `almanac: empty topic slug\\n`, exitCode: 1 };\n  }\n  if (child === parent) {\n    return {\n      stdout: \"\",\n      stderr: `almanac: topic cannot be its own parent\\n`,\n      exitCode: 1,\n    };\n  }\n\n  // Refresh the index so ad-hoc topics (ones the user tagged pages\n  // with but never formally `topics create`d) are visible to\n  // `topicExists` below.\n  await ensureFreshIndex({ repoRoot });\n\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n\n  const db = openIndex(indexDbPath(repoRoot));\n  try {\n    for (const slug of [child, parent]) {\n      if (!topicExists(file, db, slug)) {\n        return {\n          stdout: \"\",\n          stderr: `almanac: topic \"${slug}\" does not exist\\n`,\n          exitCode: 1,\n        };\n      }\n      if (findTopic(file, slug) === null) {\n        // DB-only ad-hoc topic → promote it into topics.yaml so the\n        // new DAG edge has a concrete home.\n        ensureTopic(file, slug);\n      }\n    }\n\n    const childEntry = findTopic(file, child);\n    if (childEntry === null) {\n      // Shouldn't happen after ensureTopic above — defensive.\n      return {\n        stdout: \"\",\n        stderr: `almanac: topic \"${child}\" not found\\n`,\n        exitCode: 1,\n      };\n    }\n\n    if (childEntry.parents.includes(parent)) {\n      return {\n        stdout: `edge ${child} → ${parent} already exists\\n`,\n        stderr: \"\",\n        exitCode: 0,\n      };\n    }\n\n    // Cycle check BEFORE mutation. Uses the in-memory file so the check\n    // operates on the state we're about to write — no DB round-trip needed.\n    const parentAncestors = ancestorsInFile(file, parent);\n    if (parentAncestors.has(child) || parent === child) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: adding ${parent} as parent of ${child} would create a cycle\\n`,\n        exitCode: 1,\n      };\n    }\n\n    childEntry.parents.push(parent);\n    await writeTopicsFile(yamlPath, file);\n    await runIndexer({ repoRoot });\n    return {\n      stdout: `linked ${child} → ${parent}\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  } finally {\n    db.close();\n  }\n}\n\n/**\n * `almanac topics unlink <child> <parent>`. Removes a DAG edge if it\n * exists. No-op (exit 0) if not. Never deletes topics.\n */\nexport async function runTopicsUnlink(\n  options: TopicsUnlinkOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  const child = toKebabCase(options.child);\n  const parent = toKebabCase(options.parent);\n  if (child.length === 0 || parent.length === 0) {\n    return { stdout: \"\", stderr: `almanac: empty topic slug\\n`, exitCode: 1 };\n  }\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n  const childEntry = findTopic(file, child);\n  if (childEntry === null || !childEntry.parents.includes(parent)) {\n    return {\n      stdout: `no edge ${child} → ${parent}\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n  childEntry.parents = childEntry.parents.filter((p) => p !== parent);\n  await writeTopicsFile(yamlPath, file);\n  await runIndexer({ repoRoot });\n  return {\n    stdout: `unlinked ${child} → ${parent}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// rename — `almanac topics rename <old> <new>`\n// ─────────────────────────────────────────────────────────────────────\n\n/**\n * `almanac topics rename <old> <new>`. Rewrites the slug both in\n * `topics.yaml` (as an entry key and in anyone who declared it as a\n * parent) and in every affected page's frontmatter.\n *\n * Refuses if `<new>` is already a distinct topic — \"merging\" two topics\n * should be explicit, not a silent side effect of a rename.\n */\nexport async function runTopicsRename(\n  options: TopicsRenameOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  const oldSlug = toKebabCase(options.oldSlug);\n  const newSlug = toKebabCase(options.newSlug);\n  if (oldSlug.length === 0 || newSlug.length === 0) {\n    return { stdout: \"\", stderr: `almanac: empty topic slug\\n`, exitCode: 1 };\n  }\n  if (oldSlug === newSlug) {\n    return {\n      stdout: `topic \"${oldSlug}\" unchanged\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  await ensureFreshIndex({ repoRoot });\n\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n\n  // Hoist the DB handle so the existence checks below don't reopen\n  // the index per-slug.\n  const db = openIndex(indexDbPath(repoRoot));\n  let pagesUpdated: number;\n  try {\n    // Fetch existence info. `oldInYaml` is kept as a direct reference\n    // because we mutate the entry; the DB check is only needed when\n    // the slug isn't in the file (ad-hoc-only).\n    const oldInYaml = findTopic(file, oldSlug);\n    if (!topicExists(file, db, oldSlug)) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: no such topic \"${oldSlug}\"\\n`,\n        exitCode: 1,\n      };\n    }\n\n    if (topicExists(file, db, newSlug)) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: topic \"${newSlug}\" already exists; delete it first if you intend to merge\\n`,\n        exitCode: 1,\n      };\n    }\n\n    // Rewrite `topics.yaml`: the entry itself (if present) plus any\n    // parent reference to `oldSlug`.\n    if (oldInYaml !== null) {\n      oldInYaml.slug = newSlug;\n      if (oldInYaml.title === titleCase(oldSlug)) {\n        // Title was the auto-generated default — refresh it to the new\n        // slug's title-case. 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+{"version":3,"sources":["../src/cli.ts","../src/commands/bootstrap.ts","../src/agent/auth.ts","../src/agent/prompts.ts","../src/agent/sdk.ts","../src/paths.ts","../src/commands/init.ts","../src/slug.ts","../src/registry/index.ts","../src/commands/capture.ts","../src/indexer/frontmatter.ts","../src/commands/hook.ts","../src/commands/health.ts","../src/indexer/duration.ts","../src/indexer/index.ts","../src/topics/yaml.ts","../src/indexer/paths.ts","../src/indexer/schema.ts","../src/indexer/wikilinks.ts","../src/indexer/resolveWiki.ts","../src/topics/dag.ts","../src/commands/info.ts","../src/commands/list.ts","../src/commands/path.ts","../src/commands/reindex.ts","../src/commands/search.ts","../src/commands/show.ts","../src/topics/frontmatterRewrite.ts","../src/topics/paths.ts","../src/commands/tag.ts","../src/commands/topics.ts","../src/registry/autoregister.ts","../bin/codealmanac.ts"],"sourcesContent":["import { basename } from \"node:path\";\n\nimport { Command } from \"commander\";\n\nimport { runBootstrap } from \"./commands/bootstrap.js\";\nimport { runCapture } from \"./commands/capture.js\";\nimport {\n  runHookInstall,\n  runHookStatus,\n  runHookUninstall,\n} from \"./commands/hook.js\";\nimport { runHealth } from \"./commands/health.js\";\nimport { initWiki } from \"./commands/init.js\";\nimport { runInfo } from \"./commands/info.js\";\nimport { listWikis } from \"./commands/list.js\";\nimport { runPath } from \"./commands/path.js\";\nimport { runReindex } from \"./commands/reindex.js\";\nimport { runSearch } from \"./commands/search.js\";\nimport { runShow } from \"./commands/show.js\";\nimport { runTag, runUntag } from \"./commands/tag.js\";\nimport {\n  runTopicsCreate,\n  runTopicsDelete,\n  runTopicsDescribe,\n  runTopicsLink,\n  runTopicsList,\n  runTopicsRename,\n  runTopicsShow,\n  runTopicsUnlink,\n} from \"./commands/topics.js\";\nimport { autoRegisterIfNeeded } from \"./registry/autoregister.js\";\n\n/**\n * Entry point. `bin/codealmanac.ts` hands us `process.argv` and any errors\n * bubble up to the shim for a uniform \"almanac: <message>\" output format.\n *\n * Auto-registration runs before most commands. Two exceptions:\n *   - `init` registers explicitly, so auto-register would be redundant and\n *     would race with init's own write.\n *   - `list --drop <name>` shouldn't silently re-register the repo whose\n *     entry the user is trying to remove.\n */\nexport async function run(argv: string[]): Promise<void> {\n  const program = new Command();\n\n  // Both `almanac` and `codealmanac` point at the same entry (see\n  // `package.json#bin`). Match the help header to whatever the user\n  // invoked so `codealmanac --help` doesn't incongruously read\n  // `Usage: almanac …`. Fall back to `almanac` when argv[1] isn't\n  // available (programmatic invocation, tests).\n  const invoked = argv[1] !== undefined ? basename(argv[1]) : \"almanac\";\n  const programName =\n    invoked === \"codealmanac\" ? \"codealmanac\" : \"almanac\";\n\n  program\n    .name(programName)\n    .description(\n      \"codealmanac — a living wiki for codebases, maintained by AI agents\",\n    )\n    .version(\"0.1.0\", \"-v, --version\", \"print version\");\n\n  program\n    .command(\"init\")\n    .description(\"scaffold .almanac/ in the current directory and register it\")\n    .option(\"--name <name>\", \"wiki name (defaults to the directory name)\")\n    .option(\"--description <text>\", \"one-line description of this wiki\")\n    .action(async (opts: { name?: string; description?: string }) => {\n      const result = await initWiki({\n        cwd: process.cwd(),\n        name: opts.name,\n        description: opts.description,\n      });\n      const verb = result.created ? \"initialized\" : \"updated\";\n      process.stdout.write(\n        `${verb} wiki \"${result.entry.name}\" at ${result.almanacDir}\\n`,\n      );\n    });\n\n  program\n    .command(\"list\")\n    .description(\"list registered wikis\")\n    .option(\"--json\", \"emit structured JSON\")\n    .option(\n      \"--drop <name>\",\n      \"remove a wiki from the registry (the only way entries are ever removed)\",\n    )\n    .action(async (opts: { json?: boolean; drop?: string }) => {\n      // Auto-register only makes sense for default/JSON listing. Skipping\n      // it on --drop keeps the removal operation predictable — the user's\n      // intent is to shrink the registry, not grow it mid-command.\n      if (opts.drop === undefined) {\n        await autoRegisterIfNeeded(process.cwd());\n      }\n      const result = await listWikis(opts);\n      process.stdout.write(result.stdout);\n      if (result.exitCode !== 0) {\n        process.exitCode = result.exitCode;\n      }\n    });\n\n  program\n    .command(\"search [query]\")\n    .description(\"query pages by text, topic, file mentions, or freshness\")\n    .option(\n      \"--topic <name...>\",\n      \"filter by topic (repeat for intersection)\",\n      collectOption,\n      [] as string[],\n    )\n    .option(\n      \"--mentions <path>\",\n      \"pages referencing this file or folder (trailing / = folder)\",\n    )\n    .option(\n      \"--since <duration>\",\n      \"updated within duration, by file mtime (e.g. 2w, 30d)\",\n    )\n    .option(\n      \"--stale <duration>\",\n      \"NOT updated within duration, by file mtime\",\n    )\n    .option(\"--orphan\", \"pages with no topics\")\n    .option(\"--include-archive\", \"include archived pages\")\n    .option(\"--archived\", \"archived pages only\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .option(\"--json\", \"emit structured JSON\")\n    .option(\"--limit <n>\", \"cap results\", parsePositiveInt)\n    .action(\n      async (\n        query: string | undefined,\n        opts: {\n          topic?: string[];\n          mentions?: string;\n          since?: string;\n          stale?: string;\n          orphan?: boolean;\n          includeArchive?: boolean;\n          archived?: boolean;\n          wiki?: string;\n          json?: boolean;\n          limit?: number;\n        },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runSearch({\n          cwd: process.cwd(),\n          query,\n          topics: opts.topic ?? [],\n          mentions: opts.mentions,\n          since: opts.since,\n          stale: opts.stale,\n          orphan: opts.orphan,\n          includeArchive: opts.includeArchive,\n          archived: opts.archived,\n          wiki: opts.wiki,\n          json: opts.json,\n          limit: opts.limit,\n        });\n        if (result.stderr.length > 0) process.stderr.write(result.stderr);\n        process.stdout.write(result.stdout);\n        if (result.exitCode !== 0) process.exitCode = result.exitCode;\n      },\n    );\n\n  program\n    .command(\"show [slug]\")\n    .description(\"print the markdown content of a page\")\n    .option(\"--stdin\", \"read slugs from stdin (one per line)\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (\n        slug: string | undefined,\n        opts: { stdin?: boolean; wiki?: string },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runShow({\n          cwd: process.cwd(),\n          slug,\n          stdin: opts.stdin,\n          stdinInput: opts.stdin === true ? await readStdin() : undefined,\n          wiki: opts.wiki,\n        });\n        if (result.stderr.length > 0) process.stderr.write(result.stderr);\n        process.stdout.write(result.stdout);\n        if (result.exitCode !== 0) process.exitCode = result.exitCode;\n      },\n    );\n\n  program\n    .command(\"path [slug]\")\n    .description(\"resolve a slug to its absolute file path\")\n    .option(\"--stdin\", \"read slugs from stdin (one per line)\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (\n        slug: string | undefined,\n        opts: { stdin?: boolean; wiki?: string },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runPath({\n          cwd: process.cwd(),\n          slug,\n          stdin: opts.stdin,\n          stdinInput: opts.stdin === true ? await readStdin() : undefined,\n          wiki: opts.wiki,\n        });\n        if (result.stderr.length > 0) process.stderr.write(result.stderr);\n        process.stdout.write(result.stdout);\n        if (result.exitCode !== 0) process.exitCode = result.exitCode;\n      },\n    );\n\n  program\n    .command(\"info [slug]\")\n    .description(\"print metadata for a page (topics, refs, links, lineage)\")\n    .option(\"--stdin\", \"read slugs from stdin (one per line)\")\n    .option(\"--json\", \"emit structured JSON\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (\n        slug: string | undefined,\n        opts: { stdin?: boolean; json?: boolean; wiki?: string },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runInfo({\n          cwd: process.cwd(),\n          slug,\n          stdin: opts.stdin,\n          stdinInput: opts.stdin === true ? await readStdin() : undefined,\n          json: opts.json,\n          wiki: opts.wiki,\n        });\n        if (result.stderr.length > 0) process.stderr.write(result.stderr);\n        process.stdout.write(result.stdout);\n        if (result.exitCode !== 0) process.exitCode = result.exitCode;\n      },\n    );\n\n  program\n    .command(\"reindex\")\n    .description(\"force a full rebuild of .almanac/index.db\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(async (opts: { wiki?: string }) => {\n      await autoRegisterIfNeeded(process.cwd());\n      const result = await runReindex({\n        cwd: process.cwd(),\n        wiki: opts.wiki,\n      });\n      process.stdout.write(result.stdout);\n      if (result.exitCode !== 0) process.exitCode = result.exitCode;\n    });\n\n  // ─── topics (sub-tree) ────────────────────────────────────────────\n  const topics = program\n    .command(\"topics\")\n    .description(\"manage the topic DAG (list, create, link, rename, delete)\");\n\n  // Default action for `almanac topics` with no subcommand: list.\n  topics\n    .command(\"list\", { isDefault: true })\n    .description(\"list all topics with page counts\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .option(\"--json\", \"emit structured JSON\")\n    .action(async (opts: { wiki?: string; json?: boolean }) => {\n      await autoRegisterIfNeeded(process.cwd());\n      const result = await runTopicsList({\n        cwd: process.cwd(),\n        wiki: opts.wiki,\n        json: opts.json,\n      });\n      emit(result);\n    });\n\n  topics\n    .command(\"show <slug>\")\n    .description(\"print a topic's metadata, parents, children, and pages\")\n    .option(\"--descendants\", \"include pages tagged with descendant topics\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .option(\"--json\", \"emit structured JSON\")\n    .action(\n      async (\n        slug: string,\n        opts: { descendants?: boolean; wiki?: string; json?: boolean },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runTopicsShow({\n          cwd: process.cwd(),\n          slug,\n          descendants: opts.descendants,\n          wiki: opts.wiki,\n          json: opts.json,\n        });\n        emit(result);\n      },\n    );\n\n  topics\n    .command(\"create <name>\")\n    .description(\"create a topic (rejects if --parent slug does not exist)\")\n    .option(\n      \"--parent <slug>\",\n      \"parent topic slug (repeat for multiple parents)\",\n      collectOption,\n      [] as string[],\n    )\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (\n        name: string,\n        opts: { parent?: string[]; wiki?: string },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runTopicsCreate({\n          cwd: process.cwd(),\n          name,\n          parents: opts.parent,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  topics\n    .command(\"link <child> <parent>\")\n    .description(\"add a DAG edge (cycle-checked)\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (child: string, parent: string, opts: { wiki?: string }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runTopicsLink({\n          cwd: process.cwd(),\n          child,\n          parent,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  topics\n    .command(\"unlink <child> <parent>\")\n    .description(\"remove a DAG edge\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (child: string, parent: string, opts: { wiki?: string }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runTopicsUnlink({\n          cwd: process.cwd(),\n          child,\n          parent,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  topics\n    .command(\"rename <old> <new>\")\n    .description(\"rename a topic; rewrites every affected page's frontmatter\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (oldSlug: string, newSlug: string, opts: { wiki?: string }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runTopicsRename({\n          cwd: process.cwd(),\n          oldSlug,\n          newSlug,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  topics\n    .command(\"delete <slug>\")\n    .description(\"delete a topic; untags every affected page\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(async (slug: string, opts: { wiki?: string }) => {\n      await autoRegisterIfNeeded(process.cwd());\n      const result = await runTopicsDelete({\n        cwd: process.cwd(),\n        slug,\n        wiki: opts.wiki,\n      });\n      emit(result);\n    });\n\n  topics\n    .command(\"describe <slug> <text>\")\n    .description(\"set a topic's one-line description\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (slug: string, text: string, opts: { wiki?: string }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runTopicsDescribe({\n          cwd: process.cwd(),\n          slug,\n          description: text,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  // ─── tag / untag ─────────────────────────────────────────────────\n  program\n    .command(\"tag [page] [topics...]\")\n    .description(\"add topics to a page (auto-creates missing topics)\")\n    .option(\"--stdin\", \"read page slugs from stdin (one per line)\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (\n        page: string | undefined,\n        topicsArg: string[],\n        opts: { stdin?: boolean; wiki?: string },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        // `--stdin <topic> [<topic>...]` shape: no positional page,\n        // all positionals are topics. commander gives us `page` =\n        // first positional and `topicsArg` = rest, so in --stdin mode\n        // we prepend whatever landed in `page` to the topics list.\n        const resolvedTopics = opts.stdin === true\n          ? [page, ...topicsArg].filter(\n              (t): t is string => typeof t === \"string\" && t.length > 0,\n            )\n          : topicsArg;\n        const result = await runTag({\n          cwd: process.cwd(),\n          page: opts.stdin === true ? undefined : page,\n          topics: resolvedTopics,\n          stdin: opts.stdin,\n          stdinInput: opts.stdin === true ? await readStdin() : undefined,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  program\n    .command(\"untag <page> <topic>\")\n    .description(\"remove a topic from a page's frontmatter\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (page: string, topic: string, opts: { wiki?: string }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runUntag({\n          cwd: process.cwd(),\n          page,\n          topic,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  // ─── bootstrap ───────────────────────────────────────────────────\n  // Slice 4: first Claude Agent SDK integration. Spawns the bootstrap\n  // agent on the current repo to create initial entity pages + README +\n  // topic DAG. Requires ANTHROPIC_API_KEY; refuses on populated wikis\n  // unless --force.\n  program\n    .command(\"bootstrap\")\n    .description(\n      \"spawn an agent to scan the repo and create initial wiki stubs (requires ANTHROPIC_API_KEY)\",\n    )\n    .option(\"--quiet\", \"suppress per-tool streaming; print only the final line\")\n    .option(\"--model <model>\", \"override the agent model\")\n    .option(\n      \"--force\",\n      \"overwrite an existing populated wiki (default: refuse)\",\n    )\n    .action(\n      async (opts: { quiet?: boolean; model?: string; force?: boolean }) => {\n        // No auto-register here: if this is a fresh repo the bootstrap\n        // command handles init (and therefore registration) itself. If\n        // the repo is already a wiki, capture/init have already\n        // registered it.\n        const result = await runBootstrap({\n          cwd: process.cwd(),\n          quiet: opts.quiet,\n          model: opts.model,\n          force: opts.force,\n        });\n        emit(result);\n      },\n    );\n\n  // ─── capture ─────────────────────────────────────────────────────\n  // Slice 5: writer + reviewer subagent on a Claude Code session\n  // transcript. Refuses if no `.almanac/` exists (capture is for\n  // maintaining wikis, not creating them). Transcript path resolution:\n  //  - explicit positional arg wins\n  //  - `--session <id>` matches by filename under ~/.claude/projects/\n  //  - otherwise auto-resolve the most recent transcript whose cwd\n  //    matches this repo\n  program\n    .command(\"capture [transcript]\")\n    .description(\n      \"capture knowledge from a Claude Code session transcript \" +\n        \"(auto-resolves the most recent session for this repo when no \" +\n        \"path is given; requires ANTHROPIC_API_KEY)\",\n    )\n    .option(\"--session <id>\", \"target a specific session by ID\")\n    .option(\n      \"--quiet\",\n      \"suppress per-tool streaming; print only the final summary\",\n    )\n    .option(\"--model <model>\", \"override the agent model\")\n    .action(\n      async (\n        transcript: string | undefined,\n        opts: { session?: string; quiet?: boolean; model?: string },\n      ) => {\n        // Auto-register the repo on capture: the user may have cloned a\n        // repo with `.almanac/` committed but never run init.\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runCapture({\n          cwd: process.cwd(),\n          transcriptPath: transcript,\n          sessionId: opts.session,\n          quiet: opts.quiet,\n          model: opts.model,\n        });\n        emit(result);\n      },\n    );\n\n  // ─── hook ─────────────────────────────────────────────────────────\n  // Wires codealmanac into Claude Code's SessionEnd hook via\n  // ~/.claude/settings.json. Non-interactive install/uninstall/status.\n  const hook = program\n    .command(\"hook\")\n    .description(\n      \"install, uninstall, or inspect the SessionEnd hook in ~/.claude/settings.json\",\n    );\n\n  hook\n    .command(\"install\")\n    .description(\"add a SessionEnd entry that runs 'almanac capture' on session end\")\n    .action(async () => {\n      const result = await runHookInstall();\n      emit(result);\n    });\n\n  hook\n    .command(\"uninstall\")\n    .description(\"remove codealmanac's SessionEnd entry; leaves foreign entries alone\")\n    .action(async () => {\n      const result = await runHookUninstall();\n      emit(result);\n    });\n\n  hook\n    .command(\"status\")\n    .description(\"report whether the SessionEnd hook is installed\")\n    .action(async () => {\n      const result = await runHookStatus();\n      emit(result);\n    });\n\n  // ─── health ──────────────────────────────────────────────────────\n  program\n    .command(\"health\")\n    .description(\"report wiki problems (orphans, dead refs, broken links, …)\")\n    .option(\"--topic <name>\", \"scope to a topic + its descendants\")\n    .option(\"--stale <duration>\", \"stale threshold (default 90d)\")\n    .option(\"--stdin\", \"read page slugs from stdin (limit to these pages)\")\n    .option(\"--json\", \"emit structured JSON\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (opts: {\n        topic?: string;\n        stale?: string;\n        stdin?: boolean;\n        json?: boolean;\n        wiki?: string;\n      }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runHealth({\n          cwd: process.cwd(),\n          topic: opts.topic,\n          stale: opts.stale,\n          stdin: opts.stdin,\n          stdinInput: opts.stdin === true ? await readStdin() : undefined,\n          json: opts.json,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  await program.parseAsync(argv);\n}\n\n/**\n * Uniform writer for commands that produce `{stdout, stderr, exitCode}`.\n * Used by the slice-3 topics/tag/health commands; older commands still\n * inline the same three lines and can be collapsed in a follow-up.\n */\nfunction emit(result: {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}): void {\n  if (result.stderr.length > 0) process.stderr.write(result.stderr);\n  if (result.stdout.length > 0) process.stdout.write(result.stdout);\n  if (result.exitCode !== 0) process.exitCode = result.exitCode;\n}\n\n/**\n * Commander's built-in collectable option helper. Repeatable `--topic`\n * appends; a bare call with no previous value starts a fresh array.\n */\nfunction collectOption(value: string, previous: string[]): string[] {\n  return [...previous, value];\n}\n\nfunction parsePositiveInt(value: string): number {\n  const n = Number.parseInt(value, 10);\n  if (!Number.isFinite(n) || n < 0) {\n    throw new Error(`invalid --limit \"${value}\" (expected a non-negative integer)`);\n  }\n  return n;\n}\n\n/**\n * Drain stdin to a string. Used by the `--stdin` flag on show/path/info.\n * We require an explicit opt-in rather than auto-detect TTY because\n * relying on `process.stdin.isTTY` makes the behavior surprising when\n * invoked from scripts with stdin redirected.\n */\nasync function readStdin(): Promise<string> {\n  if (process.stdin.isTTY === true) return \"\";\n  const chunks: Buffer[] = [];\n  for await (const chunk of process.stdin) {\n    chunks.push(Buffer.isBuffer(chunk) ? chunk : Buffer.from(chunk));\n  }\n  return Buffer.concat(chunks).toString(\"utf8\");\n}\n","import { createWriteStream, existsSync, type WriteStream } from \"node:fs\";\nimport { readdir } from \"node:fs/promises\";\nimport { join, relative } from \"node:path\";\n\nimport type { SDKMessage } from \"@anthropic-ai/claude-agent-sdk\";\n\nimport { assertClaudeAuth, type SpawnCliFn } from \"../agent/auth.js\";\nimport { loadPrompt } from \"../agent/prompts.js\";\nimport {\n  runAgent,\n  type AgentResult,\n  type RunAgentOptions,\n} from \"../agent/sdk.js\";\nimport { findNearestAlmanacDir, getRepoAlmanacDir } from \"../paths.js\";\nimport { initWiki } from \"./init.js\";\n\nexport interface BootstrapOptions {\n  cwd: string;\n  /** Suppress per-tool-use streaming output; print only errors + final line. */\n  quiet?: boolean;\n  /** Override the agent model. Defaults to the SDK default (sonnet-4-6). */\n  model?: string;\n  /** Overwrite a populated wiki. Default refuses with a pointer at `capture`. */\n  force?: boolean;\n  /** Injectable agent runner — tests replace this with a fake. */\n  runAgent?: (opts: RunAgentOptions) => Promise<AgentResult>;\n  /**\n   * Injectable subprocess spawner for the Claude auth-status check.\n   * Tests substitute a stub that emits canned JSON without running the\n   * bundled CLI. Production leaves this undefined and `assertClaudeAuth`\n   * falls through to `defaultSpawnCli`.\n   */\n  spawnCli?: SpawnCliFn;\n  /**\n   * Clock injection, for tests. Otherwise `Date.now()` timestamps the\n   * transcript log filename and defaults to the SDK's session_id once\n   * we receive one (the filename is chosen BEFORE the agent starts so\n   * we can stream to it).\n   */\n  now?: () => Date;\n}\n\nexport interface BootstrapResult {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * Tools the bootstrap agent is permitted to use. Bootstrap reads the repo\n * (Read/Glob/Grep), runs quick inspection commands (Bash — scoped by the\n * prompt, not by the SDK — the agent isn't expected to do anything\n * destructive), and writes scaffolding (Write/Edit). Notably absent:\n *   - `Agent` — bootstrap has no subagents (reviewer is slice 5).\n *   - `WebFetch` / `WebSearch` — prompt is explicit that we work from the\n *     repo, not the internet. Adding these would invite drift.\n *   - MCP servers — none needed for a local filesystem scan.\n */\nconst BOOTSTRAP_TOOLS = [\"Read\", \"Write\", \"Edit\", \"Glob\", \"Grep\", \"Bash\"];\n\n/**\n * `almanac bootstrap` — first Claude Agent SDK integration.\n *\n * Flow:\n *   1. Auth gate (ANTHROPIC_API_KEY). Fail fast with a clean error.\n *   2. Resolve repo root (existing `.almanac/` or cwd).\n *   3. Refuse-if-populated unless --force.\n *   4. Auto-init silently if `.almanac/` doesn't exist yet.\n *   5. Load `prompts/bootstrap.md`.\n *   6. Run the agent with BOOTSTRAP_TOOLS, cwd = repo root.\n *   7. Stream tool-uses to stdout (unless --quiet); write the full raw\n *      transcript to `.almanac/.bootstrap-<session>.log`.\n *   8. Print a final `[done]` / `[failed]` line with cost + turns.\n *\n * Non-zero exit on failure so shell users can pipe into `&&`.\n */\nexport async function runBootstrap(\n  options: BootstrapOptions,\n): Promise<BootstrapResult> {\n  // Fail before loading prompts so we don't do filesystem work on a request\n  // that can't succeed. `assertClaudeAuth` accepts either subscription\n  // OAuth (via the bundled SDK CLI) or `ANTHROPIC_API_KEY`; missing both\n  // surfaces a two-option error and MUST exit non-zero so the SessionEnd\n  // hook (which backgrounds the process and ignores stderr) doesn't\n  // treat silent auth failure as success.\n  try {\n    await assertClaudeAuth(options.spawnCli);\n  } catch (err: unknown) {\n    const msg = err instanceof Error ? err.message : String(err);\n    return {\n      stdout: \"\",\n      stderr: `almanac: ${msg}\\n`,\n      exitCode: 1,\n    };\n  }\n\n  // Repo root: honor an already-initialized wiki anywhere above us.\n  // Otherwise treat `cwd` as the root for a fresh wiki.\n  const repoRoot = findNearestAlmanacDir(options.cwd) ?? options.cwd;\n  const almanacDir = getRepoAlmanacDir(repoRoot);\n  const pagesDir = join(almanacDir, \"pages\");\n\n  // Refuse to clobber a populated wiki. `almanac capture` is the tool for\n  // maintaining wikis after bootstrap.\n  if (options.force !== true && existsSync(pagesDir)) {\n    const existing = await countMarkdownPages(pagesDir);\n    if (existing > 0) {\n      return {\n        stdout: \"\",\n        stderr:\n          `almanac: .almanac/ already initialized with ${existing} page${existing === 1 ? \"\" : \"s\"}. ` +\n          \"Use 'almanac capture' instead, or --force to overwrite.\\n\",\n        exitCode: 1,\n      };\n    }\n  }\n\n  // Auto-init silently if missing. `initWiki` is idempotent — re-running\n  // on an existing wiki is a no-op for the README / pages dir.\n  if (!existsSync(almanacDir)) {\n    try {\n      await initWiki({ cwd: repoRoot });\n    } catch (err: unknown) {\n      // Per the slice spec: auto-init failures should be loud. The user\n      // needs to know init is broken, not see a cascading agent error.\n      const msg = err instanceof Error ? err.message : String(err);\n      return {\n        stdout: \"\",\n        stderr: `almanac: init failed during bootstrap: ${msg}\\n`,\n        exitCode: 1,\n      };\n    }\n  }\n\n  const systemPrompt = await loadPrompt(\"bootstrap\");\n\n  // Transcript log filename: timestamp-based so it's sortable. The session\n  // ID from the SDK isn't known until the first message arrives — by then\n  // we'd already want somewhere to stream to. Use a clock-derived prefix\n  // that's still meaningful even on a run that fails before producing a\n  // session_id.\n  const now = options.now?.() ?? new Date();\n  const logName = `.bootstrap-${formatTimestamp(now)}.log`;\n  const logPath = join(almanacDir, logName);\n  const logStream = createWriteStream(logPath, { flags: \"w\" });\n\n  // The streaming formatter is what the user sees on stdout unless\n  // --quiet is set. The raw log captures EVERYTHING (including\n  // `stream_event` partials) for postmortem.\n  const out = process.stdout;\n  const formatter = new StreamingFormatter({\n    write: (line: string) => {\n      if (options.quiet !== true) out.write(line);\n    },\n  });\n\n  const onMessage = (msg: SDKMessage): void => {\n    // Write the raw message to the transcript. Keep one JSON per line so\n    // the log is grep-able and can be re-parsed if needed.\n    try {\n      logStream.write(`${JSON.stringify(msg)}\\n`);\n    } catch {\n      // Serialization failures are non-fatal — we'd rather keep streaming\n      // to stdout than crash because one message had a circular ref.\n    }\n    formatter.handle(msg);\n  };\n\n  const runner = options.runAgent ?? runAgent;\n\n  const userPrompt = `Begin the bootstrap now. Working directory: ${repoRoot}.`;\n\n  let result: AgentResult;\n  try {\n    result = await runner({\n      systemPrompt,\n      prompt: userPrompt,\n      allowedTools: BOOTSTRAP_TOOLS,\n      cwd: repoRoot,\n      model: options.model,\n      onMessage,\n    });\n  } finally {\n    await closeStream(logStream);\n  }\n\n  const finalLine = formatFinalLine(result, logPath, repoRoot);\n\n  if (result.success) {\n    return {\n      stdout: `${finalLine}\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  return {\n    stdout: options.quiet === true ? \"\" : `${finalLine}\\n`,\n    stderr: `almanac: bootstrap failed: ${result.error ?? \"unknown error\"}\\n`,\n    exitCode: 1,\n  };\n}\n\n/**\n * Format the final line the user sees. On success it's a one-liner with\n * cost + turns; on failure we still print the cost/turns so the user\n * knows what the partial run used. The log path is shown relative to\n * `repoRoot` to keep the line short.\n */\nfunction formatFinalLine(\n  result: AgentResult,\n  logPath: string,\n  repoRoot: string,\n): string {\n  const status = result.success ? \"done\" : \"failed\";\n  const rel = relative(repoRoot, logPath);\n  const cost = `$${result.cost.toFixed(3)}`;\n  return `[${status}] cost: ${cost}, turns: ${result.turns} (transcript: ${rel})`;\n}\n\nasync function countMarkdownPages(pagesDir: string): Promise<number> {\n  try {\n    const entries = await readdir(pagesDir, { withFileTypes: true });\n    return entries.filter((e) => e.isFile() && e.name.endsWith(\".md\")).length;\n  } catch {\n    return 0;\n  }\n}\n\nfunction closeStream(stream: WriteStream): Promise<void> {\n  return new Promise((resolve) => {\n    stream.end(() => resolve());\n  });\n}\n\nfunction formatTimestamp(d: Date): string {\n  // YYYYMMDD-HHMMSS, local time. Collision-proof enough for human use\n  // (one bootstrap per second, per repo is an acceptable ceiling).\n  const pad = (n: number): string => n.toString().padStart(2, \"0\");\n  const y = d.getFullYear();\n  const mo = pad(d.getMonth() + 1);\n  const da = pad(d.getDate());\n  const h = pad(d.getHours());\n  const mi = pad(d.getMinutes());\n  const s = pad(d.getSeconds());\n  return `${y}${mo}${da}-${h}${mi}${s}`;\n}\n\n/**\n * Translates SDK messages into one-line-per-tool-use output.\n *\n * Design rules:\n *   - One line per `tool_use` block, not per token. Users scanning the\n *     output want to see \"what the agent did\", not a tail of the\n *     assistant's prose.\n *   - `Bash` gets special formatting because the input is most usefully\n *     rendered as the command being run.\n *   - On final `result`, emit a summary line. Callers can suppress all\n *     intermediate output via `--quiet` and still get the summary.\n *   - Tool paths are shown relative to the cwd (not implemented here\n *     because the SDK doesn't give us cwd on every message; users get\n *     the raw input). The cwd-relative rendering is a nice-to-have that\n *     we can layer on later without changing the API.\n *\n * Exported for testing — `StreamingFormatter` is easier to unit-test in\n * isolation than the whole command.\n */\nexport class StreamingFormatter {\n  private readonly sink: { write: (line: string) => void };\n  /**\n   * Current agent label. Starts as \"bootstrap\"; switches when we see an\n   * `Agent` tool-use (slice 5 will exercise this). We still track it here\n   * so the formatter can stay shared between bootstrap and capture.\n   */\n  private currentAgent = \"bootstrap\";\n\n  constructor(sink: { write: (line: string) => void }) {\n    this.sink = sink;\n  }\n\n  /**\n   * Swap the top-level agent label. `capture` uses this to relabel from\n   * the default \"bootstrap\" to \"writer\" — otherwise the writer's tool-use\n   * output would render as `[bootstrap] …`, which is confusing when you're\n   * reading capture logs.\n   */\n  setAgent(name: string): void {\n    this.currentAgent = name;\n  }\n\n  handle(msg: SDKMessage): void {\n    if (msg.type === \"assistant\") {\n      for (const block of msg.message.content) {\n        if (block.type !== \"tool_use\") continue;\n        this.handleToolUse(block.name, block.input);\n      }\n      return;\n    }\n\n    if (msg.type === \"result\") {\n      // The command-level finalLine is what the user sees at the end of\n      // stdout; the formatter also emits one here so live-tailing a\n      // transcript log shows the full run. Kept terse.\n      const status =\n        msg.subtype === \"success\" ? \"done\" : `failed (${msg.subtype})`;\n      this.sink.write(\n        `[${status}] cost: $${msg.total_cost_usd.toFixed(3)}, turns: ${msg.num_turns}\\n`,\n      );\n      return;\n    }\n  }\n\n  private handleToolUse(name: string, rawInput: unknown): void {\n    const input = normalizeToolInput(rawInput);\n\n    if (name === \"Agent\") {\n      // Subagent dispatch. Track the label so subsequent tool-uses show\n      // up under the right agent bracket. The label is whatever the\n      // parent passed as `subagent_type`, falling back to \"subagent\" if\n      // the input was malformed (shouldn't happen, but defensively).\n      const sub =\n        typeof input.subagent_type === \"string\" ? input.subagent_type : \"subagent\";\n      this.currentAgent = sub;\n      this.sink.write(`[${sub}] starting\\n`);\n      return;\n    }\n\n    const summary = formatToolSummary(name, input);\n    this.sink.write(`[${this.currentAgent}] ${summary}\\n`);\n  }\n}\n\n/**\n * SDK quirk: `tool_use.input` arrives as either an object OR a\n * JSON-encoded string. Always normalize before touching fields.\n */\nfunction normalizeToolInput(raw: unknown): Record<string, unknown> {\n  if (typeof raw === \"string\") {\n    try {\n      const parsed = JSON.parse(raw);\n      if (parsed !== null && typeof parsed === \"object\") {\n        return parsed as Record<string, unknown>;\n      }\n    } catch {\n      // Fall through to empty object.\n    }\n    return {};\n  }\n  if (raw !== null && typeof raw === \"object\") {\n    return raw as Record<string, unknown>;\n  }\n  return {};\n}\n\n/**\n * Render a tool call as a single human-readable line. Not exhaustive —\n * we cover the tools bootstrap actually invokes and fall back to the\n * tool name + a terse input summary for anything else.\n */\nfunction formatToolSummary(\n  name: string,\n  input: Record<string, unknown>,\n): string {\n  switch (name) {\n    case \"Read\": {\n      const target = stringField(input, \"file_path\") ?? \"?\";\n      return `reading ${target}`;\n    }\n    case \"Write\": {\n      const target = stringField(input, \"file_path\") ?? \"?\";\n      return `writing ${target}`;\n    }\n    case \"Edit\": {\n      const target = stringField(input, \"file_path\") ?? \"?\";\n      return `editing ${target}`;\n    }\n    case \"Glob\": {\n      const pattern = stringField(input, \"pattern\") ?? \"?\";\n      return `glob ${pattern}`;\n    }\n    case \"Grep\": {\n      const pattern = stringField(input, \"pattern\") ?? \"?\";\n      return `grep ${pattern}`;\n    }\n    case \"Bash\": {\n      const command = stringField(input, \"command\") ?? \"?\";\n      // Truncate long commands so one tool-use stays one line.\n      const trimmed =\n        command.length > 80 ? `${command.slice(0, 77)}...` : command;\n      return `bash ${trimmed}`;\n    }\n    default: {\n      // Unknown or MCP tool. Show the name; omit the input to avoid\n      // spamming the terminal with arbitrary JSON.\n      return name;\n    }\n  }\n}\n\nfunction stringField(\n  input: Record<string, unknown>,\n  key: string,\n): string | undefined {\n  const value = input[key];\n  return typeof value === \"string\" ? value : undefined;\n}\n","import { spawn, type ChildProcess } from \"node:child_process\";\nimport { createRequire } from \"node:module\";\nimport { dirname, join } from \"node:path\";\n\n/**\n * Claude auth gate — accepts either an active Claude subscription login\n * OR an `ANTHROPIC_API_KEY` environment variable.\n *\n * The Claude Agent SDK delegates authentication to its bundled `cli.js`,\n * which reads OAuth credentials from `~/.claude/credentials/` (the same\n * store Claude Code uses). Users who are logged in via `claude auth login\n * --claudeai` should be able to run bootstrap/capture without ever\n * exporting an API key. Conversely, users on pay-per-token API keys\n * shouldn't be required to go through the OAuth flow.\n *\n * We spawn the bundled SDK's `cli.js auth status --json` to answer \"are\n * we logged in?\" rather than poking at the credentials file directly —\n * that's the SDK's contract, and it handles all the edge cases (token\n * expiry, org switching, consoleloginpath, …) for us.\n *\n * The CLI path is resolved via `require.resolve(\"@anthropic-ai/claude-\n * agent-sdk/package.json\")` + the `cli.js` sibling. Going through\n * `createRequire` keeps this compatible with both ESM dev mode (tsx) and\n * the bundled dist (tsup externalizes the SDK, so Node's own resolver\n * does the lookup at runtime). If the SDK isn't installed at all we fall\n * back to treating the user as unauthenticated — the assert will then\n * surface the familiar two-path error so they can at least fix it via\n * `ANTHROPIC_API_KEY`.\n */\n\nexport interface ClaudeAuthStatus {\n  loggedIn: boolean;\n  email?: string;\n  subscriptionType?: string;\n  authMethod?: string;\n}\n\nexport interface SpawnedProcess {\n  stdout: { on: (event: \"data\", cb: (data: Buffer | string) => void) => void };\n  stderr: { on: (event: \"data\", cb: (data: Buffer | string) => void) => void };\n  on: (event: \"close\" | \"error\", cb: (arg: number | null | Error) => void) => void;\n  kill: (signal?: string) => void;\n}\n\n/**\n * The subprocess spawner is injectable so tests can replace it with a\n * fake that emits canned JSON without touching the filesystem. Production\n * code uses `defaultSpawnCli` which invokes the bundled SDK CLI.\n */\nexport type SpawnCliFn = (args: string[]) => SpawnedProcess;\n\nconst AUTH_TIMEOUT_MS = 10_000;\n\n/**\n * Resolve `cli.js` from the bundled `@anthropic-ai/claude-agent-sdk`\n * install. Uses `createRequire` so the lookup works regardless of\n * whether we're running from `dist/` (where tsup externalized the SDK)\n * or directly from source.\n *\n * Throws if the SDK can't be located — `checkClaudeAuth` catches this\n * and treats the user as not-logged-in, which lets the env-var path\n * still work for users with a borked install.\n */\nfunction resolveCliJsPath(): string {\n  // `import.meta.url` points at this module (dev or dist). `createRequire`\n  // from that URL can then resolve sibling packages the same way Node's\n  // own CJS resolver would.\n  //\n  // We resolve the main entry (not `./package.json`) because the SDK's\n  // `exports` field locks subpath access — `require.resolve(\".../package.json\")`\n  // fails with `ERR_PACKAGE_PATH_NOT_EXPORTED` on current SDK versions.\n  // The main entry resolves fine; `cli.js` is its sibling in the install\n  // layout the SDK has used since day one.\n  const require = createRequire(import.meta.url);\n  const entry = require.resolve(\"@anthropic-ai/claude-agent-sdk\");\n  return join(dirname(entry), \"cli.js\");\n}\n\n/**\n * Default subprocess spawner for production use — invokes the bundled\n * SDK's `cli.js` via the same Node runtime that's running codealmanac.\n * Tests inject a fake via the `spawnCli` parameter.\n */\nexport const defaultSpawnCli: SpawnCliFn = (args: string[]) => {\n  const cliPath = resolveCliJsPath();\n  // Use `process.execPath` so we inherit the Node runtime codealmanac\n  // itself is running under — avoids PATH weirdness on systems where\n  // `node` isn't on PATH but codealmanac was installed via npm.\n  const child = spawn(process.execPath, [cliPath, ...args], {\n    stdio: [\"ignore\", \"pipe\", \"pipe\"],\n  });\n  return child as unknown as SpawnedProcess;\n};\n\n/**\n * Check whether the user is authenticated via Claude subscription OAuth.\n *\n * Spawns the bundled SDK CLI's `auth status --json`. On any failure\n * (spawn error, non-JSON stdout, non-zero exit, timeout) we return\n * `{ loggedIn: false }` rather than propagating the error — the caller\n * will fall back to the `ANTHROPIC_API_KEY` path and, if that's also\n * missing, produce a clean two-option error message.\n *\n * The 10s timeout guards against the CLI hanging on a broken network or\n * keychain prompt. In practice `auth status` is a cheap local read.\n */\nexport async function checkClaudeAuth(\n  spawnCli: SpawnCliFn = defaultSpawnCli,\n): Promise<ClaudeAuthStatus> {\n  let child: SpawnedProcess;\n  try {\n    child = spawnCli([\"auth\", \"status\", \"--json\"]);\n  } catch {\n    return { loggedIn: false };\n  }\n\n  return new Promise<ClaudeAuthStatus>((resolve) => {\n    let stdout = \"\";\n    let stderr = \"\";\n    let settled = false;\n\n    const settle = (value: ClaudeAuthStatus): void => {\n      if (settled) return;\n      settled = true;\n      clearTimeout(timer);\n      resolve(value);\n    };\n\n    const timer = setTimeout(() => {\n      try {\n        child.kill(\"SIGTERM\");\n      } catch {\n        // Kill can fail if the process already exited; nothing we can do.\n      }\n      settle({ loggedIn: false });\n    }, AUTH_TIMEOUT_MS);\n\n    child.stdout.on(\"data\", (data) => {\n      stdout += data.toString();\n    });\n    child.stderr.on(\"data\", (data) => {\n      stderr += data.toString();\n    });\n\n    child.on(\"error\", () => {\n      settle({ loggedIn: false });\n    });\n\n    child.on(\"close\", (code) => {\n      // The SDK writes `{\"loggedIn\": false, ...}` to stdout with a zero\n      // exit code when the user isn't signed in, so we only reject on\n      // non-zero + empty stdout. An empty stdout with zero exit (shouldn't\n      // happen in practice) also fails safely to `loggedIn: false`.\n      if (code !== 0 && stdout.trim().length === 0) {\n        // `stderr` isn't surfaced to the user here — the caller's error\n        // message covers both auth paths — but it would be captured by\n        // `stderr` if we ever wanted to log it for debugging.\n        void stderr;\n        settle({ loggedIn: false });\n        return;\n      }\n      try {\n        const parsed = JSON.parse(stdout.trim()) as Record<string, unknown>;\n        const loggedIn = parsed.loggedIn === true;\n        const out: ClaudeAuthStatus = { loggedIn };\n        if (typeof parsed.email === \"string\") out.email = parsed.email;\n        if (typeof parsed.subscriptionType === \"string\") {\n          out.subscriptionType = parsed.subscriptionType;\n        }\n        if (typeof parsed.authMethod === \"string\") {\n          out.authMethod = parsed.authMethod;\n        }\n        settle(out);\n      } catch {\n        settle({ loggedIn: false });\n      }\n    });\n  });\n}\n\n/**\n * Human-readable error when neither auth path is available. The text is\n * deliberately verbose — users hitting this wall for the first time\n * deserve both options in front of them, not a terse hint.\n */\nexport const UNAUTHENTICATED_MESSAGE =\n  \"not authenticated to Claude.\\n\\n\" +\n  \"Option 1 — use your Claude subscription (Pro/Max):\\n\" +\n  \"  claude auth login --claudeai\\n\\n\" +\n  \"Option 2 — use a pay-per-token API key:\\n\" +\n  \"  Get one at https://console.anthropic.com\\n\" +\n  \"  export ANTHROPIC_API_KEY=sk-ant-...\\n\\n\" +\n  \"Verify with: claude auth status\";\n\n/**\n * Assert that at least one auth path is satisfied. Prefers subscription\n * auth (fewer surprises for Claude Pro/Max users) but accepts\n * `ANTHROPIC_API_KEY` as a fallback. On failure throws with\n * `code = \"CLAUDE_AUTH_MISSING\"` so callers can distinguish this from\n * other errors if they ever want to.\n *\n * Returns the resolved auth status so callers that want to display the\n * logged-in email in a preamble can do so without a second subprocess.\n */\nexport async function assertClaudeAuth(\n  spawnCli: SpawnCliFn = defaultSpawnCli,\n): Promise<ClaudeAuthStatus> {\n  const status = await checkClaudeAuth(spawnCli);\n  if (status.loggedIn) {\n    return status;\n  }\n  const apiKey = process.env.ANTHROPIC_API_KEY;\n  if (apiKey !== undefined && apiKey.length > 0) {\n    // Signal to callers that we're on the API-key path. Not \"loggedIn\"\n    // in the OAuth sense, but the SDK will pick up the env var and\n    // succeed — so we return a status that tells bootstrap/capture the\n    // gate is open.\n    return { loggedIn: true, authMethod: \"apiKey\" };\n  }\n  const err = new Error(UNAUTHENTICATED_MESSAGE);\n  (err as { code?: string }).code = \"CLAUDE_AUTH_MISSING\";\n  throw err;\n}\n\n// Internal re-export — helps keep the public type surface minimal while\n// still letting tests import the `ChildProcess` shape when needed.\nexport type { ChildProcess };\n","import { existsSync } from \"node:fs\";\nimport { readFile } from \"node:fs/promises\";\nimport path from \"node:path\";\nimport { fileURLToPath } from \"node:url\";\n\n/**\n * Loads bundled prompt text from the `prompts/` directory that ships with\n * the npm package. Used by `almanac bootstrap` (slice 4) and `almanac\n * capture` (slice 5).\n *\n * ## Why not embed the prompts as TS string literals?\n *\n * The non-negotiable from the spec (see CLAUDE.md → \"Non-negotiables\"):\n * \"Prompts are shipped from the npm package. They live in `prompts/` at\n * repo root, are bundled into `files` in `package.json`, and the agent\n * harness reads them from the package install path at runtime.\"\n *\n * Keeping them as separate files means they can be reviewed as prose,\n * diffed meaningfully, and (in the future) edited by users without\n * rebuilding the package.\n *\n * ## Path resolution\n *\n * Two runtime layouts need to work:\n *\n *   1. **Installed (`npm i -g codealmanac`).** The entry point lives at\n *      `dist/codealmanac.js`; prompts at `prompts/*.md`. Walking up from\n *      `import.meta.url` (`.../<pkg>/dist/codealmanac.js`) one level and\n *      into `prompts/` hits the right directory.\n *\n *   2. **Source dev.** During `npm run dev`, tsup emits to `dist/` just\n *      like in production, so case 1 applies. Tests import\n *      `src/agent/prompts.ts` directly via tsx/vitest; `import.meta.url`\n *      points at `src/agent/prompts.ts`. Walking up two levels from there\n *      lands at the repo root, where `prompts/` also lives.\n *\n * We probe a small list of candidates in order and use the first that\n * contains all three expected prompt files. This keeps a single source of\n * truth — the `prompts/` directory on disk — without baking in whether\n * we're running from `dist/` or `src/`.\n */\n\nexport type PromptName = \"bootstrap\" | \"writer\" | \"reviewer\";\n\nconst PROMPT_NAMES: readonly PromptName[] = [\n  \"bootstrap\",\n  \"writer\",\n  \"reviewer\",\n];\n\n/**\n * Override the prompts directory, for tests. Production code should never\n * call this — the auto-resolution handles both installed + source layouts.\n */\nlet overrideDir: string | null = null;\n\nexport function setPromptsDirForTesting(dir: string | null): void {\n  overrideDir = dir;\n}\n\n/**\n * Resolve the prompts directory by probing candidate locations. Cached\n * after the first call so repeated `loadPrompt()` calls don't stat the\n * filesystem more than once per process.\n */\nlet resolvedDir: string | null = null;\n\nexport function resolvePromptsDir(): string {\n  if (overrideDir !== null) return overrideDir;\n  if (resolvedDir !== null) return resolvedDir;\n\n  const here = path.dirname(fileURLToPath(import.meta.url));\n\n  // Candidates, most-specific first. Each path is where `prompts/` MIGHT\n  // live given some plausible bundle layout. The first one that exists\n  // and contains our three expected files wins.\n  const candidates = [\n    // Bundled dist layout: `.../<pkg>/dist/codealmanac.js` → `../prompts`\n    path.resolve(here, \"..\", \"prompts\"),\n    // Source layout: `.../<pkg>/src/agent/prompts.ts` → `../../prompts`\n    path.resolve(here, \"..\", \"..\", \"prompts\"),\n    // Defensive fallback: if tsup someday emits a nested `dist/src/agent`,\n    // walk up three levels.\n    path.resolve(here, \"..\", \"..\", \"..\", \"prompts\"),\n  ];\n\n  for (const dir of candidates) {\n    if (isPromptsDir(dir)) {\n      resolvedDir = dir;\n      return dir;\n    }\n  }\n\n  // If none matched, give a helpful error with the candidates we tried.\n  // This typically means the package was installed without the `prompts/`\n  // dir included — shouldn't happen unless someone broke `files` in\n  // package.json.\n  throw new Error(\n    \"could not locate bundled prompts/ directory. Tried:\\n\" +\n      candidates.map((c) => `  - ${c}`).join(\"\\n\"),\n  );\n}\n\nfunction isPromptsDir(dir: string): boolean {\n  if (!existsSync(dir)) return false;\n  // Require all three prompts to be present. A half-populated directory\n  // is worse than not finding one — we'd rather error early.\n  return PROMPT_NAMES.every((name) =>\n    existsSync(path.join(dir, `${name}.md`)),\n  );\n}\n\nexport async function loadPrompt(name: PromptName): Promise<string> {\n  const dir = resolvePromptsDir();\n  return readFile(path.join(dir, `${name}.md`), \"utf8\");\n}\n","import { query } from \"@anthropic-ai/claude-agent-sdk\";\nimport type {\n  AgentDefinition,\n  SDKMessage,\n} from \"@anthropic-ai/claude-agent-sdk\";\n\n/**\n * Thin wrapper around `@anthropic-ai/claude-agent-sdk`'s `query()`. This is\n * the ONLY module that imports from the SDK — every other command imports\n * from here. Slice 5 (capture) reuses this wrapper unchanged.\n *\n * Why a wrapper at all:\n *   1. Sets defaults (`maxTurns`, `includePartialMessages`, model) once so\n *      commands stay small.\n *   2. Translates the SDK's rich message types into a {cost, turns, result}\n *      summary the commands actually care about.\n *\n * The auth gate lives in `src/agent/auth.ts`. Commands call\n * `assertClaudeAuth()` BEFORE `runAgent` so we fail with a clean two-path\n * error before the SDK generator spins up. `runAgent` itself doesn't\n * re-check — the SDK reads whichever of (subscription OAuth,\n * `ANTHROPIC_API_KEY`) is present.\n *\n * Keep this module SMALL. If a feature can live in the caller, it should.\n */\n\nexport interface RunAgentOptions {\n  /** Full system prompt text — usually loaded from `prompts/*.md`. */\n  systemPrompt: string;\n  /** User prompt / kick-off message. */\n  prompt: string;\n  /** Tool allowlist, e.g. `[\"Read\", \"Write\", \"Edit\", \"Glob\", \"Grep\", \"Bash\"]`. */\n  allowedTools: string[];\n  /**\n   * Subagent definitions (slice 5 passes `{ reviewer: ... }`). Defaults to\n   * `{}` — bootstrap has no subagents.\n   */\n  agents?: Record<string, AgentDefinition>;\n  /** Working directory the agent's tools operate in (repo root). */\n  cwd: string;\n  /**\n   * Model override. Defaults to `claude-sonnet-4-6`. Note the FULL form —\n   * `options.model` requires `claude-sonnet-4-6`, not `sonnet`.\n   */\n  model?: string;\n  /**\n   * Hard cap on turns. Defaults to 100. SDK enforces this as a strict stop\n   * (no graceful wrap-up turn), so set generously.\n   */\n  maxTurns?: number;\n  /**\n   * Observer called for every SDK message. The formatter (streaming\n   * output, transcript log) runs here.\n   */\n  onMessage?: (msg: SDKMessage) => void;\n}\n\nexport interface AgentResult {\n  /** `true` when the SDK emitted a `result` with `subtype: \"success\"`. */\n  success: boolean;\n  /** Total USD cost reported by the final `result` message. */\n  cost: number;\n  /** Number of turns the agent used. */\n  turns: number;\n  /** The assistant's final textual result, if any. */\n  result: string;\n  /** Session ID captured from the first assistant/result message. */\n  sessionId?: string;\n  /** Populated when `success === false`. */\n  error?: string;\n}\n\n/**\n * Run an agent to completion. Iterates the SDK's `AsyncGenerator` and\n * returns a summary. Any thrown error in the `for await` becomes a\n * `success: false` result with the error message attached — we don't\n * propagate because the caller wants to write transcripts + print\n * formatted output regardless of outcome.\n *\n * The caller is responsible for running `assertClaudeAuth()` BEFORE\n * loading prompts or printing progress — see `bootstrap.ts`/`capture.ts`.\n * `runAgent` itself no longer re-checks; the SDK will happily pick up\n * whichever of (subscription OAuth, `ANTHROPIC_API_KEY`) the environment\n * provides.\n */\nexport async function runAgent(opts: RunAgentOptions): Promise<AgentResult> {\n\n  const q = query({\n    prompt: opts.prompt,\n    options: {\n      systemPrompt: opts.systemPrompt,\n      allowedTools: opts.allowedTools,\n      agents: opts.agents ?? {},\n      cwd: opts.cwd,\n      model: opts.model ?? \"claude-sonnet-4-6\",\n      maxTurns: opts.maxTurns ?? 100,\n      // REQUIRED for streaming text deltas. Without it, `stream_event`\n      // messages never fire and the CLI has no progress visibility during\n      // long turns. See docs/research/agent-sdk.md §12 pitfall #1.\n      includePartialMessages: true,\n    },\n  });\n\n  let cost = 0;\n  let turns = 0;\n  let result = \"\";\n  let sessionId: string | undefined;\n  let success = false;\n  let errorMsg: string | undefined;\n\n  try {\n    for await (const msg of q) {\n      opts.onMessage?.(msg);\n\n      // Capture session_id from the first message that carries it.\n      // Per the research doc, it appears on the first `assistant` or on\n      // the `result` — whichever arrives first.\n      if (\n        sessionId === undefined &&\n        typeof (msg as { session_id?: unknown }).session_id === \"string\"\n      ) {\n        sessionId = (msg as { session_id: string }).session_id;\n      }\n\n      if (msg.type === \"result\") {\n        // `SDKResultMessage = SDKResultSuccess | SDKResultError`. Both\n        // carry `total_cost_usd` and `num_turns`; only success has\n        // `result` (the final assistant text).\n        cost = msg.total_cost_usd;\n        turns = msg.num_turns;\n        if (msg.subtype === \"success\") {\n          success = true;\n          result = msg.result;\n        } else {\n          success = false;\n          errorMsg =\n            // `SDKResultError` variants don't carry a `result` string; the\n            // useful detail lives in `errors` (array of strings) or the\n            // subtype itself (e.g. \"error_max_turns\").\n            (msg.errors?.join(\"; \") ?? \"\") || `agent error: ${msg.subtype}`;\n        }\n      }\n    }\n  } catch (err: unknown) {\n    errorMsg = err instanceof Error ? err.message : String(err);\n    success = false;\n  }\n\n  return { success, cost, turns, result, sessionId, error: errorMsg };\n}\n","import { existsSync } from \"node:fs\";\nimport { homedir } from \"node:os\";\nimport { dirname, isAbsolute, join, resolve } from \"node:path\";\n\n/**\n * Absolute path to the user-level `~/.almanac/` directory.\n *\n * All global state (the registry, future global config) lives here, not in\n * the repo. We resolve this via `os.homedir()` rather than `$HOME` so the\n * CLI behaves the same on macOS, Linux, and Windows.\n */\nexport function getGlobalAlmanacDir(): string {\n  return join(homedir(), \".almanac\");\n}\n\n/**\n * Absolute path to the global registry file.\n *\n * The registry is the single source of truth for \"which wikis exist on this\n * machine.\" It is intentionally stored outside any repo so it survives\n * branch switches, clones, and repo deletions.\n */\nexport function getRegistryPath(): string {\n  return join(getGlobalAlmanacDir(), \"registry.json\");\n}\n\n/**\n * Repo-level `.almanac/` path for a given working directory (not resolved —\n * just `join(cwd, \".almanac\")`). Use `findNearestAlmanacDir` when you need\n * to walk upward like git does.\n */\nexport function getRepoAlmanacDir(cwd: string): string {\n  return join(cwd, \".almanac\");\n}\n\n/**\n * Walk upward from `startDir` looking for a directory that contains\n * `.almanac/`. Returns the absolute path to the repo root (the directory\n * containing `.almanac/`), or `null` if none is found before hitting the\n * filesystem root.\n *\n * Mirrors how `git` locates the enclosing repository. This lets `almanac`\n * work from any subdirectory inside a repo, not just the root.\n *\n * We explicitly skip the global `~/.almanac/` directory. It shares the\n * `.almanac` name with the per-repo wiki dir, but it's not a wiki — it\n * only holds the registry and global state. If the user runs `almanac\n * init` anywhere inside their home directory (outside a real wiki), we\n * must NOT treat `~` as an enclosing wiki root. Otherwise init would try\n * to register the home dir itself as a wiki.\n */\nexport function findNearestAlmanacDir(startDir: string): string | null {\n  const globalDir = getGlobalAlmanacDir();\n  let current = isAbsolute(startDir) ? startDir : resolve(startDir);\n\n  // Walk until we hit the filesystem root. `dirname(\"/\")` returns `\"/\"`,\n  // so the loop terminates when we stop ascending.\n  while (true) {\n    const candidate = join(current, \".almanac\");\n    if (candidate !== globalDir && existsSync(candidate)) {\n      return current;\n    }\n    const parent = dirname(current);\n    if (parent === current) {\n      return null;\n    }\n    current = parent;\n  }\n}\n","import { existsSync } from \"node:fs\";\nimport { mkdir, readFile, writeFile } from \"node:fs/promises\";\nimport { basename, join } from \"node:path\";\n\nimport { findNearestAlmanacDir, getRepoAlmanacDir } from \"../paths.js\";\nimport { toKebabCase } from \"../slug.js\";\nimport {\n  addEntry,\n  ensureGlobalDir,\n  type RegistryEntry,\n} from \"../registry/index.js\";\n\nexport interface InitOptions {\n  cwd: string;\n  name?: string;\n  description?: string;\n}\n\nexport interface InitResult {\n  entry: RegistryEntry;\n  almanacDir: string;\n  created: boolean; // false if .almanac/ already existed (idempotent re-init)\n}\n\n/**\n * Scaffold `.almanac/` in the repo and register it globally.\n *\n * Idempotent: running `init` on a repo that already has `.almanac/` is\n * fine — we re-register (refreshing the name/description) and skip\n * anything that already exists. We never overwrite a user-authored\n * `README.md` or touch existing pages.\n *\n * If `cwd` lives inside a subdirectory of an existing wiki, we walk up to\n * the wiki root and operate there. `almanac init` from `src/nested/`\n * should update the enclosing wiki, not create a nested one at\n * `src/nested/.almanac/` (which would fragment the registry and leave a\n * confusing orphan `.almanac/` on disk).\n */\nexport async function initWiki(options: InitOptions): Promise<InitResult> {\n  // If cwd is already inside a wiki, prefer that root. Otherwise treat\n  // cwd as the new wiki root.\n  const repoRoot = findNearestAlmanacDir(options.cwd) ?? options.cwd;\n\n  const almanacDir = getRepoAlmanacDir(repoRoot);\n  const pagesDir = join(almanacDir, \"pages\");\n  const readmePath = join(almanacDir, \"README.md\");\n\n  const alreadyExisted = existsSync(almanacDir);\n\n  await mkdir(pagesDir, { recursive: true });\n\n  if (!existsSync(readmePath)) {\n    await writeFile(readmePath, starterReadme(), \"utf8\");\n  }\n\n  await ensureGitignoreHasIndexDb(repoRoot);\n\n  const name = toKebabCase(options.name ?? basename(repoRoot));\n  if (name.length === 0) {\n    throw new Error(\n      \"could not derive a wiki name from the current directory; pass --name\",\n    );\n  }\n\n  const description = (options.description ?? \"\").trim();\n\n  await ensureGlobalDir();\n  const entry: RegistryEntry = {\n    name,\n    description,\n    path: repoRoot,\n    registered_at: new Date().toISOString(),\n  };\n  await addEntry(entry);\n\n  return { entry, almanacDir, created: !alreadyExisted };\n}\n\n/**\n * Ensure `.gitignore` in the repo root contains the codealmanac-derived\n * files that should never be committed.\n *\n * We ignore three paths:\n *   - `.almanac/index.db`        — the SQLite index (derived)\n *   - `.almanac/index.db-wal`    — WAL mode sidecar (present during writes)\n *   - `.almanac/index.db-shm`    — shared-memory sidecar (WAL mode)\n *\n * All three are derived from the markdown pages. The sidecars only show\n * up while better-sqlite3 has the DB open and can vanish between `git\n * status` calls, but explicitly ignoring them prevents \"dirty worktree\"\n * noise during active reindexing.\n *\n * We add the block regardless of whether the file exists (creating\n * `.gitignore` if needed), and we add any target lines that aren't\n * already present. Existing targets are left alone. If none of the\n * target lines need adding, the file is not touched at all.\n *\n * Formatting: when we do append, we guarantee exactly one blank line\n * between the prior content and our appended block. If the `# codealmanac`\n * header is already present but new targets need adding, we just append\n * the missing lines (no duplicate header).\n */\nasync function ensureGitignoreHasIndexDb(cwd: string): Promise<void> {\n  const path = join(cwd, \".gitignore\");\n  const targets = [\n    \".almanac/index.db\",\n    \".almanac/index.db-wal\",\n    \".almanac/index.db-shm\",\n  ];\n\n  let existing = \"\";\n  if (existsSync(path)) {\n    existing = await readFile(path, \"utf8\");\n  }\n\n  // Normalize to line comparison to avoid false negatives on trailing\n  // whitespace or CRLF line endings.\n  const lines = existing.split(/\\r?\\n/).map((l) => l.trim());\n  const missing = targets.filter((t) => !lines.includes(t));\n  if (missing.length === 0) return;\n\n  const hasHeader = lines.includes(\"# codealmanac\");\n  const block = hasHeader\n    ? missing.join(\"\\n\") + \"\\n\"\n    : `# codealmanac\\n${missing.join(\"\\n\")}\\n`;\n\n  // Three cases for the separator before the appended block:\n  //  - empty file: no separator needed\n  //  - ends with newline: one more newline produces a single blank line\n  //  - no trailing newline: two newlines (one to terminate the last line,\n  //    one for the blank separator)\n  const sep =\n    existing.length === 0 ? \"\" : existing.endsWith(\"\\n\") ? \"\\n\" : \"\\n\\n\";\n  await writeFile(path, `${existing}${sep}${block}`, \"utf8\");\n}\n\n/**\n * The starter `.almanac/README.md` content. Based on the \"Wiki README\" and\n * \"Notability bar\" sections of the design spec. Kept opinionated but short\n * (~70 lines) — the user is expected to edit it to fit the repo.\n */\nfunction starterReadme(): string {\n  return `# Wiki\n\nThis is the codealmanac wiki for this repository. It captures the knowledge\nthe code itself can't say — decisions, flows, invariants, gotchas, incidents.\n\nThe primary reader is an AI coding agent. The secondary reader is a human\nskimming to understand the shape of the codebase. Write accordingly: dense,\nfactual, linked.\n\n## Notability bar\n\nWrite a page when there is **non-obvious knowledge that will help a future\nagent**. Specifically:\n\n- A decision that took discussion, research, or trial-and-error\n- A gotcha discovered through failure\n- A cross-cutting flow that spans multiple files and isn't obvious from any\n  one of them\n- A constraint or invariant not visible from the code\n- An entity (technology, service, system) referenced by multiple pages\n\nDo not write pages that restate what the code does. Do not write pages of\ninference — only of observation. Silence is an acceptable outcome.\n\n## Topic taxonomy\n\nTopics form a DAG; pages can belong to multiple topics. Start with these and\ngrow as the wiki does:\n\n- \\`stack\\` — technologies and services we use (frameworks, databases, APIs)\n- \\`systems\\` — custom systems we built (auth, billing, search)\n- \\`flows\\` — multi-file processes end-to-end (checkout-flow, publish-flow)\n- \\`decisions\\` — \"why X over Y\"\n- \\`incidents\\` — recorded failures and their fixes\n- \\`concepts\\` — shared vocabulary specific to this codebase\n\nDomain topics (\\`auth\\`, \\`payments\\`, \\`frontend\\`, \\`backend\\`) live alongside\nthese. A page about JWT rotation belongs to both \\`auth\\` and \\`decisions\\`.\n\n## Page shapes\n\nFour shapes cover most of what gets written. They are suggestions, not a\nschema — a page that fits none of them is fine.\n\n- **Entity** — a stable named thing (Supabase, Stripe, the search service)\n- **Decision** — why we chose X over Y\n- **Flow** — how a multi-file process works end-to-end\n- **Gotcha** — a specific surprise, failure, or constraint\n\n## Writing conventions\n\n- Every sentence contains a specific fact. If it doesn't, cut it.\n- Neutral tone. \"is\", not \"serves as\". No \"plays a pivotal role\", no\n  interpretive \"-ing\" clauses, no vague attribution (\"experts argue\").\n- No hedging or knowledge-gap disclaimers. If you don't know, don't write\n  the sentence.\n- Prose first. Bullets for genuine lists. Tables only for structured\n  comparison.\n- No formulaic conclusions. End with the last substantive fact.\n\n## Linking\n\nOne \\`[[...]]\\` syntax for everything, disambiguated by content:\n\n- \\`[[checkout-flow]]\\` — page slug\n- \\`[[src/checkout/handler.ts]]\\` — file reference\n- \\`[[src/checkout/]]\\` — folder reference (trailing slash)\n- \\`[[other-wiki:slug]]\\` — cross-wiki reference\n\nEvery page should link to at least one entity when possible. A page with no\nentity link is suspect.\n\n## Pages live in \\`.almanac/pages/\\`\n\nOne markdown file per page, kebab-case slug. Frontmatter carries \\`topics:\\`\nand optional \\`files:\\`. The rest is prose.\n`;\n}\n","/**\n * Canonical kebab-case slugifier used across the codebase.\n *\n * One function, three callers:\n *   - `registry/index.ts` — wiki name slugs (both auto-derived and\n *     user-supplied via `--name`)\n *   - `indexer/index.ts` — page filename → slug and topic → slug\n *   - `indexer/wikilinks.ts` — wikilink target → slug for resolution\n *\n * All three want the same behavior: lowercased, non-alphanumeric runs\n * collapse to a single hyphen, leading/trailing hyphens trimmed. Keeping\n * this in one place avoids a class of bug where an unusual input (e.g.\n * `Checkout_Flow`) produces different slugs depending on which layer\n * slugified it.\n *\n * Rules:\n *   - Lowercase\n *   - Non-alphanumeric runs collapse to a single hyphen\n *   - Leading/trailing hyphens trimmed\n */\nexport function toKebabCase(input: string): string {\n  return input\n    .toLowerCase()\n    .replace(/[^a-z0-9]+/g, \"-\")\n    .replace(/^-+|-+$/g, \"\");\n}\n","import { mkdir, readFile, rename, writeFile } from \"node:fs/promises\";\nimport { dirname } from \"node:path\";\n\nimport { getGlobalAlmanacDir, getRegistryPath } from \"../paths.js\";\nimport { toKebabCase } from \"../slug.js\";\n\n// Re-export so existing import sites (`from \"../registry/index.js\"`) keep\n// working without a mechanical fan-out. The canonical home is `../slug.js`.\nexport { toKebabCase };\n\n/**\n * One entry in `~/.almanac/registry.json`.\n *\n * `name` is the canonical kebab-case slug the user types. `path` is the\n * absolute repo root (the directory that contains `.almanac/`). We store\n * absolute paths so cross-wiki resolution works regardless of the caller's\n * cwd.\n */\nexport interface RegistryEntry {\n  name: string;\n  description: string;\n  path: string;\n  registered_at: string;\n}\n\n/**\n * Read the registry file into memory.\n *\n * A missing file is not an error — it's the first-run state, which we\n * treat as an empty registry. A malformed file IS an error; we surface it\n * rather than silently clobbering the user's data.\n */\nexport async function readRegistry(): Promise<RegistryEntry[]> {\n  const path = getRegistryPath();\n  let raw: string;\n  try {\n    raw = await readFile(path, \"utf8\");\n  } catch (err: unknown) {\n    if (isNodeError(err) && err.code === \"ENOENT\") {\n      return [];\n    }\n    throw err;\n  }\n\n  const trimmed = raw.trim();\n  if (trimmed.length === 0) {\n    return [];\n  }\n\n  let parsed: unknown;\n  try {\n    parsed = JSON.parse(trimmed);\n  } catch (err: unknown) {\n    const message = err instanceof Error ? err.message : String(err);\n    throw new Error(`registry at ${path} is not valid JSON: ${message}`);\n  }\n\n  if (!Array.isArray(parsed)) {\n    throw new Error(`registry at ${path} must be a JSON array`);\n  }\n\n  // Validate every entry. We do NOT silently coerce missing `name` or\n  // `path` — an entry with `name: \"\"` would be unremovable via `--drop`\n  // and an empty `path` would match any `findEntry({ path: \"\" })` call.\n  // If someone hand-edited the registry into a bad state, surfacing the\n  // error is strictly better than limping along with corrupt data.\n  return parsed.map((item, idx) => {\n    if (typeof item !== \"object\" || item === null) {\n      throw new Error(`registry entry ${idx} is not an object`);\n    }\n    const e = item as Record<string, unknown>;\n    const name = typeof e.name === \"string\" ? e.name : \"\";\n    const path = typeof e.path === \"string\" ? e.path : \"\";\n    if (name.length === 0) {\n      throw new Error(`registry entry ${idx} is missing a non-empty \"name\"`);\n    }\n    if (path.length === 0) {\n      throw new Error(`registry entry ${idx} is missing a non-empty \"path\"`);\n    }\n    return {\n      name,\n      description: typeof e.description === \"string\" ? e.description : \"\",\n      path,\n      registered_at:\n        typeof e.registered_at === \"string\" ? e.registered_at : \"\",\n    };\n  });\n}\n\n/**\n * Persist the registry to disk. Creates `~/.almanac/` if it doesn't exist.\n *\n * We write with a trailing newline and 2-space indentation so the file is\n * diff-friendly if someone ever commits or inspects it manually.\n *\n * The write is atomic: we write to `registry.json.tmp` and then rename,\n * which is an atomic operation on every mainstream filesystem. This\n * matters because two concurrent `almanac init` (or autoregister) calls\n * from different shells would otherwise race on a partial write and\n * corrupt the file — a single `rename` means one wins cleanly and the\n * other's contents are simply dropped.\n */\nexport async function writeRegistry(entries: RegistryEntry[]): Promise<void> {\n  const path = getRegistryPath();\n  await mkdir(dirname(path), { recursive: true });\n  const body = `${JSON.stringify(entries, null, 2)}\\n`;\n  const tmpPath = `${path}.tmp`;\n  await writeFile(tmpPath, body, \"utf8\");\n  await rename(tmpPath, path);\n}\n\n/**\n * macOS (HFS+/APFS default) and Windows (NTFS default) are case-insensitive\n * but case-preserving. `/Users/x/Project` and `/Users/x/project` are the\n * same directory. We must treat them as the same registry entry, or a\n * single `almanac init` from a differently-cased cwd would duplicate the\n * row. Linux is case-sensitive — do not normalize there.\n *\n * Callers still store the original casing; only comparisons are lowercased.\n */\nfunction pathsEqual(a: string, b: string): boolean {\n  if (process.platform === \"darwin\" || process.platform === \"win32\") {\n    return a.toLowerCase() === b.toLowerCase();\n  }\n  return a === b;\n}\n\n/**\n * Add (or replace) an entry in the registry.\n *\n * Uniqueness is enforced on BOTH `name` and `path`: a repo can only appear\n * once, and a name can only refer to one repo. If either matches, we\n * replace the existing entry rather than creating a duplicate. This is\n * what makes auto-registration idempotent.\n */\nexport async function addEntry(entry: RegistryEntry): Promise<RegistryEntry[]> {\n  const existing = await readRegistry();\n  const filtered = existing.filter(\n    (e) => e.name !== entry.name && !pathsEqual(e.path, entry.path),\n  );\n  filtered.push(entry);\n  await writeRegistry(filtered);\n  return filtered;\n}\n\n/**\n * Remove an entry by name. Returns the removed entry (or `null` if none\n * matched). Only `almanac list --drop <name>` calls this — we never drop\n * automatically, even for unreachable paths.\n */\nexport async function dropEntry(name: string): Promise<RegistryEntry | null> {\n  const existing = await readRegistry();\n  const idx = existing.findIndex((e) => e.name === name);\n  if (idx === -1) {\n    return null;\n  }\n  const [removed] = existing.splice(idx, 1);\n  await writeRegistry(existing);\n  return removed ?? null;\n}\n\n/**\n * Find an entry by either name or absolute path. Used by auto-registration\n * to decide whether the current repo is already known.\n *\n * Path comparison is case-insensitive on macOS/Windows (see `pathsEqual`).\n */\nexport async function findEntry(params: {\n  name?: string;\n  path?: string;\n}): Promise<RegistryEntry | null> {\n  const entries = await readRegistry();\n  for (const entry of entries) {\n    if (params.name !== undefined && entry.name === params.name) return entry;\n    if (params.path !== undefined && pathsEqual(entry.path, params.path)) {\n      return entry;\n    }\n  }\n  return null;\n}\n\n/**\n * Ensure the global `.almanac/` directory exists. Safe to call repeatedly;\n * `mkdir recursive` is a no-op when the directory already exists.\n */\nexport async function ensureGlobalDir(): Promise<void> {\n  await mkdir(getGlobalAlmanacDir(), { recursive: true });\n}\n\nfunction isNodeError(err: unknown): err is NodeJS.ErrnoException {\n  return err instanceof Error && \"code\" in err;\n}\n","import { createHash } from \"node:crypto\";\nimport {\n  createWriteStream,\n  existsSync,\n  statSync,\n  type WriteStream,\n} from \"node:fs\";\nimport { readFile, readdir, stat } from \"node:fs/promises\";\nimport { homedir } from \"node:os\";\nimport { basename, join, relative } from \"node:path\";\n\nimport type { AgentDefinition, SDKMessage } from \"@anthropic-ai/claude-agent-sdk\";\n\nimport { assertClaudeAuth, type SpawnCliFn } from \"../agent/auth.js\";\nimport { loadPrompt } from \"../agent/prompts.js\";\nimport {\n  runAgent,\n  type AgentResult,\n  type RunAgentOptions,\n} from \"../agent/sdk.js\";\nimport { parseFrontmatter } from \"../indexer/frontmatter.js\";\nimport { findNearestAlmanacDir, getRepoAlmanacDir } from \"../paths.js\";\nimport { StreamingFormatter } from \"./bootstrap.js\";\n\nexport interface CaptureOptions {\n  cwd: string;\n  /** Explicit transcript path. Skips auto-resolution. */\n  transcriptPath?: string;\n  /** Target a specific session ID. */\n  sessionId?: string;\n  /** Suppress per-tool-use streaming; print only the final summary line. */\n  quiet?: boolean;\n  /** Model override. Defaults to the SDK default (sonnet-4-6). */\n  model?: string;\n  /** Injectable agent runner — tests replace this with a fake. */\n  runAgent?: (opts: RunAgentOptions) => Promise<AgentResult>;\n  /**\n   * Injectable spawner for the Claude auth-status subprocess. Tests pass\n   * a stub; production uses `defaultSpawnCli` which shells out to the\n   * bundled SDK's `cli.js`.\n   */\n  spawnCli?: SpawnCliFn;\n  /** Clock injection for deterministic log filenames in tests. */\n  now?: () => Date;\n  /**\n   * Override the Claude Code projects directory when auto-resolving a\n   * transcript. Production code leaves this undefined and we fall back to\n   * `~/.claude/projects`; tests point it at a fixture dir.\n   */\n  claudeProjectsDir?: string;\n}\n\nexport interface CaptureResult {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * Tools the writer agent is permitted to use.\n *\n *   - `Read` — read the session transcript, existing wiki pages, source files\n *   - `Write` / `Edit` — create and update pages under `.almanac/pages/`\n *   - `Glob` / `Grep` — navigate the wiki and source code\n *   - `Bash` — interrogate the wiki via `almanac search/show/info/list`\n *   - `Agent` — invoke the reviewer subagent\n *\n * `WebFetch`/`WebSearch` are intentionally absent: the writer should work\n * from the transcript + repo, not the open internet.\n */\nconst WRITER_TOOLS = [\"Read\", \"Write\", \"Edit\", \"Glob\", \"Grep\", \"Bash\", \"Agent\"];\n\n/**\n * Tools the reviewer subagent is permitted to use. The absence of\n * `Write`/`Edit`/`Agent` is the *only* thing preventing the reviewer from\n * editing files or chaining to further subagents — the SDK enforces this\n * based on the `tools` field in the `AgentDefinition`.\n */\nconst REVIEWER_TOOLS = [\"Read\", \"Grep\", \"Glob\", \"Bash\"];\n\nconst REVIEWER_DESCRIPTION =\n  \"Reviews proposed wiki changes against the full knowledge base for \" +\n  \"cohesion, duplication, missing links, notability, and writing conventions.\";\n\n/**\n * `almanac capture` — writer agent + reviewer subagent on a session transcript.\n *\n * Flow:\n *   1. Auth gate (ANTHROPIC_API_KEY).\n *   2. Resolve repo root (walk up for `.almanac/`). Refuse if none.\n *   3. Resolve transcript path (arg, --session, or auto-resolve from\n *      Claude Code's session storage).\n *   4. Snapshot `.almanac/pages/` BEFORE the agent runs so we can compute\n *      a created/updated/archived summary when it finishes.\n *   5. Load `prompts/writer.md` + `prompts/reviewer.md`. Build a reviewer\n *      `AgentDefinition` with read-only tools.\n *   6. Run the writer agent with the reviewer registered under `agents`.\n *   7. Stream tool-uses via the shared `StreamingFormatter` (unless --quiet).\n *   8. Diff the snapshot → emit `[done] N updated, M created, K archived …`.\n *\n * Empty outcomes (writer wrote nothing) exit 0 with a clear \"notability bar\"\n * message — per the writer prompt, silence is a valid output.\n */\nexport async function runCapture(\n  options: CaptureOptions,\n): Promise<CaptureResult> {\n  // Fail before any filesystem work. `assertClaudeAuth` accepts either\n  // subscription OAuth (via the bundled SDK CLI) or `ANTHROPIC_API_KEY`;\n  // missing both surfaces a two-option error with exit 1 so the\n  // SessionEnd hook (which backgrounds + redirects to a sidecar log)\n  // doesn't silently treat auth failure as a successful capture.\n  try {\n    await assertClaudeAuth(options.spawnCli);\n  } catch (err: unknown) {\n    const msg = err instanceof Error ? err.message : String(err);\n    return {\n      stdout: \"\",\n      stderr: `almanac: ${msg}\\n`,\n      exitCode: 1,\n    };\n  }\n\n  // Resolve the repo root by walking up for `.almanac/`. Unlike bootstrap,\n  // capture refuses to run when no wiki exists — the writer needs existing\n  // pages to read against, and auto-initing here would hide the fact that\n  // the user skipped `almanac bootstrap`.\n  const repoRoot = findNearestAlmanacDir(options.cwd);\n  if (repoRoot === null) {\n    return {\n      stdout: \"\",\n      stderr:\n        \"almanac: no .almanac/ found in this directory or any parent. \" +\n        \"Run 'almanac init' or 'almanac bootstrap' first.\\n\",\n      exitCode: 1,\n    };\n  }\n\n  const almanacDir = getRepoAlmanacDir(repoRoot);\n  const pagesDir = join(almanacDir, \"pages\");\n\n  // Resolve the transcript path up front. Doing this before we open a log\n  // stream keeps bad-arg errors uncluttered by side effects.\n  const transcriptResolution = await resolveTranscript({\n    repoRoot,\n    explicit: options.transcriptPath,\n    sessionId: options.sessionId,\n    claudeProjectsDir: options.claudeProjectsDir,\n  });\n  if (!transcriptResolution.ok) {\n    return {\n      stdout: \"\",\n      stderr: `almanac: ${transcriptResolution.error}\\n`,\n      exitCode: 1,\n    };\n  }\n  const transcriptPath = transcriptResolution.path;\n\n  // Snapshot the pages dir BEFORE the writer runs. We compare against it\n  // after the agent exits to compute a created/updated/archived tally.\n  // Doing this in TS (not via the agent's self-reporting) means the summary\n  // stays trustworthy even if the writer gets confused about what it did.\n  const snapshotBefore = await snapshotPages(pagesDir);\n\n  // Load the two prompts. Kept sequential rather than parallel — both files\n  // are tiny and the second read is cache-warm.\n  const systemPrompt = await loadPrompt(\"writer\");\n  const reviewerPrompt = await loadPrompt(\"reviewer\");\n\n  const agents: Record<string, AgentDefinition> = {\n    reviewer: {\n      description: REVIEWER_DESCRIPTION,\n      prompt: reviewerPrompt,\n      tools: REVIEWER_TOOLS,\n    },\n  };\n\n  // Transcript log filename: timestamp-based so repeated runs don't clobber\n  // each other. We don't have the SDK session_id yet (it's on the first\n  // message), and filesystem writes need a destination before the stream\n  // begins.\n  const now = options.now?.() ?? new Date();\n  const logName = `.capture-${formatTimestamp(now)}.log`;\n  const logPath = join(almanacDir, logName);\n  const logStream = createWriteStream(logPath, { flags: \"w\" });\n\n  const out = process.stdout;\n  const formatter = new StreamingFormatter({\n    write: (line: string) => {\n      if (options.quiet !== true) out.write(line);\n    },\n  });\n  // The shared StreamingFormatter defaults its currentAgent to \"bootstrap\"\n  // because bootstrap was the first command to use it. For capture the\n  // writer owns the top-level turn, so relabel.\n  formatter.setAgent(\"writer\");\n\n  const onMessage = (msg: SDKMessage): void => {\n    try {\n      logStream.write(`${JSON.stringify(msg)}\\n`);\n    } catch {\n      // Best-effort: one unserializable message shouldn't kill the whole\n      // stream. Humans read the log; if a line is missing they can re-run.\n    }\n    formatter.handle(msg);\n  };\n\n  // Pass an ABSOLUTE path for the transcript so the writer doesn't have to\n  // guess at cwd semantics. Everything else (`.almanac/pages/`) is already\n  // relative to the cwd the SDK gives its tools.\n  const userPrompt =\n    `Capture this coding session.\\n` +\n    `Transcript: ${transcriptPath}.\\n` +\n    `Working directory: ${repoRoot}.`;\n\n  const runner = options.runAgent ?? runAgent;\n\n  let result: AgentResult;\n  try {\n    result = await runner({\n      systemPrompt,\n      prompt: userPrompt,\n      allowedTools: WRITER_TOOLS,\n      agents,\n      cwd: repoRoot,\n      model: options.model,\n      // Capture sessions can touch many pages; give it more headroom than\n      // bootstrap. The SDK treats `maxTurns` as a hard stop — better to\n      // overshoot than to cut off mid-review.\n      maxTurns: 150,\n      onMessage,\n    });\n  } finally {\n    await closeStream(logStream);\n  }\n\n  const snapshotAfter = await snapshotPages(pagesDir);\n  const delta = diffSnapshots(snapshotBefore, snapshotAfter);\n\n  if (!result.success) {\n    return {\n      stdout: \"\",\n      stderr:\n        `almanac: capture failed: ${result.error ?? \"unknown error\"}\\n` +\n        `(transcript: ${relative(repoRoot, logPath)})\\n`,\n      exitCode: 1,\n    };\n  }\n\n  const summary = formatSummary(result, delta, logPath, repoRoot);\n\n  return {\n    stdout: `${summary}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\n// ─── Transcript resolution ────────────────────────────────────────────────\n\ninterface ResolvedTranscript {\n  ok: true;\n  path: string;\n}\ninterface FailedTranscript {\n  ok: false;\n  error: string;\n}\n\n/**\n * Resolve the transcript path from the three possible sources, in priority:\n *   1. Explicit positional arg (`almanac capture <path>`).\n *   2. `--session <id>`: find the single `.jsonl` matching that ID.\n *   3. Auto-resolve: most recent `.jsonl` under Claude Code's projects dir\n *      whose parent directory hashes to `repoRoot`. If multiple candidates\n *      or none match, return an error directing the user to pass a path.\n *\n * Claude Code names the per-project directory with a path-hash that we\n * can't deterministically reproduce without reading Claude Code's source.\n * Rather than guess at the hashing scheme, we scan all project dirs, pick\n * the one whose most recent transcript mentions the `repoRoot` in its\n * `cwd` field, and take the newest `.jsonl` from there.\n */\nasync function resolveTranscript(args: {\n  repoRoot: string;\n  explicit?: string;\n  sessionId?: string;\n  claudeProjectsDir?: string;\n}): Promise<ResolvedTranscript | FailedTranscript> {\n  if (args.explicit !== undefined && args.explicit.length > 0) {\n    if (!existsSync(args.explicit)) {\n      return {\n        ok: false,\n        error: `transcript not found: ${args.explicit}`,\n      };\n    }\n    return { ok: true, path: args.explicit };\n  }\n\n  const projectsDir =\n    args.claudeProjectsDir ?? join(homedir(), \".claude\", \"projects\");\n  if (!existsSync(projectsDir)) {\n    return {\n      ok: false,\n      error:\n        `could not auto-resolve transcript; ${projectsDir} does not exist. ` +\n        `Pass --session <id> or <transcript-path>.`,\n    };\n  }\n\n  const allTranscripts = await collectTranscripts(projectsDir);\n\n  if (args.sessionId !== undefined && args.sessionId.length > 0) {\n    const expected = `${args.sessionId}.jsonl`;\n    const match = allTranscripts.find((t) => basename(t.path) === expected);\n    if (match === undefined) {\n      return {\n        ok: false,\n        error:\n          `no transcript found for session ${args.sessionId} under ${projectsDir}`,\n      };\n    }\n    return { ok: true, path: match.path };\n  }\n\n  // Auto-resolve: prefer transcripts whose `cwd` field matches `repoRoot`,\n  // then fall back to the most recently modified if no cwd match is found.\n  // We read a peek of each transcript (not the whole file) to check the\n  // cwd — JSONL's first line typically carries it.\n  const matches = await filterTranscriptsByCwd(allTranscripts, args.repoRoot);\n\n  if (matches.length === 0) {\n    return {\n      ok: false,\n      error:\n        `could not auto-resolve transcript under ${projectsDir}; ` +\n        `no session matches cwd ${args.repoRoot}. ` +\n        `Pass --session <id> or <transcript-path>.`,\n    };\n  }\n\n  // Sort by mtime desc and pick the newest.\n  matches.sort((a, b) => b.mtime - a.mtime);\n  return { ok: true, path: matches[0]!.path };\n}\n\ninterface TranscriptEntry {\n  path: string;\n  mtime: number;\n}\n\nasync function collectTranscripts(\n  projectsDir: string,\n): Promise<TranscriptEntry[]> {\n  const out: TranscriptEntry[] = [];\n  let topLevel: string[];\n  try {\n    topLevel = await readdir(projectsDir);\n  } catch {\n    return out;\n  }\n  for (const name of topLevel) {\n    const projectDir = join(projectsDir, name);\n    let entries: string[];\n    try {\n      entries = await readdir(projectDir);\n    } catch {\n      continue;\n    }\n    for (const entry of entries) {\n      if (!entry.endsWith(\".jsonl\")) continue;\n      const full = join(projectDir, entry);\n      try {\n        const st = await stat(full);\n        if (st.isFile()) {\n          out.push({ path: full, mtime: st.mtimeMs });\n        }\n      } catch {\n        // Transient read error, skip.\n      }\n    }\n  }\n  return out;\n}\n\n/**\n * Keep only transcripts whose first session record mentions a `cwd` that\n * matches `repoRoot` (exact string match). We also match on the Claude\n * Code project-hash heuristic: the per-project dir name is usually the\n * absolute repo path with `/` replaced by `-`. Falling back to the hash\n * heuristic means we still resolve sanely when the JSONL format changes.\n */\nasync function filterTranscriptsByCwd(\n  transcripts: TranscriptEntry[],\n  repoRoot: string,\n): Promise<TranscriptEntry[]> {\n  const dirHash = `-${repoRoot.replace(/^\\/+/, \"\").replace(/\\//g, \"-\")}`;\n\n  const byDirName = transcripts.filter((t) => {\n    const parent = basename(join(t.path, \"..\"));\n    return parent === dirHash || parent.endsWith(dirHash);\n  });\n  if (byDirName.length > 0) return byDirName;\n\n  // Fallback: peek into each JSONL for a `\"cwd\":\"<repoRoot>\"` needle.\n  const needle = `\"cwd\":\"${repoRoot}\"`;\n  const hits: TranscriptEntry[] = [];\n  for (const t of transcripts) {\n    try {\n      const head = await readHead(t.path, 4096);\n      if (head.includes(needle)) hits.push(t);\n    } catch {\n      continue;\n    }\n  }\n  return hits;\n}\n\nasync function readHead(path: string, bytes: number): Promise<string> {\n  // Small files — just read the whole thing. We only call this on .jsonl\n  // files, which can be large, so cap at `bytes` via slicing.\n  const content = await readFile(path, \"utf8\");\n  return content.length > bytes ? content.slice(0, bytes) : content;\n}\n\n// ─── Snapshot / delta ─────────────────────────────────────────────────────\n\ninterface PageSnapshotEntry {\n  slug: string;\n  /** SHA-256 of file bytes — cheap, stable, avoids relying on mtime. */\n  hash: string;\n  /** `true` when the frontmatter has `archived_at` set. */\n  archived: boolean;\n}\n\ntype PageSnapshot = Map<string, PageSnapshotEntry>;\n\nasync function snapshotPages(pagesDir: string): Promise<PageSnapshot> {\n  const out: PageSnapshot = new Map();\n  if (!existsSync(pagesDir)) return out;\n\n  let entries: string[];\n  try {\n    entries = await readdir(pagesDir);\n  } catch {\n    return out;\n  }\n  for (const entry of entries) {\n    if (!entry.endsWith(\".md\")) continue;\n    const slug = entry.slice(0, -3);\n    const full = join(pagesDir, entry);\n    try {\n      const st = statSync(full);\n      if (!st.isFile()) continue;\n      const content = await readFile(full, \"utf8\");\n      const hash = createHash(\"sha256\").update(content).digest(\"hex\");\n      const fm = parseFrontmatter(content);\n      out.set(slug, {\n        slug,\n        hash,\n        archived: fm.archived_at !== null,\n      });\n    } catch {\n      continue;\n    }\n  }\n  return out;\n}\n\ninterface SnapshotDelta {\n  created: number;\n  updated: number;\n  archived: number;\n}\n\nfunction diffSnapshots(\n  before: PageSnapshot,\n  after: PageSnapshot,\n): SnapshotDelta {\n  let created = 0;\n  let updated = 0;\n  let archived = 0;\n\n  for (const [slug, entry] of after) {\n    const prev = before.get(slug);\n    if (prev === undefined) {\n      created += 1;\n      continue;\n    }\n    if (prev.hash !== entry.hash) {\n      // An edit that flips a page from active → archived counts as\n      // \"archived\", not \"updated\" — the archive is the semantically\n      // interesting thing.\n      if (!prev.archived && entry.archived) {\n        archived += 1;\n      } else {\n        updated += 1;\n      }\n    }\n  }\n  // Note: we deliberately don't track deleted pages. The writer prompt\n  // tells agents to archive (via frontmatter), not delete — a page that\n  // disappears entirely is a protocol violation worth surfacing, but not\n  // by silently counting it in the summary.\n\n  return { created, updated, archived };\n}\n\n// ─── Formatting ───────────────────────────────────────────────────────────\n\nfunction formatSummary(\n  result: AgentResult,\n  delta: SnapshotDelta,\n  logPath: string,\n  repoRoot: string,\n): string {\n  const rel = relative(repoRoot, logPath);\n  const cost = `$${result.cost.toFixed(3)}`;\n  const { created, updated, archived } = delta;\n\n  if (created === 0 && updated === 0 && archived === 0) {\n    return (\n      `[capture] no new knowledge met the notability bar (0 pages written), ` +\n      `cost: ${cost}, turns: ${result.turns} (transcript: ${rel})`\n    );\n  }\n\n  return (\n    `[done] ${updated} page${updated === 1 ? \"\" : \"s\"} updated, ` +\n    `${created} created, ` +\n    `${archived} archived, ` +\n    `cost: ${cost}, turns: ${result.turns} (transcript: ${rel})`\n  );\n}\n\nfunction formatTimestamp(d: Date): string {\n  const pad = (n: number): string => n.toString().padStart(2, \"0\");\n  return (\n    `${d.getFullYear()}${pad(d.getMonth() + 1)}${pad(d.getDate())}-` +\n    `${pad(d.getHours())}${pad(d.getMinutes())}${pad(d.getSeconds())}`\n  );\n}\n\nfunction closeStream(stream: WriteStream): Promise<void> {\n  return new Promise((resolve) => {\n    stream.end(() => resolve());\n  });\n}\n","import yaml from \"js-yaml\";\n\nexport interface Frontmatter {\n  title?: string;\n  topics: string[];\n  files: string[];\n  archived_at: number | null;\n  superseded_by: string | null;\n  supersedes: string | null;\n  /**\n   * The body of the file with frontmatter removed, for FTS5 and H1 fallback.\n   * Always populated even when the file has no frontmatter.\n   */\n  body: string;\n}\n\n/**\n * Pull YAML frontmatter off the top of a markdown file and coerce the\n * relevant fields. Unknown fields are tolerated silently — the wiki should\n * accept fields we don't understand yet without spewing warnings at the\n * user (future slices might consume them).\n *\n * Failure modes:\n *   - No frontmatter at all → `{ topics: [], files: [], ..., body: raw }`.\n *     This is legal; a heading + prose is a valid page.\n *   - Malformed YAML → warning to stderr, treated as \"no frontmatter\". We\n *     choose not to throw so a single bad file doesn't tank a reindex.\n *\n * Note on `archived_at`: authors write this as a YAML date (`2026-04-15`),\n * which `js-yaml` parses to a JS `Date`. We also tolerate ISO-8601 strings\n * and raw numbers. Everything else gets dropped (treated as \"not\n * archived\"). Storing epoch seconds keeps `--since`/`--stale`/`archived`\n * arithmetic trivial at query time.\n */\nexport function parseFrontmatter(raw: string): Frontmatter {\n  const empty: Frontmatter = {\n    topics: [],\n    files: [],\n    archived_at: null,\n    superseded_by: null,\n    supersedes: null,\n    body: raw,\n  };\n\n  // Frontmatter fence MUST start on line 1 — a `---` partway through the\n  // document is just a horizontal rule. Be strict about the opening delim\n  // so we don't accidentally strip section headers.\n  if (!raw.startsWith(\"---\")) {\n    return empty;\n  }\n\n  // Tolerate either Unix or Windows line endings. We read the first line\n  // explicitly to confirm it's only `---` (no trailing content).\n  const match = raw.match(/^---\\r?\\n([\\s\\S]*?)\\r?\\n---\\r?\\n?([\\s\\S]*)$/);\n  if (match === null) {\n    return empty;\n  }\n\n  const yamlBody = match[1] ?? \"\";\n  const body = match[2] ?? \"\";\n\n  let parsed: unknown;\n  try {\n    parsed = yaml.load(yamlBody);\n  } catch (err: unknown) {\n    const message = err instanceof Error ? err.message : String(err);\n    process.stderr.write(`almanac: malformed frontmatter (${message})\\n`);\n    return empty;\n  }\n\n  if (parsed === null || parsed === undefined) {\n    return { ...empty, body };\n  }\n  if (typeof parsed !== \"object\" || Array.isArray(parsed)) {\n    // Someone wrote a YAML scalar or list as the document root — not a\n    // mapping, so no fields for us to extract. Treat as empty but keep the\n    // post-fence body so FTS5 still gets content.\n    return { ...empty, body };\n  }\n\n  const obj = parsed as Record<string, unknown>;\n\n  return {\n    title: coerceString(obj.title),\n    topics: coerceStringArray(obj.topics),\n    files: coerceStringArray(obj.files),\n    archived_at: coerceEpochSeconds(obj.archived_at),\n    superseded_by: coerceString(obj.superseded_by) ?? null,\n    supersedes: coerceString(obj.supersedes) ?? null,\n    body,\n  };\n}\n\n/**\n * H1 fallback for title when frontmatter has none.\n *\n * Only considers the first 40 lines of the body — any real wiki page has\n * its H1 near the top. NOTE: `String.prototype.split(sep, limit)` still\n * splits the whole string internally and then truncates; it's not an\n * early-bail iteration. For the multi-megabyte files we might see in\n * practice this is still cheap (one regex pass, no allocation per-line\n * beyond the 40 we keep), so we favor the clearer code over hand-rolled\n * line iteration.\n */\nexport function firstH1(body: string): string | undefined {\n  const lines = body.split(/\\r?\\n/, 40);\n  for (const line of lines) {\n    const m = line.match(/^#\\s+(.+?)\\s*#*\\s*$/);\n    if (m !== null) {\n      return m[1];\n    }\n  }\n  return undefined;\n}\n\nfunction coerceString(v: unknown): string | undefined {\n  if (typeof v === \"string\" && v.trim().length > 0) return v.trim();\n  return undefined;\n}\n\nfunction coerceStringArray(v: unknown): string[] {\n  if (!Array.isArray(v)) return [];\n  const out: string[] = [];\n  for (const item of v) {\n    if (typeof item === \"string\" && item.trim().length > 0) {\n      out.push(item.trim());\n    }\n  }\n  return out;\n}\n\n/**\n * Coerce a frontmatter `archived_at` value (YAML Date, ISO string, or raw\n * epoch number) into epoch seconds. Returns `null` for anything we can't\n * make sense of — pages with an unrecognizable `archived_at` are treated as\n * active rather than silently marked archived, which is the safer default.\n */\nfunction coerceEpochSeconds(v: unknown): number | null {\n  if (v instanceof Date) {\n    return Math.floor(v.getTime() / 1000);\n  }\n  if (typeof v === \"number\" && Number.isFinite(v)) {\n    return Math.floor(v);\n  }\n  if (typeof v === \"string\" && v.trim().length > 0) {\n    const t = Date.parse(v.trim());\n    if (!Number.isNaN(t)) {\n      return Math.floor(t / 1000);\n    }\n  }\n  return null;\n}\n","import { existsSync } from \"node:fs\";\nimport { mkdir, readFile, rename, writeFile } from \"node:fs/promises\";\nimport { homedir } from \"node:os\";\nimport path from \"node:path\";\nimport { fileURLToPath } from \"node:url\";\n\n/**\n * `almanac hook install|uninstall|status` — wires the bundled\n * `hooks/almanac-capture.sh` into `~/.claude/settings.json` as a\n * `SessionEnd` hook.\n *\n * Design notes:\n *\n * - **Idempotent.** `install` twice leaves one entry, not two. We match by\n *   `command` string equality — if the user replaces our absolute path\n *   with a symlink pointing at the same script, we'll treat it as foreign.\n *   That's acceptable; the `status` output shows the path we'd use, so the\n *   user can reconcile manually.\n *\n * - **Refuse foreign entries.** If `SessionEnd` is already populated with\n *   a command we don't recognize, we print the existing value and exit\n *   non-zero. Claude Code lets users wire their own hooks (notifications,\n *   git autocommit scripts, etc.) and silently replacing them would be\n *   rude.\n *\n * - **Atomic write.** `settings.json` is small but heavily touched by\n *   Claude Code. Writing via tmp-file + rename avoids corrupting the file\n *   if we crash mid-write.\n *\n * - **Non-interactive.** No prompts, no confirmations. The caller is\n *   already making an intentional choice by running `almanac hook\n *   install`.\n */\n\nexport interface HookCommandOptions {\n  /**\n   * Override the hook script path. Production code leaves this undefined\n   * and we resolve the bundled `hooks/almanac-capture.sh`. Tests pass a\n   * fixture path to avoid depending on the runtime-install layout.\n   */\n  hookScriptPath?: string;\n  /**\n   * Override `~/.claude/settings.json`. Tests sandbox this to a tmpdir;\n   * production code leaves it undefined.\n   */\n  settingsPath?: string;\n}\n\nexport interface HookCommandResult {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\nconst HOOK_TIMEOUT_SECONDS = 10;\n\ninterface SessionEndEntry {\n  type: \"command\";\n  command: string;\n  timeout?: number;\n}\n\n/**\n * Claude Code's `settings.json` is a free-form JSON object; we only care\n * about the `hooks.SessionEnd` array. Preserve everything else verbatim so\n * we don't drop user settings when we write the file back.\n */\ntype SettingsJson = Record<string, unknown> & {\n  hooks?: Record<string, SessionEndEntry[] | undefined>;\n};\n\nexport async function runHookInstall(\n  options: HookCommandOptions = {},\n): Promise<HookCommandResult> {\n  const script = resolveHookScriptPath(options);\n  if (!script.ok) {\n    return { stdout: \"\", stderr: `almanac: ${script.error}\\n`, exitCode: 1 };\n  }\n\n  const settingsPath = resolveSettingsPath(options);\n  const settings = await readSettings(settingsPath);\n  const existing = (settings.hooks?.SessionEnd ?? []).slice();\n\n  // Find any existing entry with our exact command. If found, the install\n  // is a no-op (idempotent). If SessionEnd has OTHER commands alongside\n  // ours, leave them alone — the user might be composing multiple hooks.\n  const ourEntries = existing.filter((e) => e.command === script.path);\n  const foreignEntries = existing.filter((e) => e.command !== script.path);\n\n  // If the sole existing entry looks like ours-but-on-a-different-path\n  // (e.g. an old install from a different node_modules), replace it so we\n  // don't double-fire on session end. Heuristic: command ends with\n  // `almanac-capture.sh`. We accept this specific rename; unrelated\n  // commands still block.\n  const stale = foreignEntries.filter((e) =>\n    e.command.endsWith(\"almanac-capture.sh\"),\n  );\n  const unrelated = foreignEntries.filter(\n    (e) => !e.command.endsWith(\"almanac-capture.sh\"),\n  );\n\n  if (unrelated.length > 0) {\n    const existingStr = unrelated.map((e) => `  - ${e.command}`).join(\"\\n\");\n    return {\n      stdout: \"\",\n      stderr:\n        `almanac: SessionEnd hook already has a foreign entry:\\n${existingStr}\\n` +\n        `Remove it manually from ${settingsPath} if you want almanac to manage the hook.\\n`,\n      exitCode: 1,\n    };\n  }\n\n  if (ourEntries.length > 0 && stale.length === 0) {\n    return {\n      stdout: `almanac: SessionEnd hook already installed at ${script.path}\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  // Compose the new SessionEnd array: keep our one entry (fresh), drop any\n  // stale almanac entries.\n  const newEntries: SessionEndEntry[] = [\n    {\n      type: \"command\",\n      command: script.path,\n      timeout: HOOK_TIMEOUT_SECONDS,\n    },\n  ];\n\n  settings.hooks = { ...(settings.hooks ?? {}), SessionEnd: newEntries };\n  await writeSettings(settingsPath, settings);\n\n  return {\n    stdout:\n      `almanac: SessionEnd hook installed\\n` +\n      `  script: ${script.path}\\n` +\n      `  settings: ${settingsPath}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\nexport async function runHookUninstall(\n  options: HookCommandOptions = {},\n): Promise<HookCommandResult> {\n  const settingsPath = resolveSettingsPath(options);\n\n  if (!existsSync(settingsPath)) {\n    return {\n      stdout: `almanac: SessionEnd hook not installed (no settings file)\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  const settings = await readSettings(settingsPath);\n  const existing = (settings.hooks?.SessionEnd ?? []).slice();\n\n  // Remove ONLY our entries — anything else stays. We treat any entry with\n  // a command ending in `almanac-capture.sh` as ours (handles the case\n  // where the bundled path moved between `npm i` locations).\n  const kept = existing.filter((e) => !e.command.endsWith(\"almanac-capture.sh\"));\n  const removed = existing.length - kept.length;\n\n  if (removed === 0) {\n    return {\n      stdout: `almanac: SessionEnd hook not installed\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  if (settings.hooks !== undefined) {\n    if (kept.length === 0) {\n      // Empty SessionEnd array confuses some linters; drop the key when\n      // nothing's left.\n      const { SessionEnd: _dropped, ...rest } = settings.hooks;\n      void _dropped;\n      settings.hooks = rest;\n    } else {\n      settings.hooks = { ...settings.hooks, SessionEnd: kept };\n    }\n\n    // If `hooks` itself is now empty (user had only our SessionEnd entry\n    // and no other hook categories), drop the `hooks` key entirely so\n    // uninstall leaves the settings file in the same shape it would be\n    // in had we never run install. An empty `\"hooks\": {}` is an obvious\n    // breadcrumb in commit diffs.\n    if (Object.keys(settings.hooks).length === 0) {\n      delete settings.hooks;\n    }\n  }\n\n  await writeSettings(settingsPath, settings);\n\n  return {\n    stdout: `almanac: SessionEnd hook removed\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\nexport async function runHookStatus(\n  options: HookCommandOptions = {},\n): Promise<HookCommandResult> {\n  const script = resolveHookScriptPath(options);\n  const settingsPath = resolveSettingsPath(options);\n\n  if (!existsSync(settingsPath)) {\n    return {\n      stdout:\n        `SessionEnd hook: not installed\\n` +\n        `settings: ${settingsPath} (does not exist)\\n` +\n        (script.ok ? `script would be: ${script.path}\\n` : \"\"),\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  const settings = await readSettings(settingsPath);\n  const existing = settings.hooks?.SessionEnd ?? [];\n  const ours = existing.find((e) => e.command.endsWith(\"almanac-capture.sh\"));\n\n  if (ours === undefined) {\n    const foreign = existing\n      .map((e) => `  - ${e.command}`)\n      .join(\"\\n\");\n    return {\n      stdout:\n        `SessionEnd hook: not installed\\n` +\n        `settings: ${settingsPath}\\n` +\n        (existing.length > 0\n          ? `(${existing.length} foreign entr${existing.length === 1 ? \"y\" : \"ies\"} present:\\n${foreign})\\n`\n          : \"\") +\n        (script.ok ? `script would be: ${script.path}\\n` : \"\"),\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  return {\n    stdout:\n      `SessionEnd hook: installed\\n` +\n      `script: ${ours.command}\\n` +\n      `settings: ${settingsPath}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\n// ─── Helpers ─────────────────────────────────────────────────────────────\n\nfunction resolveSettingsPath(options: HookCommandOptions): string {\n  if (options.settingsPath !== undefined) return options.settingsPath;\n  return path.join(homedir(), \".claude\", \"settings.json\");\n}\n\ntype ScriptResolution =\n  | { ok: true; path: string }\n  | { ok: false; error: string };\n\n/**\n * Locate the bundled `hooks/almanac-capture.sh`. Mirrors\n * `resolvePromptsDir` from `src/agent/prompts.ts`: two plausible layouts\n * (installed dist vs. source dev), probe each.\n */\nfunction resolveHookScriptPath(options: HookCommandOptions): ScriptResolution {\n  if (options.hookScriptPath !== undefined) {\n    return { ok: true, path: options.hookScriptPath };\n  }\n\n  const here = path.dirname(fileURLToPath(import.meta.url));\n\n  const candidates = [\n    // Bundled: `.../codealmanac/dist/codealmanac.js` → `../hooks/…`\n    path.resolve(here, \"..\", \"hooks\", \"almanac-capture.sh\"),\n    // Source: `.../codealmanac/src/commands/hook.ts` → `../../hooks/…`\n    path.resolve(here, \"..\", \"..\", \"hooks\", \"almanac-capture.sh\"),\n    // Defensive nested fallback.\n    path.resolve(here, \"..\", \"..\", \"..\", \"hooks\", \"almanac-capture.sh\"),\n  ];\n\n  for (const candidate of candidates) {\n    if (existsSync(candidate)) {\n      return { ok: true, path: candidate };\n    }\n  }\n\n  return {\n    ok: false,\n    error:\n      `could not locate hooks/almanac-capture.sh. Tried:\\n` +\n      candidates.map((c) => `  - ${c}`).join(\"\\n\"),\n  };\n}\n\nasync function readSettings(settingsPath: string): Promise<SettingsJson> {\n  if (!existsSync(settingsPath)) return {};\n  try {\n    const raw = await readFile(settingsPath, \"utf8\");\n    if (raw.trim().length === 0) return {};\n    const parsed = JSON.parse(raw) as unknown;\n    if (parsed === null || typeof parsed !== \"object\") return {};\n    return parsed as SettingsJson;\n  } catch (err: unknown) {\n    const msg = err instanceof Error ? err.message : String(err);\n    throw new Error(`failed to read ${settingsPath}: ${msg}`);\n  }\n}\n\nasync function writeSettings(\n  settingsPath: string,\n  settings: SettingsJson,\n): Promise<void> {\n  const dir = path.dirname(settingsPath);\n  await mkdir(dir, { recursive: true });\n\n  // Atomic write: JSON.stringify → tmp file → rename. `rename` within the\n  // same filesystem is atomic on POSIX; Claude Code never sees a partial\n  // file. Formatted with 2-space indent to match the existing settings.\n  const tmp = `${settingsPath}.almanac-tmp-${process.pid}`;\n  const body = `${JSON.stringify(settings, null, 2)}\\n`;\n  await writeFile(tmp, body, \"utf8\");\n  await rename(tmp, settingsPath);\n}\n","import { existsSync } from \"node:fs\";\nimport { readFile } from \"node:fs/promises\";\nimport { basename, join } from \"node:path\";\n\nimport fg from \"fast-glob\";\nimport type Database from \"better-sqlite3\";\n\nimport { parseDuration } from \"../indexer/duration.js\";\nimport { ensureFreshIndex } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\nimport { findEntry } from \"../registry/index.js\";\nimport { toKebabCase } from \"../slug.js\";\nimport { subtreeInDb } from \"../topics/dag.js\";\n\n/**\n * `almanac health` — flag problems in the wiki.\n *\n * Eight independent categories, each checked against the current index\n * and filesystem. Categories never throw each other off; one failing\n * is not a reason to skip the others.\n *\n * Scoping:\n *   - `--topic <slug>` narrows every page-scoped category to pages\n *     tagged with that topic OR any descendant topic (DAG traversal).\n *     Topic-level categories (`empty_topics`) are narrowed to the\n *     subtree itself.\n *   - `--stdin` reads page slugs from stdin and limits page-scoped\n *     categories to that set.\n *\n * Output:\n *   - default: human-readable, grouped by category with counts.\n *   - `--json`: one big object, shape = `HealthReport`.\n */\n\nexport interface HealthReport {\n  orphans: { slug: string }[];\n  stale: { slug: string; days_since_update: number }[];\n  dead_refs: { slug: string; path: string }[];\n  broken_links: { source_slug: string; target_slug: string }[];\n  broken_xwiki: { source_slug: string; target_wiki: string; target_slug: string }[];\n  empty_topics: { slug: string }[];\n  empty_pages: { slug: string }[];\n  slug_collisions: { slug: string; paths: string[] }[];\n}\n\nexport interface HealthOptions {\n  cwd: string;\n  wiki?: string;\n  topic?: string;\n  stale?: string;\n  stdin?: boolean;\n  stdinInput?: string;\n  json?: boolean;\n}\n\nexport interface HealthCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * Default `--stale` window. 90 days matches the spec. Users can tune\n * with `--stale <duration>` using the shared parser.\n */\nconst DEFAULT_STALE_SECONDS = 90 * 24 * 60 * 60;\n\nexport async function runHealth(\n  options: HealthOptions,\n): Promise<HealthCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  await ensureFreshIndex({ repoRoot });\n\n  const almanacDir = join(repoRoot, \".almanac\");\n  const pagesDir = join(almanacDir, \"pages\");\n  const db = openIndex(join(almanacDir, \"index.db\"));\n\n  try {\n    const staleSeconds = options.stale !== undefined\n      ? parseDuration(options.stale)\n      : DEFAULT_STALE_SECONDS;\n\n    const scope = resolveScope(db, options);\n\n    const report: HealthReport = {\n      orphans: findOrphans(db, scope),\n      stale: findStale(db, scope, staleSeconds),\n      dead_refs: await findDeadRefs(db, scope, repoRoot),\n      broken_links: findBrokenLinks(db, scope),\n      broken_xwiki: await findBrokenXwiki(db, scope),\n      empty_topics: findEmptyTopics(db, scope),\n      empty_pages: await findEmptyPages(db, scope, pagesDir),\n      slug_collisions: await findSlugCollisions(pagesDir),\n    };\n\n    if (options.json === true) {\n      return {\n        stdout: `${JSON.stringify(report, null, 2)}\\n`,\n        stderr: \"\",\n        exitCode: 0,\n      };\n    }\n\n    return {\n      stdout: formatReport(report),\n      stderr: \"\",\n      exitCode: 0,\n    };\n  } finally {\n    db.close();\n  }\n}\n\ninterface HealthScope {\n  /** When non-null, restrict page-scoped checks to these slugs. */\n  pages: Set<string> | null;\n  /** When non-null, restrict topic-scoped checks to these slugs. */\n  topics: Set<string> | null;\n}\n\n/**\n * Compute the active page/topic scope from `--topic` and `--stdin`\n * flags. Both null = no restriction (report everything).\n */\nfunction resolveScope(db: Database.Database, options: HealthOptions): HealthScope {\n  let pages: Set<string> | null = null;\n  let topics: Set<string> | null = null;\n\n  if (options.topic !== undefined) {\n    const rootSlug = toKebabCase(options.topic);\n    if (rootSlug.length > 0) {\n      const subtree = subtreeInDb(db, rootSlug);\n      topics = new Set(subtree);\n      const placeholders = subtree.map(() => \"?\").join(\", \");\n      const rows = db\n        .prepare<unknown[], { page_slug: string }>(\n          `SELECT DISTINCT page_slug FROM page_topics\n           WHERE topic_slug IN (${placeholders})`,\n        )\n        .all(...subtree);\n      pages = new Set(rows.map((r) => r.page_slug));\n    }\n  }\n\n  if (options.stdin === true && options.stdinInput !== undefined) {\n    const stdinPages = new Set<string>();\n    for (const line of options.stdinInput.split(/\\r?\\n/)) {\n      const s = line.trim();\n      if (s.length > 0) stdinPages.add(s);\n    }\n    // Intersect with any existing topic-scoped set.\n    if (pages === null) pages = stdinPages;\n    else {\n      const out = new Set<string>();\n      for (const s of stdinPages) if (pages.has(s)) out.add(s);\n      pages = out;\n    }\n  }\n\n  return { pages, topics };\n}\n\nfunction inPageScope(scope: HealthScope, slug: string): boolean {\n  if (scope.pages === null) return true;\n  return scope.pages.has(slug);\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// individual checks\n// ─────────────────────────────────────────────────────────────────────\n\n/**\n * Pages with zero `topics:`. Archived pages are exempt — the spec\n * excludes them from search by default and they're inherently\n * \"retired\", not \"abandoned\".\n */\nfunction findOrphans(\n  db: Database.Database,\n  scope: HealthScope,\n): { slug: string }[] {\n  const rows = db\n    .prepare<[], { slug: string }>(\n      `SELECT p.slug FROM pages p\n       WHERE p.archived_at IS NULL\n         AND NOT EXISTS (\n           SELECT 1 FROM page_topics pt WHERE pt.page_slug = p.slug\n         )\n       ORDER BY p.slug`,\n    )\n    .all();\n  return rows.filter((r) => inPageScope(scope, r.slug));\n}\n\n/**\n * Active pages whose `updated_at` is older than `staleSeconds`. We\n * report `days_since_update` rather than a raw timestamp because the\n * spec's example output (\"old-architecture (124 days)\") shows that.\n */\nfunction findStale(\n  db: Database.Database,\n  scope: HealthScope,\n  staleSeconds: number,\n): { slug: string; days_since_update: number }[] {\n  const now = Math.floor(Date.now() / 1000);\n  const threshold = now - staleSeconds;\n  const rows = db\n    .prepare<[number], { slug: string; updated_at: number }>(\n      `SELECT slug, updated_at FROM pages\n       WHERE archived_at IS NULL AND updated_at < ?\n       ORDER BY updated_at ASC`,\n    )\n    .all(threshold);\n  return rows\n    .filter((r) => inPageScope(scope, r.slug))\n    .map((r) => ({\n      slug: r.slug,\n      days_since_update: Math.floor((now - r.updated_at) / (60 * 60 * 24)),\n    }));\n}\n\n/**\n * `file_refs` whose target paths no longer exist on disk. We `stat`\n * each referenced path, relative to the repo root, and report misses.\n *\n * Only checks active pages — archived pages are allowed to reference\n * files that have since been deleted (that's often why they were\n * archived in the first place).\n *\n * We stat the `original_path` (author's casing) rather than the\n * lowercased `path` — on case-sensitive filesystems like Linux, stat\n * of a lowercased alias of `src/Dockerfile` returns ENOENT even\n * though the file exists. macOS and Windows are case-insensitive so\n * either form resolves there; using the original consistently means\n * the code behaves identically on every host.\n */\nasync function findDeadRefs(\n  db: Database.Database,\n  scope: HealthScope,\n  repoRoot: string,\n): Promise<{ slug: string; path: string }[]> {\n  const rows = db\n    .prepare<\n      [],\n      { slug: string; path: string; original_path: string; is_dir: number }\n    >(\n      `SELECT p.slug, r.path, r.original_path, r.is_dir\n       FROM file_refs r\n       JOIN pages p ON p.slug = r.page_slug\n       WHERE p.archived_at IS NULL\n       ORDER BY p.slug, r.path`,\n    )\n    .all();\n  const out: { slug: string; path: string }[] = [];\n  for (const r of rows) {\n    if (!inPageScope(scope, r.slug)) continue;\n    const abs = join(repoRoot, r.original_path);\n    if (!existsSync(abs)) {\n      // Surface the author's casing in the report — matches what's in\n      // the user's frontmatter/wikilink, which is what they'll search\n      // for when fixing the miss.\n      out.push({ slug: r.slug, path: r.original_path });\n    }\n  }\n  return out;\n}\n\n/**\n * Wikilinks whose target slug has no row in `pages`. Every other\n * page-scoped check filters archived source pages out; this one and\n * `findBrokenXwiki` follow the same rule so the report doesn't flag\n * broken links from pages that have been retired.\n */\nfunction findBrokenLinks(\n  db: Database.Database,\n  scope: HealthScope,\n): { source_slug: string; target_slug: string }[] {\n  const rows = db\n    .prepare<[], { source_slug: string; target_slug: string }>(\n      `SELECT w.source_slug, w.target_slug\n       FROM wikilinks w\n       JOIN pages src ON src.slug = w.source_slug\n       LEFT JOIN pages tgt ON tgt.slug = w.target_slug\n       WHERE tgt.slug IS NULL AND src.archived_at IS NULL\n       ORDER BY w.source_slug, w.target_slug`,\n    )\n    .all();\n  return rows.filter((r) => inPageScope(scope, r.source_slug));\n}\n\n/**\n * Cross-wiki links whose target wiki isn't registered OR whose path\n * is unreachable. Per the plan we stop at \"wiki unregistered or path\n * missing\" — walking into the other wiki's `index.db` to check the\n * slug exists is explicitly out of scope for slice 3 (documented in\n * the plan). A follow-up slice can deepen this.\n */\nasync function findBrokenXwiki(\n  db: Database.Database,\n  scope: HealthScope,\n): Promise<{ source_slug: string; target_wiki: string; target_slug: string }[]> {\n  const rows = db\n    .prepare<\n      [],\n      { source_slug: string; target_wiki: string; target_slug: string }\n    >(\n      // Same archived-source filter as `findBrokenLinks`. Retired pages\n      // shouldn't spam the report with links to wikis that may have\n      // been intentionally retired too.\n      `SELECT x.source_slug, x.target_wiki, x.target_slug\n       FROM cross_wiki_links x\n       JOIN pages src ON src.slug = x.source_slug\n       WHERE src.archived_at IS NULL\n       ORDER BY x.source_slug, x.target_wiki, x.target_slug`,\n    )\n    .all();\n  const out: { source_slug: string; target_wiki: string; target_slug: string }[] = [];\n  // Cache the registry lookup so we only resolve each wiki once.\n  const reachableCache = new Map<string, boolean>();\n  for (const r of rows) {\n    if (!inPageScope(scope, r.source_slug)) continue;\n    let ok = reachableCache.get(r.target_wiki);\n    if (ok === undefined) {\n      const entry = await findEntry({ name: r.target_wiki });\n      ok = entry !== null && existsSync(join(entry.path, \".almanac\"));\n      reachableCache.set(r.target_wiki, ok);\n    }\n    if (!ok) {\n      out.push({\n        source_slug: r.source_slug,\n        target_wiki: r.target_wiki,\n        target_slug: r.target_slug,\n      });\n    }\n  }\n  return out;\n}\n\n/** Topics with zero pages. */\nfunction findEmptyTopics(\n  db: Database.Database,\n  scope: HealthScope,\n): { slug: string }[] {\n  const rows = db\n    .prepare<[], { slug: string }>(\n      `SELECT t.slug FROM topics t\n       WHERE NOT EXISTS (\n         SELECT 1 FROM page_topics pt WHERE pt.topic_slug = t.slug\n       )\n       ORDER BY t.slug`,\n    )\n    .all();\n  if (scope.topics === null) return rows;\n  return rows.filter((r) => scope.topics!.has(r.slug));\n}\n\n/**\n * Pages whose body is effectively empty — only frontmatter, maybe a\n * heading, no prose. \"Empty\" = after dropping frontmatter and heading\n * lines, the remaining non-blank non-whitespace content is < 40\n * characters. This matches the test from the plan: \"a page with only\n * frontmatter + heading is empty; with a paragraph it's not.\"\n *\n * Archived pages are exempt — deliberately minimal archive stubs\n * shouldn't be flagged.\n */\nasync function findEmptyPages(\n  db: Database.Database,\n  scope: HealthScope,\n  pagesDir: string,\n): Promise<{ slug: string }[]> {\n  const rows = db\n    .prepare<[], { slug: string; file_path: string }>(\n      `SELECT slug, file_path FROM pages\n       WHERE archived_at IS NULL\n       ORDER BY slug`,\n    )\n    .all();\n  const out: { slug: string }[] = [];\n  for (const r of rows) {\n    if (!inPageScope(scope, r.slug)) continue;\n    let raw: string;\n    try {\n      raw = await readFile(r.file_path, \"utf8\");\n    } catch {\n      continue;\n    }\n    // Strip frontmatter if present.\n    const m = raw.match(/^---\\r?\\n[\\s\\S]*?\\r?\\n---\\r?\\n?([\\s\\S]*)$/);\n    const body = m !== null ? (m[1] ?? \"\") : raw;\n    // \"Empty\" = after dropping frontmatter, heading lines, and blank\n    // lines, nothing non-trivial remains. A single-line wikilink or\n    // one-sentence paragraph counts as content; a page with only a\n    // heading (or a heading + whitespace) does not.\n    //\n    // `pagesDir` is accepted for parity with future content-resolution\n    // checks (e.g., resolving includes); referenced so lint doesn't\n    // complain about an unused parameter.\n    void pagesDir;\n    const hasSubstance = body\n      .split(/\\r?\\n/)\n      .some((l) => {\n        const t = l.trim();\n        if (t.length === 0) return false;\n        if (t.startsWith(\"#\")) return false;\n        return true;\n      });\n    if (!hasSubstance) {\n      out.push({ slug: r.slug });\n    }\n  }\n  return out;\n}\n\n/**\n * Walk `.almanac/pages/` and group filenames by their kebab-cased\n * slug. Any slug with >1 filename is a collision. We rescan rather\n * than reading a persisted table — indexing surfaces collisions only\n * as warnings, so a dedicated rescan gives us a definitive answer\n * without adding a new table.\n */\nasync function findSlugCollisions(\n  pagesDir: string,\n): Promise<{ slug: string; paths: string[] }[]> {\n  if (!existsSync(pagesDir)) return [];\n  const files = await fg(\"**/*.md\", {\n    cwd: pagesDir,\n    absolute: false,\n    onlyFiles: true,\n    caseSensitiveMatch: true,\n  });\n  const bySlug = new Map<string, string[]>();\n  for (const rel of files) {\n    const slug = toKebabCase(basename(rel, \".md\"));\n    if (slug.length === 0) continue;\n    const list = bySlug.get(slug) ?? [];\n    list.push(rel);\n    bySlug.set(slug, list);\n  }\n  const out: { slug: string; paths: string[] }[] = [];\n  for (const [slug, paths] of bySlug.entries()) {\n    if (paths.length > 1) {\n      out.push({ slug, paths: paths.sort() });\n    }\n  }\n  out.sort((a, b) => a.slug.localeCompare(b.slug));\n  return out;\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// pretty-print\n// ─────────────────────────────────────────────────────────────────────\n\nfunction formatReport(r: HealthReport): string {\n  const sections: string[] = [];\n  sections.push(\n    section(\n      \"orphans\",\n      r.orphans.length,\n      r.orphans.map((o) => `  ${o.slug}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"stale\",\n      r.stale.length,\n      r.stale.map((s) => `  ${s.slug}     (${s.days_since_update} days)`),\n    ),\n  );\n  sections.push(\n    section(\n      \"dead-refs\",\n      r.dead_refs.length,\n      r.dead_refs.map((d) => `  ${d.slug}  references ${d.path} (missing)`),\n    ),\n  );\n  sections.push(\n    section(\n      \"broken-links\",\n      r.broken_links.length,\n      r.broken_links.map(\n        (b) => `  ${b.source_slug} → ${b.target_slug} (target does not exist)`,\n      ),\n    ),\n  );\n  sections.push(\n    section(\n      \"broken-xwiki\",\n      r.broken_xwiki.length,\n      r.broken_xwiki.map(\n        (b) =>\n          `  ${b.source_slug} → ${b.target_wiki}:${b.target_slug} (wiki unregistered or unreachable)`,\n      ),\n    ),\n  );\n  sections.push(\n    section(\n      \"empty-topics\",\n      r.empty_topics.length,\n      r.empty_topics.map((e) => `  ${e.slug}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"empty-pages\",\n      r.empty_pages.length,\n      r.empty_pages.map((e) => `  ${e.slug}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"slug-collisions\",\n      r.slug_collisions.length,\n      r.slug_collisions.map((c) => `  ${c.slug}: ${c.paths.join(\", \")}`),\n    ),\n  );\n  return `${sections.join(\"\\n\\n\")}\\n`;\n}\n\nfunction section(label: string, count: number, lines: string[]): string {\n  if (count === 0) return `${label} (0): (ok)`;\n  return `${label} (${count}):\\n${lines.join(\"\\n\")}`;\n}\n","/**\n * Parse a compact duration string of the form `<N><unit>` into seconds.\n *\n * Accepted units (from the spec, `--since` / `--stale`):\n *   - `m` — minutes\n *   - `h` — hours\n *   - `d` — days\n *   - `w` — weeks\n *\n * Examples: `2w` → 1209600, `30d` → 2592000, `12h` → 43200.\n *\n * Anything else throws — the CLI surfaces the error with the usual\n * `almanac: <message>` prefix, which is clearer than silently treating\n * `2weeks` or `30 days` as zero.\n */\nexport function parseDuration(input: string): number {\n  const trimmed = input.trim();\n  const m = trimmed.match(/^(\\d+)([mhdw])$/);\n  if (m === null) {\n    throw new Error(\n      `invalid duration \"${input}\" (expected Nw, Nd, Nh, or Nm — e.g. 2w, 30d)`,\n    );\n  }\n  const n = Number.parseInt(m[1] ?? \"0\", 10);\n  const unit = m[2];\n  switch (unit) {\n    case \"m\":\n      return n * 60;\n    case \"h\":\n      return n * 60 * 60;\n    case \"d\":\n      return n * 60 * 60 * 24;\n    case \"w\":\n      return n * 60 * 60 * 24 * 7;\n    default:\n      // Unreachable — regex pins the unit — but satisfies exhaustiveness.\n      throw new Error(`invalid duration unit \"${unit ?? \"\"}\"`);\n  }\n}\n","import { createHash } from \"node:crypto\";\nimport { existsSync, statSync } from \"node:fs\";\nimport { readFile, utimes } from \"node:fs/promises\";\nimport { basename, join, relative } from \"node:path\";\n\nimport fg from \"fast-glob\";\nimport type Database from \"better-sqlite3\";\n\nimport { toKebabCase } from \"../slug.js\";\nimport { loadTopicsFile, titleCase } from \"../topics/yaml.js\";\nimport { firstH1, parseFrontmatter } from \"./frontmatter.js\";\nimport {\n  normalizePath,\n  normalizePathPreservingCase,\n  looksLikeDir,\n} from \"./paths.js\";\nimport { openIndex } from \"./schema.js\";\nimport { extractWikilinks } from \"./wikilinks.js\";\n\n/**\n * Filename relative to the `.almanac/` dir where the topic DAG + metadata\n * lives. The indexer loads it on every reindex; the topics commands\n * mutate it atomically. Keep this in sync with `src/topics/paths.ts`'s\n * `topicsYamlPath` — duplicated here only so the indexer doesn't import\n * a second \"where is it\" helper.\n */\nconst TOPICS_YAML_FILENAME = \"topics.yaml\";\n\nexport interface IndexContext {\n  /** Absolute path to the repo root (the dir containing `.almanac/`). */\n  repoRoot: string;\n}\n\nexport interface IndexResult {\n  /** Pages parsed or re-parsed during this run. Zero when the DB was already up to date. */\n  changed: number;\n  /** Pages present in the DB before this run but missing from disk. */\n  removed: number;\n  /**\n   * Pages on disk at the end of this run — i.e. files that made it all the\n   * way through to the index. Skipped files (slug collisions, unreadable,\n   * un-sluggable filenames) are NOT counted here. Use `filesSeen` for the\n   * raw count of `.md` files encountered on disk.\n   *\n   * Alias retained for backwards-compat with existing tests/consumers; new\n   * code should prefer `pagesIndexed` for clarity.\n   */\n  total: number;\n  /** Pages that made it into the index. Same number as `total`. */\n  pagesIndexed: number;\n  /**\n   * Count of `.md` files found under `pages/` before any filtering. Always\n   * `>= pagesIndexed`; the difference is `filesSkipped`.\n   */\n  filesSeen: number;\n  /**\n   * Files dropped before making it into the index — slug collisions,\n   * un-sluggable filenames, or filesystem races (deleted/unreadable mid-run).\n   * Covered by stderr warnings when non-zero.\n   */\n  filesSkipped: number;\n}\n\n// Glob is relative to `pagesDir` (which is `.almanac/pages/`), so this is\n// just \"every .md at any depth\" — not `pages/**/*.md`, because we've\n// already `cd`'d into `pages/` logically.\nconst PAGES_GLOB = \"**/*.md\";\n\n/**\n * The \"front door\" for query commands. Runs the indexer only if the DB is\n * missing or at least one page is newer than it. Meant to be cheap — the\n * common case is \"nothing changed, mtime check returns fast, we're done\".\n *\n * The spec is explicit: \"Reindex is implicit and invisible. If the user\n * didn't didn't explicitly run `reindex`, they shouldn't see reindex\n * output. Silent by default.\" So this function never writes to stdout;\n * warnings (slug collisions, bad frontmatter) still go to stderr.\n */\nexport async function ensureFreshIndex(ctx: IndexContext): Promise<IndexResult> {\n  const almanacDir = join(ctx.repoRoot, \".almanac\");\n  const dbPath = join(almanacDir, \"index.db\");\n  const pagesDir = join(almanacDir, \"pages\");\n\n  if (!existsSync(pagesDir)) {\n    // No pages dir = nothing to index. Open/create the DB so downstream\n    // queries can run against an empty schema rather than crashing on a\n    // missing file.\n    const db = openIndex(dbPath);\n    db.close();\n    return emptyResult();\n  }\n\n  if (\n    !existsSync(dbPath) ||\n    pagesNewerThan(pagesDir, dbPath) ||\n    topicsYamlNewerThan(almanacDir, dbPath)\n  ) {\n    return runIndexer(ctx);\n  }\n  return emptyResult();\n}\n\nfunction emptyResult(): IndexResult {\n  return {\n    changed: 0,\n    removed: 0,\n    total: 0,\n    pagesIndexed: 0,\n    filesSeen: 0,\n    filesSkipped: 0,\n  };\n}\n\n/**\n * Force a full reindex. Identical to `ensureFreshIndex` except it runs\n * the indexer unconditionally. Exposed for `almanac reindex`.\n */\nexport async function runIndexer(ctx: IndexContext): Promise<IndexResult> {\n  const almanacDir = join(ctx.repoRoot, \".almanac\");\n  const dbPath = join(almanacDir, \"index.db\");\n  const pagesDir = join(almanacDir, \"pages\");\n\n  const db = openIndex(dbPath);\n  let result: IndexResult;\n  try {\n    result = await indexPagesInto(db, pagesDir);\n    // After pages are indexed, reconcile the topics table against\n    // `.almanac/topics.yaml` (if present). `indexPagesInto` has already\n    // lazily inserted rows for every topic slug mentioned in page\n    // frontmatter with a title-cased title; `applyTopicsYaml` now\n    // promotes the declared title/description and rewrites parent edges\n    // for those topics that live in the file.\n    await applyTopicsYaml(db, join(almanacDir, TOPICS_YAML_FILENAME));\n  } finally {\n    db.close();\n  }\n\n  // Bump the DB mtime to \"now\" after a successful reindex (even a no-op\n  // one). Otherwise, a page file with a future mtime (clock skew,\n  // `git checkout` preserving source mtimes) would trigger `ensureFreshIndex`\n  // on every query: the freshness check sees `page.mtime > db.mtime`,\n  // reindex runs, finds no content-hash changes, and the DB mtime stays\n  // stale — locking us into a reindex-on-every-query loop. Touching the\n  // DB mtime makes the comparison monotonic.\n  try {\n    const now = new Date();\n    await utimes(dbPath, now, now);\n  } catch {\n    // Touching mtime is a freshness optimization; failures here are\n    // non-fatal and the reindex result is still correct.\n  }\n  return result;\n}\n\ninterface ExistingRow {\n  slug: string;\n  content_hash: string;\n  file_path: string;\n}\n\nasync function indexPagesInto(\n  db: Database.Database,\n  pagesDir: string,\n): Promise<IndexResult> {\n  const files = await fg(PAGES_GLOB, {\n    cwd: pagesDir,\n    absolute: false,\n    onlyFiles: true,\n    caseSensitiveMatch: true,\n  });\n\n  // Load the current state of the index into memory so we can diff against\n  // what's on disk. This is cheap even at 10k pages (one INTEGER + two\n  // short strings per row).\n  const existingRows = db\n    .prepare<[], ExistingRow>(\"SELECT slug, content_hash, file_path FROM pages\")\n    .all();\n  const existingBySlug = new Map<string, ExistingRow>();\n  for (const row of existingRows) existingBySlug.set(row.slug, row);\n\n  // First pass: decide what to do with each file on disk. We record the\n  // intent here so the transaction below can run synchronously — mixing\n  // async file reads into a better-sqlite3 transaction doesn't work\n  // (transactions are sync).\n  const planned: Array<{\n    slug: string;\n    title: string;\n    filePath: string;\n    fullPath: string;\n    contentHash: string;\n    updatedAt: number;\n    archivedAt: number | null;\n    supersededBy: string | null;\n    topics: string[];\n    frontmatterFiles: string[];\n    wikilinks: ReturnType<typeof extractWikilinks>;\n    content: string;\n  }> = [];\n  const seenSlugs = new Set<string>();\n  let filesSkipped = 0;\n\n  for (const rel of files) {\n    const fullPath = join(pagesDir, rel);\n    const base = basename(rel, \".md\");\n    const slug = toKebabCase(base);\n    if (slug.length === 0) {\n      process.stderr.write(\n        `almanac: skipping \"${rel}\" — filename has no slug-able characters\\n`,\n      );\n      filesSkipped++;\n      continue;\n    }\n    if (slug !== base) {\n      // Filename isn't already canonical kebab-case. Warn, but still\n      // index under the canonical slug. `almanac health` (slice 3) will\n      // surface these as a proper report.\n      process.stderr.write(\n        `almanac: warning — \"${rel}\" is not canonical; indexed as slug \"${slug}\"\\n`,\n      );\n    }\n    if (seenSlugs.has(slug)) {\n      // Two files slugify to the same slug. Keep the first, skip the\n      // rest — health will flag this properly in slice 3.\n      process.stderr.write(\n        `almanac: warning — slug \"${slug}\" collides with an earlier file; skipping \"${rel}\"\\n`,\n      );\n      filesSkipped++;\n      continue;\n    }\n\n    // `fast-glob` gave us the list in one shot, but by the time we stat\n    // and read each file it can have been deleted, renamed, or swapped\n    // (editors that save via rename-swap expose this briefly). A single\n    // such race shouldn't tank the whole reindex — matches the malformed-\n    // YAML behavior (\"one bad file doesn't stop the others\"). We narrow\n    // to ENOENT/EACCES so genuine I/O failures (EIO, EMFILE, etc.) still\n    // surface.\n    let st: ReturnType<typeof statSync>;\n    let raw: string;\n    try {\n      st = statSync(fullPath);\n      raw = await readFile(fullPath, \"utf8\");\n    } catch (err: unknown) {\n      if (\n        err instanceof Error &&\n        \"code\" in err &&\n        (err.code === \"ENOENT\" || err.code === \"EACCES\")\n      ) {\n        process.stderr.write(\n          `almanac: skipping \"${rel}\" — ${err.message}\\n`,\n        );\n        filesSkipped++;\n        continue;\n      }\n      throw err;\n    }\n\n    seenSlugs.add(slug);\n    const updatedAt = Math.floor(st.mtimeMs / 1000);\n\n    // Content-hash skip: if the hash matches what's in the DB and the\n    // file path hasn't moved, we can leave this page's rows alone. This\n    // is the fast-path for \"user ran a query; one page was touched\".\n    const contentHash = hashContent(raw);\n    const existing = existingBySlug.get(slug);\n    if (\n      existing !== undefined &&\n      existing.content_hash === contentHash &&\n      existing.file_path === fullPath\n    ) {\n      continue;\n    }\n\n    const fm = parseFrontmatter(raw);\n    const title = fm.title ?? firstH1(fm.body) ?? base;\n    const links = extractWikilinks(fm.body);\n\n    planned.push({\n      slug,\n      title,\n      filePath: rel,\n      fullPath,\n      contentHash,\n      updatedAt,\n      archivedAt: fm.archived_at,\n      supersededBy: fm.superseded_by,\n      topics: fm.topics,\n      frontmatterFiles: fm.files,\n      wikilinks: links,\n      content: fm.body,\n    });\n  }\n\n  // Compute deletions: anything in the DB whose slug isn't on disk\n  // anymore (or whose file slugifies to a different slug now).\n  const toDelete: string[] = [];\n  for (const slug of existingBySlug.keys()) {\n    if (!seenSlugs.has(slug)) toDelete.push(slug);\n  }\n\n  const deleteByPage = db.prepare<[string]>(\"DELETE FROM pages WHERE slug = ?\");\n  const deleteFtsByPage = db.prepare<[string]>(\n    \"DELETE FROM fts_pages WHERE slug = ?\",\n  );\n\n  const replacePage = db.prepare<\n    [string, string, string, string, number, number | null, string | null]\n  >(\n    `INSERT INTO pages (slug, title, file_path, content_hash, updated_at, archived_at, superseded_by)\n     VALUES (?, ?, ?, ?, ?, ?, ?)\n     ON CONFLICT(slug) DO UPDATE SET\n       title         = excluded.title,\n       file_path     = excluded.file_path,\n       content_hash  = excluded.content_hash,\n       updated_at    = excluded.updated_at,\n       archived_at   = excluded.archived_at,\n       superseded_by = excluded.superseded_by`,\n  );\n\n  const deletePageTopics = db.prepare<[string]>(\n    \"DELETE FROM page_topics WHERE page_slug = ?\",\n  );\n  const insertPageTopic = db.prepare<[string, string]>(\n    \"INSERT OR IGNORE INTO page_topics (page_slug, topic_slug) VALUES (?, ?)\",\n  );\n  // Seed ad-hoc topics with a title-cased default. If the topic is\n  // later declared in `.almanac/topics.yaml`, `applyTopicsYaml` will\n  // promote the title/description to whatever the file says. We set the\n  // title here (rather than leaving NULL) so `topics list` and\n  // `health --topic` have a display name even before a user writes to\n  // topics.yaml.\n  const insertTopic = db.prepare<[string, string]>(\n    \"INSERT OR IGNORE INTO topics (slug, title) VALUES (?, ?)\",\n  );\n\n  const deleteFileRefs = db.prepare<[string]>(\n    \"DELETE FROM file_refs WHERE page_slug = ?\",\n  );\n  const insertFileRef = db.prepare<[string, string, string, number]>(\n    \"INSERT OR IGNORE INTO file_refs (page_slug, path, original_path, is_dir) VALUES (?, ?, ?, ?)\",\n  );\n\n  const deleteWikilinks = db.prepare<[string]>(\n    \"DELETE FROM wikilinks WHERE source_slug = ?\",\n  );\n  const insertWikilink = db.prepare<[string, string]>(\n    \"INSERT OR IGNORE INTO wikilinks (source_slug, target_slug) VALUES (?, ?)\",\n  );\n\n  const deleteXwiki = db.prepare<[string]>(\n    \"DELETE FROM cross_wiki_links WHERE source_slug = ?\",\n  );\n  const insertXwiki = db.prepare<[string, string, string]>(\n    \"INSERT OR IGNORE INTO cross_wiki_links (source_slug, target_wiki, target_slug) VALUES (?, ?, ?)\",\n  );\n\n  const insertFts = db.prepare<[string, string, string]>(\n    \"INSERT INTO fts_pages (slug, title, content) VALUES (?, ?, ?)\",\n  );\n\n  const apply = db.transaction(() => {\n    for (const slug of toDelete) {\n      // `fts_pages` is an FTS5 virtual table — FK cascades do NOT propagate\n      // into it, so we must delete FTS rows explicitly before relying on\n      // `DELETE FROM pages` to cascade-clean the four real tables\n      // (page_topics, file_refs, wikilinks, cross_wiki_links). If this\n      // explicit delete ever gets removed, orphaned FTS rows will show up\n      // as phantom search hits pointing at non-existent slugs.\n      deleteFtsByPage.run(slug);\n      deleteByPage.run(slug); // CASCADE cleans page_topics, file_refs, wikilinks, cross_wiki_links\n    }\n\n    for (const p of planned) {\n      // page_topics/file_refs/wikilinks/cross_wiki_links all cascade on\n      // delete, so the cleanest \"replace\" story is: delete-then-insert\n      // the per-page rows under the same transaction. Doing it this way\n      // (rather than `ON CONFLICT DO UPDATE` per row) keeps the logic\n      // uniform and makes \"remove a topic from frontmatter\" work.\n      deletePageTopics.run(p.slug);\n      deleteFileRefs.run(p.slug);\n      deleteWikilinks.run(p.slug);\n      deleteXwiki.run(p.slug);\n      // Same virtual-table reason as the deletion branch above — FTS5\n      // rows do not cascade, so clean them by hand before reinserting.\n      deleteFtsByPage.run(p.slug);\n\n      replacePage.run(\n        p.slug,\n        p.title,\n        p.fullPath,\n        p.contentHash,\n        p.updatedAt,\n        p.archivedAt,\n        p.supersededBy,\n      );\n\n      for (const topic of p.topics) {\n        const topicSlug = toKebabCase(topic);\n        if (topicSlug.length === 0) continue;\n        insertTopic.run(topicSlug, titleCase(topicSlug));\n        insertPageTopic.run(p.slug, topicSlug);\n      }\n\n      // Frontmatter `files:` — normalize each entry, inferring directness\n      // from its trailing slash. Authors who write `src/payments` (no\n      // trailing slash) are asserting a file; this matches how `[[...]]`\n      // classifies the same string. We store both the lowercased form\n      // (for `--mentions` GLOB queries) and the casing-preserving form\n      // (for dead-ref `existsSync` on case-sensitive filesystems).\n      for (const raw of p.frontmatterFiles) {\n        const isDir = looksLikeDir(raw);\n        const path = normalizePath(raw, isDir);\n        const originalPath = normalizePathPreservingCase(raw, isDir);\n        if (path.length === 0) continue;\n        insertFileRef.run(p.slug, path, originalPath, isDir ? 1 : 0);\n      }\n\n      // Inline `[[...]]` extracted from body.\n      for (const ref of p.wikilinks) {\n        switch (ref.kind) {\n          case \"page\":\n            insertWikilink.run(p.slug, ref.target);\n            break;\n          case \"file\":\n            insertFileRef.run(p.slug, ref.path, ref.originalPath, 0);\n            break;\n          case \"folder\":\n            insertFileRef.run(p.slug, ref.path, ref.originalPath, 1);\n            break;\n          case \"xwiki\":\n            insertXwiki.run(p.slug, ref.wiki, ref.target);\n            break;\n        }\n      }\n\n      insertFts.run(p.slug, p.title, p.content);\n    }\n  });\n  apply();\n\n  // `relative` keeps lint happy about unused imports; total is just the\n  // count of .md files we saw on this pass.\n  void relative;\n  const pagesIndexed = seenSlugs.size;\n  return {\n    changed: planned.length,\n    removed: toDelete.length,\n    total: pagesIndexed,\n    pagesIndexed,\n    filesSeen: files.length,\n    filesSkipped,\n  };\n}\n\n/**\n * Return true if any `pages/**\\/*.md` has an mtime strictly greater than\n * the index DB's mtime. We walk with `fast-glob` rather than shell out to\n * `find` for portability.\n *\n * This is the \"should we reindex?\" check. It's intentionally cheap —\n * `fast-glob` with `stats: true` gives us mtimes without a second `stat`\n * round-trip.\n */\nfunction pagesNewerThan(pagesDir: string, dbPath: string): boolean {\n  let dbMtime: number;\n  try {\n    dbMtime = statSync(dbPath).mtimeMs;\n  } catch {\n    return true;\n  }\n\n  // Synchronous walk — `fg.sync` is fine at this scale and keeps the\n  // decision path simple (we don't need to await inside every CLI entry).\n  const entries = fg.sync(PAGES_GLOB, {\n    cwd: pagesDir,\n    absolute: true,\n    onlyFiles: true,\n    stats: true,\n  }) as Array<{ path: string; stats?: { mtimeMs: number } }>;\n\n  for (const entry of entries) {\n    const mtime = entry.stats?.mtimeMs;\n    if (mtime !== undefined && mtime > dbMtime) return true;\n  }\n  return false;\n}\n\nfunction hashContent(raw: string): string {\n  return createHash(\"sha256\").update(raw).digest(\"hex\");\n}\n\n/**\n * Return true if `topics.yaml` has an mtime strictly greater than the\n * index DB's mtime. This is the topics-side mirror of `pagesNewerThan`\n * — mutations to `topics.yaml` (title/description/parents) aren't\n * visible from any page mtime, so we need a separate freshness hook\n * for the file itself.\n *\n * Missing `topics.yaml` → false. Absence is legal and means \"no topic\n * metadata, only whatever pages declare\". A missing file doesn't\n * invalidate the existing index.\n */\nfunction topicsYamlNewerThan(almanacDir: string, dbPath: string): boolean {\n  const path = join(almanacDir, \"topics.yaml\");\n  if (!existsSync(path)) return false;\n  let dbMtime: number;\n  try {\n    dbMtime = statSync(dbPath).mtimeMs;\n  } catch {\n    return true;\n  }\n  try {\n    const st = statSync(path);\n    return st.mtimeMs > dbMtime;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Apply the contents of `.almanac/topics.yaml` to SQLite.\n *\n * Called at the tail of every reindex. For each entry in the file we\n * upsert a row into `topics` (with title + description) and rewrite\n * that topic's edges in `topic_parents`. Topics that were ad-hoc-only\n * before (mentioned in page frontmatter, never `almanac topics\n * create`d) get their display name promoted to whatever is in the\n * file.\n *\n * Importantly, we do NOT delete `topics` rows that live only in page\n * frontmatter — those are legal, per the spec (\"any slug mentioned in\n * pages' `topics:` frontmatter gets a row, even if not in\n * topics.yaml\"). We also do NOT clear `topic_parents` wholesale; we\n * rewrite edges for each declared topic but leave untouched rows for\n * ad-hoc topics (which by definition have no declared parents).\n *\n * Missing file = no-op. This is the \"no topic metadata yet\" state and\n * callers shouldn't have to paper over it.\n */\nasync function applyTopicsYaml(\n  db: Database.Database,\n  topicsYamlPath: string,\n): Promise<void> {\n  if (!existsSync(topicsYamlPath)) return;\n  let file;\n  try {\n    file = await loadTopicsFile(topicsYamlPath);\n  } catch (err: unknown) {\n    const message = err instanceof Error ? err.message : String(err);\n    process.stderr.write(`almanac: ${message}\\n`);\n    return;\n  }\n\n  const upsertTopic = db.prepare<[string, string, string | null]>(\n    `INSERT INTO topics (slug, title, description) VALUES (?, ?, ?)\n     ON CONFLICT(slug) DO UPDATE SET\n       title = excluded.title,\n       description = excluded.description`,\n  );\n  const clearParents = db.prepare<[string]>(\n    \"DELETE FROM topic_parents WHERE child_slug = ?\",\n  );\n  const insertParent = db.prepare<[string, string]>(\n    \"INSERT OR IGNORE INTO topic_parents (child_slug, parent_slug) VALUES (?, ?)\",\n  );\n\n  // Collect every slug we consider \"declared\" — in topics.yaml or\n  // referenced by any page_topics row. Anything outside this set is\n  // stale (e.g., a topic that used to be in the file before a rename\n  // or delete, or an ad-hoc slug whose only page just got untagged).\n  // Those get removed so `empty-topics` doesn't falsely flag them.\n  const declared = new Set<string>();\n  for (const t of file.topics) declared.add(t.slug);\n  const adHoc = db\n    .prepare<[], { topic_slug: string }>(\n      \"SELECT DISTINCT topic_slug FROM page_topics\",\n    )\n    .all();\n  for (const r of adHoc) declared.add(r.topic_slug);\n\n  const apply = db.transaction(() => {\n    for (const t of file.topics) {\n      upsertTopic.run(t.slug, t.title, t.description);\n      clearParents.run(t.slug);\n      for (const parent of t.parents) {\n        if (parent === t.slug) continue;\n        insertParent.run(t.slug, parent);\n      }\n    }\n\n    // Prune stale topic rows + any edges attached to them. We do this\n    // last so the upserts above have already promoted declared slugs.\n    const existing = db\n      .prepare<[], { slug: string }>(\"SELECT slug FROM topics\")\n      .all();\n    const deleteTopic = db.prepare<[string]>(\"DELETE FROM topics WHERE slug = ?\");\n    const deleteEdgesByChild = db.prepare<[string]>(\n      \"DELETE FROM topic_parents WHERE child_slug = ?\",\n    );\n    const deleteEdgesByParent = db.prepare<[string]>(\n      \"DELETE FROM topic_parents WHERE parent_slug = ?\",\n    );\n    for (const r of existing) {\n      if (declared.has(r.slug)) continue;\n      deleteEdgesByChild.run(r.slug);\n      deleteEdgesByParent.run(r.slug);\n      deleteTopic.run(r.slug);\n    }\n  });\n  apply();\n}\n","import { existsSync } from \"node:fs\";\nimport { mkdir, readFile, rename, writeFile } from \"node:fs/promises\";\nimport { dirname } from \"node:path\";\n\nimport yaml from \"js-yaml\";\n\nimport { toKebabCase } from \"../slug.js\";\n\n/**\n * One entry in `.almanac/topics.yaml` — the source of truth for topic\n * metadata (title, description, DAG parents). Pages are still the source\n * of truth for which pages belong to which topics; this file only holds\n * the topic-level attributes.\n *\n * `slug` is the canonical kebab-case key used everywhere downstream\n * (SQLite `topics.slug`, page frontmatter `topics:` entries, wikilink\n * targets). `title` is the human-readable name the user typed at create\n * time. `description` is a free-form one-liner (or null when unset).\n * `parents` is the DAG edge list — kept as an array of slugs rather than\n * a nested structure so round-tripping stays boring and a user eyeballing\n * the file can see the full graph.\n */\nexport interface TopicEntry {\n  slug: string;\n  title: string;\n  description: string | null;\n  parents: string[];\n}\n\nexport interface TopicsFile {\n  topics: TopicEntry[];\n}\n\n/**\n * Load `.almanac/topics.yaml` into a `TopicsFile`. A missing file is not\n * an error — it's the first-run state, which we treat as \"no topic\n * metadata, only whatever the pages declare in frontmatter\". Malformed\n * YAML IS an error; we surface it rather than silently clobbering the\n * user's committed source of truth.\n *\n * The return shape is always normalized — callers don't have to guard\n * for missing `topics` key, wrong types, or absent `parents` arrays.\n */\nexport async function loadTopicsFile(path: string): Promise<TopicsFile> {\n  if (!existsSync(path)) {\n    return { topics: [] };\n  }\n  let raw: string;\n  try {\n    raw = await readFile(path, \"utf8\");\n  } catch (err: unknown) {\n    if (isNodeError(err) && err.code === \"ENOENT\") {\n      return { topics: [] };\n    }\n    throw err;\n  }\n\n  const trimmed = raw.trim();\n  if (trimmed.length === 0) {\n    return { topics: [] };\n  }\n\n  let parsed: unknown;\n  try {\n    parsed = yaml.load(raw);\n  } catch (err: unknown) {\n    const message = err instanceof Error ? err.message : String(err);\n    throw new Error(`topics.yaml at ${path} is not valid YAML: ${message}`);\n  }\n\n  if (parsed === null || parsed === undefined) {\n    return { topics: [] };\n  }\n\n  if (typeof parsed !== \"object\" || Array.isArray(parsed)) {\n    throw new Error(`topics.yaml at ${path} must be a mapping`);\n  }\n\n  const obj = parsed as Record<string, unknown>;\n  const rawTopics = obj.topics;\n  if (rawTopics === undefined || rawTopics === null) {\n    return { topics: [] };\n  }\n  if (!Array.isArray(rawTopics)) {\n    throw new Error(`topics.yaml at ${path} — \"topics\" must be a list`);\n  }\n\n  const topics: TopicEntry[] = [];\n  for (const item of rawTopics) {\n    if (typeof item !== \"object\" || item === null || Array.isArray(item)) {\n      continue;\n    }\n    const entry = item as Record<string, unknown>;\n    const slugRaw = entry.slug;\n    if (typeof slugRaw !== \"string\" || slugRaw.trim().length === 0) continue;\n    const slug = toKebabCase(slugRaw);\n    if (slug.length === 0) continue;\n    const title =\n      typeof entry.title === \"string\" && entry.title.trim().length > 0\n        ? entry.title.trim()\n        : titleCase(slug);\n    const description =\n      typeof entry.description === \"string\" &&\n      entry.description.trim().length > 0\n        ? entry.description.trim()\n        : null;\n    const parents: string[] = [];\n    if (Array.isArray(entry.parents)) {\n      for (const p of entry.parents) {\n        if (typeof p === \"string\" && p.trim().length > 0) {\n          const ps = toKebabCase(p);\n          if (ps.length > 0 && ps !== slug && !parents.includes(ps)) {\n            parents.push(ps);\n          }\n        }\n      }\n    }\n    topics.push({ slug, title, description, parents });\n  }\n\n  return { topics };\n}\n\n/**\n * Write a `TopicsFile` atomically — tmp file + rename, same pattern as\n * the registry. A half-written topics.yaml would corrupt the user's\n * committed source of truth, so we never write in place.\n *\n * Ordering: topics are sorted by slug for stable diffs. Parents within\n * each entry stay in the order the caller passed them (semantically an\n * ordered list — topics.yaml is the place a user can visibly reason\n * about \"primary parent first\", even though SQLite treats them as a\n * set).\n *\n * We emit a leading comment so first-time readers know the file is\n * edited by the CLI and what its role is.\n */\nexport async function writeTopicsFile(\n  path: string,\n  file: TopicsFile,\n): Promise<void> {\n  const sorted = [...file.topics].sort((a, b) => a.slug.localeCompare(b.slug));\n  const doc = {\n    topics: sorted.map((t) => {\n      // Emit all four keys in a stable order: slug, title, description,\n      // parents. description is emitted as `null` in YAML when unset so\n      // the schema stays consistent across entries (js-yaml renders the\n      // literal word `null`, not the `~` shorthand).\n      return {\n        slug: t.slug,\n        title: t.title,\n        description: t.description,\n        parents: t.parents,\n      };\n    }),\n  };\n\n  const header =\n    `# .almanac/topics.yaml — source of truth for topic metadata.\\n` +\n    `# Managed by \\`almanac topics\\` commands. User-added comments\\n` +\n    `# between entries will be stripped on the next write (js-yaml\\n` +\n    `# doesn't round-trip comments). Edit at your own risk — or use the\\n` +\n    `# CLI (\\`almanac topics create|link|describe|rename|delete\\`)\\n` +\n    `# which preserves the structure correctly.\\n`;\n  const body = yaml.dump(doc, {\n    lineWidth: 100,\n    noRefs: true,\n    sortKeys: false,\n  });\n  const content = `${header}${body}`;\n  const tmpPath = `${path}.tmp`;\n  // mkdir parent in case `.almanac/` vanished (shouldn't, but cheap insurance)\n  const parent = dirname(path);\n  if (!existsSync(parent)) {\n    await mkdir(parent, { recursive: true });\n  }\n  await writeFile(tmpPath, content, \"utf8\");\n  await rename(tmpPath, path);\n}\n\n/**\n * Look up a topic by slug. Returns `null` when the slug is absent —\n * callers distinguish \"declared in topics.yaml\" from \"ad-hoc (only\n * appears in page frontmatter)\" based on this.\n */\nexport function findTopic(file: TopicsFile, slug: string): TopicEntry | null {\n  for (const t of file.topics) {\n    if (t.slug === slug) return t;\n  }\n  return null;\n}\n\n/**\n * Ensure a topic entry exists. If missing, inserts a minimal entry with\n * title-cased title and null description. Returns the (possibly new)\n * entry. Used by `tag`, `topics create` (with `--parent auto-creating`),\n * and `topics link` (auto-creating child/parent on demand).\n */\nexport function ensureTopic(file: TopicsFile, slug: string): TopicEntry {\n  const existing = findTopic(file, slug);\n  if (existing !== null) return existing;\n  const entry: TopicEntry = {\n    slug,\n    title: titleCase(slug),\n    description: null,\n    parents: [],\n  };\n  file.topics.push(entry);\n  return entry;\n}\n\n/**\n * Convert a slug back to a human-ish title: `auth-flow` → `Auth Flow`.\n * Used as the fallback title when the caller didn't provide one\n * (auto-creation paths, ad-hoc slugs coming from page frontmatter).\n */\nexport function titleCase(slug: string): string {\n  if (slug.length === 0) return slug;\n  return slug\n    .split(\"-\")\n    .filter((s) => s.length > 0)\n    .map((s) => `${s[0]?.toUpperCase() ?? \"\"}${s.slice(1)}`)\n    .join(\" \");\n}\n\nfunction isNodeError(err: unknown): err is NodeJS.ErrnoException {\n  return err instanceof Error && \"code\" in err;\n}\n","/**\n * Path normalization for the file/folder references stored in `file_refs`\n * and for the query input passed to `--mentions`.\n *\n * The same function runs over both sides so a value written at index time\n * and a value looked up at query time compare byte-for-byte. If this ever\n * drifts between writers and readers, `--mentions` starts silently missing\n * matches — apply one canonicalization, not two.\n *\n * Rules (from the spec, Correctness):\n *   - Lowercase (macOS filesystems are case-insensitive, so the wiki treats\n *     `Src/Checkout/` and `src/checkout/` as the same path)\n *   - Forward slashes only (never backslashes from Windows-authored content)\n *   - No leading `./`\n *   - Collapse redundant slashes (`src//checkout/` → `src/checkout/`)\n *   - Trailing `/` iff the caller says it's a directory\n *\n * The `isDir` flag is a signal carried alongside the path — we don't infer\n * it from the raw string here, because frontmatter `files:` entries and the\n * inline `[[...]]` classifier both decide directness themselves and pass\n * the answer in. Having one place decide and one place normalize keeps the\n * directory inference rule testable in isolation.\n */\nexport function normalizePath(raw: string, isDir: boolean): string {\n  const normalized = normalizeShape(raw, isDir);\n  return normalized.toLowerCase();\n}\n\n/**\n * Normalize shape without lowercasing — preserves the author's casing.\n * Used to store `original_path` in `file_refs` so dead-ref checks on\n * case-sensitive filesystems (Linux, `git` checkouts with core.ignorecase\n * false) stat the actual path on disk rather than a lowercased alias.\n *\n * Everything else about the result is identical to `normalizePath`:\n * forward slashes, no `./`, no duplicate slashes, trailing `/` iff\n * `isDir`. The ONLY difference is the final `.toLowerCase()` is skipped.\n */\nexport function normalizePathPreservingCase(raw: string, isDir: boolean): string {\n  return normalizeShape(raw, isDir);\n}\n\nfunction normalizeShape(raw: string, isDir: boolean): string {\n  let s = raw.trim();\n\n  // Windows-style backslashes → forward slashes. We never want to store\n  // backslashes; a path authored on Windows and checked in should match\n  // the same path authored on macOS.\n  s = s.replace(/\\\\+/g, \"/\");\n\n  // Drop a leading `./` — it's syntactic noise and authors inconsistently\n  // include it. `./src/checkout/` and `src/checkout/` must hash equal.\n  while (s.startsWith(\"./\")) s = s.slice(2);\n\n  // Collapse any run of slashes to a single slash. This also normalizes\n  // `src//checkout/` and accidental doubled slashes from string concat.\n  s = s.replace(/\\/+/g, \"/\");\n\n  // Strip any trailing slashes before re-applying the directory marker —\n  // this way we don't care if the caller fed us `src/checkout` or\n  // `src/checkout/` as a directory; we impose our own rule.\n  s = s.replace(/\\/+$/, \"\");\n\n  if (isDir) {\n    // Directories ALWAYS end with a trailing slash. This is what lets the\n    // GLOB queries distinguish `src/checkout/` (the directory) from\n    // `src/checkout` (a file with no extension) without ambiguity.\n    return `${s}/`;\n  }\n  return s;\n}\n\n/**\n * Infer `isDir` from the raw string the author wrote. Only used at the\n * point of parsing frontmatter `files:` entries and inline `[[...]]`\n * references — everywhere else, `isDir` is already known from context.\n *\n * Rule: trailing `/` (after backslash normalization) means directory.\n */\nexport function looksLikeDir(raw: string): boolean {\n  const s = raw.trim().replace(/\\\\+/g, \"/\");\n  return s.endsWith(\"/\");\n}\n","import Database from \"better-sqlite3\";\n\n/**\n * Schema DDL, applied on every open. All statements are `CREATE ... IF NOT\n * EXISTS` so this is idempotent — handy when the file already exists but\n * was written by an older version, and tolerable because the schema is\n * append-only (new tables don't collide).\n *\n * Departures from the raw spec, explained:\n *   - `page_topics.topic_slug` has no FK to `topics(slug)`. Topics are\n *     created lazily when a page declares them; a strict FK would force us\n *     to upsert topic rows before the page rows, which doesn't buy us\n *     anything in slice 2 and locks us out of slice 3's \"no explicit topic\n *     registration needed\" behavior.\n *   - `wikilinks.target_slug` / `cross_wiki_links.target_slug` also have\n *     no FK — these can be intentionally broken (unwritten target page),\n *     and `almanac health` will surface them in slice 3.\n *\n * `file_refs` carries TWO forms of each path:\n *   - `path`          — normalized + lowercased, used for GLOB/equality\n *                       queries (`--mentions`). Stable across casing\n *                       choices on macOS/Windows.\n *   - `original_path` — as-written (normalized slashes, no `./`, trailing\n *                       `/` for dirs), preserving the author's casing.\n *                       Used for filesystem stats (dead-refs on\n *                       case-sensitive filesystems like Linux) and for\n *                       user-facing display (`almanac info`).\n *\n * See also: `SCHEMA_VERSION` below and the migration logic in `openIndex`.\n */\nconst SCHEMA_DDL = `\nCREATE TABLE IF NOT EXISTS pages (\n  slug          TEXT PRIMARY KEY,\n  title         TEXT,\n  file_path     TEXT NOT NULL,\n  content_hash  TEXT NOT NULL,\n  updated_at    INTEGER NOT NULL,\n  archived_at   INTEGER,\n  superseded_by TEXT\n);\n\nCREATE TABLE IF NOT EXISTS topics (\n  slug        TEXT PRIMARY KEY,\n  title       TEXT,\n  description TEXT\n);\n\nCREATE TABLE IF NOT EXISTS page_topics (\n  page_slug  TEXT NOT NULL REFERENCES pages(slug) ON DELETE CASCADE,\n  topic_slug TEXT NOT NULL,\n  PRIMARY KEY (page_slug, topic_slug)\n);\n\nCREATE TABLE IF NOT EXISTS topic_parents (\n  child_slug  TEXT NOT NULL,\n  parent_slug TEXT NOT NULL,\n  PRIMARY KEY (child_slug, parent_slug),\n  CHECK (child_slug != parent_slug)\n);\n\nCREATE TABLE IF NOT EXISTS file_refs (\n  page_slug     TEXT NOT NULL REFERENCES pages(slug) ON DELETE CASCADE,\n  path          TEXT NOT NULL,\n  original_path TEXT NOT NULL,\n  is_dir        INTEGER NOT NULL,\n  PRIMARY KEY (page_slug, path)\n);\nCREATE INDEX IF NOT EXISTS idx_file_refs_path ON file_refs(path);\n\nCREATE TABLE IF NOT EXISTS wikilinks (\n  source_slug TEXT NOT NULL REFERENCES pages(slug) ON DELETE CASCADE,\n  target_slug TEXT NOT NULL,\n  PRIMARY KEY (source_slug, target_slug)\n);\n\nCREATE TABLE IF NOT EXISTS cross_wiki_links (\n  source_slug TEXT NOT NULL REFERENCES pages(slug) ON DELETE CASCADE,\n  target_wiki TEXT NOT NULL,\n  target_slug TEXT NOT NULL,\n  PRIMARY KEY (source_slug, target_wiki, target_slug)\n);\n\n-- NOTE: virtual FTS5 table — ON DELETE CASCADE from pages does NOT apply.\n-- The indexer must explicitly DELETE FROM fts_pages whenever it removes\n-- or replaces a page row, or we leak orphaned FTS rows.\nCREATE VIRTUAL TABLE IF NOT EXISTS fts_pages USING fts5(slug, title, content);\n`;\n\n/**\n * Bump this whenever the schema changes in a backwards-incompatible way.\n * On open we compare the stored `user_version` against this constant; if\n * it's lower, we drop the affected tables so the next `runIndexer` can\n * rebuild them. Full reindex is cheap (everything lives on disk as\n * markdown), so \"drop + recreate\" is simpler than ALTER TABLE migrations.\n *\n * Version history:\n *   1 — initial slice-2 schema\n *   2 — slice-3-review: added `file_refs.original_path`\n */\nconst SCHEMA_VERSION = 2;\n\n/**\n * Open `index.db` and apply the schema. Foreign keys are off by default in\n * SQLite; we turn them on per-connection so the ON DELETE CASCADE on\n * `pages` actually fires when we delete stale rows during incremental\n * reindex.\n *\n * We don't wrap this open in a transaction — `CREATE ... IF NOT EXISTS` is\n * safe to run repeatedly and the FTS5 virtual-table creation is already\n * atomic.\n *\n * Migration: if the DB was created by an older schema (`user_version` <\n * `SCHEMA_VERSION`), we drop the tables whose shape changed and let the\n * CREATE IF NOT EXISTS below rebuild them. The next `runIndexer` repopulates\n * from the filesystem — cheap and avoids the ALTER TABLE dance.\n */\nexport function openIndex(dbPath: string): Database.Database {\n  const db = new Database(dbPath);\n  // WAL journal mode is persistent — once set, it's recorded in the DB\n  // header and survives close/open cycles. Check first and only switch if\n  // we're not already there; this avoids a redundant pragma write on every\n  // query command.\n  const mode = db.pragma(\"journal_mode\", { simple: true });\n  if (typeof mode !== \"string\" || mode.toLowerCase() !== \"wal\") {\n    db.pragma(\"journal_mode = WAL\");\n  }\n  db.pragma(\"foreign_keys = ON\");\n\n  const rawVersion = db.pragma(\"user_version\", { simple: true });\n  const currentVersion = typeof rawVersion === \"number\" ? rawVersion : 0;\n  if (currentVersion < SCHEMA_VERSION) {\n    // Drop tables whose shape changed. `file_refs` got `original_path`\n    // as of v2; easiest to drop it entirely so CREATE IF NOT EXISTS\n    // runs with the new definition. Pages/topics/links are untouched.\n    db.exec(\"DROP TABLE IF EXISTS file_refs\");\n    // The indexer's fast-path skips pages whose content_hash matches,\n    // which means a migration-dropped `file_refs` wouldn't get\n    // repopulated until a page changed. Clear the hash column so the\n    // next reindex treats every page as changed and rebuilds its\n    // file_refs/wikilinks/cross-wiki rows. Table may not exist yet on\n    // a brand-new DB, so swallow errors.\n    try {\n      db.exec(\"UPDATE pages SET content_hash = ''\");\n    } catch {\n      // pages table didn't exist yet; the upcoming CREATE IF NOT EXISTS\n      // takes care of a fresh install.\n    }\n    db.pragma(`user_version = ${SCHEMA_VERSION}`);\n  }\n\n  db.exec(SCHEMA_DDL);\n  return db;\n}\n","import { toKebabCase } from \"../slug.js\";\nimport {\n  looksLikeDir,\n  normalizePath,\n  normalizePathPreservingCase,\n} from \"./paths.js\";\n\n/**\n * One parsed `[[...]]` reference from a page body. Classification is\n * deterministic and content-based — see `classifyWikilink` below.\n *\n * Callers dispatch on `kind`:\n *   - `page`    → row in `wikilinks`\n *   - `file`    → row in `file_refs` with `is_dir = 0`\n *   - `folder`  → row in `file_refs` with `is_dir = 1`\n *   - `xwiki`   → row in `cross_wiki_links`\n *\n * File/folder refs carry TWO forms of the path:\n *   - `path`         — lowercased (for `--mentions` lookups)\n *   - `originalPath` — as-written (for filesystem stats on case-sensitive\n *                      systems and for user-facing display)\n */\nexport type WikilinkRef =\n  | { kind: \"page\"; target: string }\n  | { kind: \"file\"; path: string; originalPath: string }\n  | { kind: \"folder\"; path: string; originalPath: string }\n  | { kind: \"xwiki\"; wiki: string; target: string };\n\n/**\n * Rules from the spec (\"Classification rules\"), applied in order:\n *\n *   1. Contains `:` before any `/`  → cross-wiki reference (`wiki:slug`)\n *   2. Contains `/`                  → file or folder reference\n *          - Trailing `/` = folder\n *          - Otherwise    = file\n *   3. Otherwise                     → page slug wikilink\n *\n * Edge cases the test suite pins down:\n *   - `[[a:b/c]]`      → xwiki (colon is before the slash, rule 1 wins)\n *   - `[[src/a:b]]`    → file (slash is before the colon, rule 2 wins)\n *   - `[[./x]]`        → the leading `./` is stripped by `normalizePath`,\n *                        so this lands in `file_refs` as `x`. A bare `./x`\n *                        with no inner slash would classify as a file.\n *   - `[[foo|display]]`→ Obsidian-style display text is stripped; we key\n *                        on the target only. A future slice could surface\n *                        display text in `almanac info`.\n */\nexport function classifyWikilink(raw: string): WikilinkRef | null {\n  // Strip Obsidian-style `|display` suffix — we don't index display text\n  // in slice 2, but we want the classifier to see the real target.\n  const pipe = raw.indexOf(\"|\");\n  let body = pipe === -1 ? raw : raw.slice(0, pipe);\n  body = body.trim();\n  if (body.length === 0) return null;\n\n  const firstColon = body.indexOf(\":\");\n  const firstSlash = body.indexOf(\"/\");\n\n  // Rule 1: cross-wiki, `wiki:slug`. Only if the colon comes before any\n  // slash — otherwise `src/urls.ts:42` (hypothetical) would wrongly\n  // classify as xwiki.\n  if (firstColon !== -1 && (firstSlash === -1 || firstColon < firstSlash)) {\n    const wiki = body.slice(0, firstColon).trim();\n    const target = body.slice(firstColon + 1).trim();\n    if (wiki.length === 0 || target.length === 0) return null;\n    return { kind: \"xwiki\", wiki, target };\n  }\n\n  // Rule 2: file or folder. The `/` may be anywhere including trailing.\n  if (firstSlash !== -1) {\n    const isDir = looksLikeDir(body);\n    const path = normalizePath(body, isDir);\n    const originalPath = normalizePathPreservingCase(body, isDir);\n    if (path.length === 0) return null;\n    return isDir\n      ? { kind: \"folder\", path, originalPath }\n      : { kind: \"file\", path, originalPath };\n  }\n\n  // Rule 3: page slug wikilink. Authors might write `Checkout Flow` or\n  // `Checkout_Flow` by accident — slugify defensively so backlinks still\n  // resolve in those cases.\n  const target = toKebabCase(body);\n  if (target.length === 0) return null;\n  return { kind: \"page\", target };\n}\n\n/**\n * Walk a markdown body and pull every `[[...]]` reference. We scan the\n * whole body rather than try to skip code blocks — the spec is explicit:\n * \"Prose outside `[[...]]` is just prose. No backtick-path heuristics, no\n * false positives from code blocks or log output.\" A `[[foo]]` inside a\n * fenced code block is still a wikilink. Authors who genuinely need a\n * literal `[[x]]` in code can escape one of the brackets.\n */\nexport function extractWikilinks(body: string): WikilinkRef[] {\n  const out: WikilinkRef[] = [];\n  const re = /\\[\\[([^\\]\\n]+)\\]\\]/g;\n  let m: RegExpExecArray | null;\n  while ((m = re.exec(body)) !== null) {\n    const ref = classifyWikilink(m[1] ?? \"\");\n    if (ref !== null) out.push(ref);\n  }\n  return out;\n}\n","import { existsSync } from \"node:fs\";\nimport { join } from \"node:path\";\n\nimport { findNearestAlmanacDir } from \"../paths.js\";\nimport { findEntry } from \"../registry/index.js\";\n\n/**\n * Figure out which repo root a query command should run against.\n *\n * Two modes, in order of precedence:\n *   1. `--wiki <name>`  — look it up in the global registry. Fails\n *      explicitly if the name isn't registered or its path has gone\n *      missing (unmounted drive, deleted repo). No silent fallback, which\n *      would hide the real problem from the user.\n *   2. default — walk up from `cwd` like git does. Fails if we're not\n *      inside a `.almanac/` repo.\n *\n * Returns the absolute path to the repo root (the directory containing\n * `.almanac/`).\n *\n * NOTE (spec contract, not yet implemented): when `--all` lands in a\n * future slice, it must silently skip wikis whose paths have gone\n * unreachable — the asymmetry with `--wiki <name>` is deliberate.\n * Explicit lookup is loud about failures (user named a specific wiki);\n * bulk `--all` is quiet (user asked \"whatever's available\"). Don't\n * unify the error behavior when adding `--all`.\n */\nexport async function resolveWikiRoot(params: {\n  cwd: string;\n  wiki?: string;\n}): Promise<string> {\n  if (params.wiki !== undefined) {\n    const entry = await findEntry({ name: params.wiki });\n    if (entry === null) {\n      throw new Error(`no registered wiki named \"${params.wiki}\"`);\n    }\n    if (!existsSync(join(entry.path, \".almanac\"))) {\n      throw new Error(\n        `wiki \"${params.wiki}\" path is unreachable (${entry.path})`,\n      );\n    }\n    return entry.path;\n  }\n\n  const nearest = findNearestAlmanacDir(params.cwd);\n  if (nearest === null) {\n    throw new Error(\n      \"no .almanac/ found in this directory or any parent; run `almanac init` first\",\n    );\n  }\n  return nearest;\n}\n","import type Database from \"better-sqlite3\";\n\nimport type { TopicsFile } from \"./yaml.js\";\n\n/**\n * Depth cap for all recursive traversals of the topics DAG. Belt and\n * suspenders alongside the `CHECK (child_slug != parent_slug)` on the\n * `topic_parents` table — even if a cycle somehow slipped into the data\n * (hand-edited `topics.yaml`, past bug), the CTE can't runaway.\n *\n * 32 is chosen as \"deeper than any real human-authored taxonomy will\n * ever go\". A 32-level topic hierarchy is absurd; anything hitting this\n * cap is almost certainly a cycle.\n */\nexport const DAG_DEPTH_CAP = 32;\n\n/**\n * Given a `topics.yaml` in memory, compute the set of ancestors of a\n * given slug (not including the slug itself). Used by `topics link`\n * to check whether a proposed edge would create a cycle.\n *\n * Running off the in-memory file lets `link` validate BEFORE touching\n * either the DB or the YAML, so a refusal doesn't leave half the state\n * mutated. Depth-capped with the same constant as the SQLite CTE.\n */\nexport function ancestorsInFile(\n  file: TopicsFile,\n  slug: string,\n): Set<string> {\n  // Build a child → parents map once.\n  const parentsOf = new Map<string, string[]>();\n  for (const t of file.topics) {\n    parentsOf.set(t.slug, t.parents);\n  }\n  const ancestors = new Set<string>();\n  // BFS, depth-capped. We stop descending when we've hit the cap or\n  // revisit an already-seen node (self-loop defense).\n  let frontier: string[] = parentsOf.get(slug) ?? [];\n  let depth = 0;\n  while (frontier.length > 0 && depth < DAG_DEPTH_CAP) {\n    const next: string[] = [];\n    for (const node of frontier) {\n      if (ancestors.has(node)) continue;\n      ancestors.add(node);\n      const ps = parentsOf.get(node);\n      if (ps !== undefined) next.push(...ps);\n    }\n    frontier = next;\n    depth += 1;\n  }\n  return ancestors;\n}\n\n/**\n * Return all descendants of a given topic slug via the SQLite\n * `topic_parents` table. Depth-capped at `DAG_DEPTH_CAP`.\n *\n * Used by `topics show --descendants` to expand a topic's page list\n * through its subtopics. The query is a canonical recursive CTE; we\n * `UNION` (not `UNION ALL`) so cycles in the data don't spin forever.\n */\nexport function descendantsInDb(\n  db: Database.Database,\n  slug: string,\n): string[] {\n  const rows = db\n    .prepare<[string, number], { slug: string }>(\n      `WITH RECURSIVE desc(slug, depth) AS (\n         SELECT child_slug, 1 FROM topic_parents WHERE parent_slug = ?\n         UNION\n         SELECT tp.child_slug, d.depth + 1\n         FROM topic_parents tp\n         JOIN desc d ON tp.parent_slug = d.slug\n         WHERE d.depth < ?\n       )\n       SELECT DISTINCT slug FROM desc ORDER BY slug`,\n    )\n    .all(slug, DAG_DEPTH_CAP)\n    .map((r) => r.slug);\n  return rows;\n}\n\n/**\n * Return the subtree rooted at `slug` (the slug itself + all\n * descendants). Convenience wrapper used by `health --topic` to scope\n * reports through the DAG.\n */\nexport function subtreeInDb(db: Database.Database, slug: string): string[] {\n  return [slug, ...descendantsInDb(db, slug)];\n}\n","import { join } from \"node:path\";\n\nimport type Database from \"better-sqlite3\";\n\nimport { ensureFreshIndex } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\n\nexport interface InfoOptions {\n  cwd: string;\n  slug?: string;\n  stdin?: boolean;\n  stdinInput?: string;\n  json?: boolean;\n  wiki?: string;\n}\n\nexport interface InfoRecord {\n  slug: string;\n  title: string | null;\n  file_path: string;\n  updated_at: number;\n  archived_at: number | null;\n  superseded_by: string | null;\n  supersedes: string[]; // pages that declare superseded_by = this slug\n  topics: string[];\n  file_refs: Array<{ path: string; is_dir: boolean }>;\n  wikilinks_out: string[];\n  wikilinks_in: string[];\n  cross_wiki_links: Array<{ wiki: string; target: string }>;\n}\n\nexport interface InfoCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * `almanac info <slug>` — structured view of one page.\n *\n * Human-readable output groups the fields into labeled sections; `--json`\n * emits the raw record. Bulk mode (`--stdin`) defaults to JSON output\n * (array of records) because interleaved human-readable blobs are hard to\n * parse downstream.\n *\n * Backlinks (`wikilinks_in`) are computed per call — there's no\n * materialized reverse index in slice 2, which keeps indexing simple and\n * the query is trivial at the size of a normal wiki.\n */\nexport async function runInfo(\n  options: InfoOptions,\n): Promise<InfoCommandOutput> {\n  const repoRoot = await resolveWikiRoot({\n    cwd: options.cwd,\n    wiki: options.wiki,\n  });\n  await ensureFreshIndex({ repoRoot });\n\n  const dbPath = join(repoRoot, \".almanac\", \"index.db\");\n  const db = openIndex(dbPath);\n\n  try {\n    const slugs = collectSlugs(options);\n    if (slugs.length === 0) {\n      return {\n        stdout: \"\",\n        stderr: \"almanac: info requires a slug (or --stdin)\\n\",\n        exitCode: 1,\n      };\n    }\n\n    const records: InfoRecord[] = [];\n    const missing: string[] = [];\n    for (const slug of slugs) {\n      const rec = fetchInfo(db, slug);\n      if (rec === null) {\n        missing.push(slug);\n        continue;\n      }\n      records.push(rec);\n    }\n\n    const bulk = options.stdin === true;\n    const jsonOut = options.json === true || bulk;\n\n    // JSON shape rule (consumers depend on this being predictable):\n    //   --stdin        → always array of records (even for a single slug)\n    //   positional     → always a single object (never an array)\n    // The previous implementation accidentally reshaped \"positional with\n    // zero records\" as an array and positional with one record as an\n    // object, which made downstream callers have to sniff the shape.\n    // Now: `info --stdin` gives you a list to iterate; `info <slug>` gives\n    // you one record to dot-access.\n    let stdout: string;\n    if (jsonOut) {\n      if (bulk) {\n        stdout = `${JSON.stringify(records, null, 2)}\\n`;\n      } else {\n        // Positional mode: we already short-circuited on empty slugs,\n        // and a missing page is in `missing[]` — so `records` is either\n        // length 1 (found) or length 0 (missing). For length 0 we emit\n        // `null` so the shape is still object-ish, not an empty array.\n        const only = records[0] ?? null;\n        stdout = `${JSON.stringify(only, null, 2)}\\n`;\n      }\n    } else {\n      stdout = records.map(formatHumanReadable).join(\"\\n\");\n    }\n\n    const stderr = missing\n      .map((s) => `almanac: no such page \"${s}\"\\n`)\n      .join(\"\");\n    return {\n      stdout,\n      stderr,\n      exitCode: missing.length > 0 ? 1 : 0,\n    };\n  } finally {\n    db.close();\n  }\n}\n\nfunction fetchInfo(db: Database.Database, slug: string): InfoRecord | null {\n  const pageRow = db\n    .prepare<\n      [string],\n      {\n        slug: string;\n        title: string | null;\n        file_path: string;\n        updated_at: number;\n        archived_at: number | null;\n        superseded_by: string | null;\n      }\n    >(\n      \"SELECT slug, title, file_path, updated_at, archived_at, superseded_by FROM pages WHERE slug = ?\",\n    )\n    .get(slug);\n  if (pageRow === undefined) return null;\n\n  const topics = db\n    .prepare<[string], { topic_slug: string }>(\n      \"SELECT topic_slug FROM page_topics WHERE page_slug = ? ORDER BY topic_slug\",\n    )\n    .all(slug)\n    .map((r) => r.topic_slug);\n\n  const refs = db\n    .prepare<[string], { original_path: string; is_dir: number }>(\n      // Display the author's casing (`original_path`), not the\n      // lowercased lookup form. The lowercased `path` column is the\n      // query key for `--mentions`; it's not a user-facing string.\n      \"SELECT original_path, is_dir FROM file_refs WHERE page_slug = ? ORDER BY original_path\",\n    )\n    .all(slug)\n    .map((r) => ({ path: r.original_path, is_dir: r.is_dir === 1 }));\n\n  const linksOut = db\n    .prepare<[string], { target_slug: string }>(\n      \"SELECT target_slug FROM wikilinks WHERE source_slug = ? ORDER BY target_slug\",\n    )\n    .all(slug)\n    .map((r) => r.target_slug);\n\n  const linksIn = db\n    .prepare<[string], { source_slug: string }>(\n      \"SELECT source_slug FROM wikilinks WHERE target_slug = ? ORDER BY source_slug\",\n    )\n    .all(slug)\n    .map((r) => r.source_slug);\n\n  const xwiki = db\n    .prepare<[string], { target_wiki: string; target_slug: string }>(\n      \"SELECT target_wiki, target_slug FROM cross_wiki_links WHERE source_slug = ? ORDER BY target_wiki, target_slug\",\n    )\n    .all(slug)\n    .map((r) => ({ wiki: r.target_wiki, target: r.target_slug }));\n\n  // \"Pages that say `supersedes: <me>`\" — the reverse side of this\n  // page's `superseded_by` field. We read this from `pages` rather than\n  // a dedicated column because the spec (deliberately) doesn't index\n  // `supersedes:` as its own table — the relationship is already implicit\n  // in whoever points at us.\n  const supersedesRows = db\n    .prepare<[string], { slug: string }>(\n      \"SELECT slug FROM pages WHERE superseded_by = ? ORDER BY slug\",\n    )\n    .all(slug)\n    .map((r) => r.slug);\n\n  return {\n    slug: pageRow.slug,\n    title: pageRow.title,\n    file_path: pageRow.file_path,\n    updated_at: pageRow.updated_at,\n    archived_at: pageRow.archived_at,\n    superseded_by: pageRow.superseded_by,\n    supersedes: supersedesRows,\n    topics,\n    file_refs: refs,\n    wikilinks_out: linksOut,\n    wikilinks_in: linksIn,\n    cross_wiki_links: xwiki,\n  };\n}\n\nfunction collectSlugs(options: InfoOptions): string[] {\n  if (options.stdin === true && options.stdinInput !== undefined) {\n    return options.stdinInput\n      .split(/\\r?\\n/)\n      .map((s) => s.trim())\n      .filter((s) => s.length > 0);\n  }\n  if (options.slug !== undefined && options.slug.length > 0) {\n    return [options.slug];\n  }\n  return [];\n}\n\nfunction formatHumanReadable(rec: InfoRecord): string {\n  const lines: string[] = [];\n  lines.push(`slug:          ${rec.slug}`);\n  lines.push(`title:         ${rec.title ?? \"—\"}`);\n  lines.push(`file:          ${rec.file_path}`);\n  lines.push(`updated_at:    ${new Date(rec.updated_at * 1000).toISOString()}`);\n  if (rec.archived_at !== null) {\n    lines.push(\n      `archived_at:   ${new Date(rec.archived_at * 1000).toISOString()}`,\n    );\n  }\n  if (rec.superseded_by !== null) {\n    lines.push(`superseded_by: ${rec.superseded_by}`);\n  }\n  if (rec.supersedes.length > 0) {\n    lines.push(`supersedes:    ${rec.supersedes.join(\", \")}`);\n  }\n  lines.push(`topics:        ${rec.topics.length > 0 ? rec.topics.join(\", \") : \"—\"}`);\n  lines.push(\"file_refs:\");\n  if (rec.file_refs.length === 0) {\n    lines.push(\"  —\");\n  } else {\n    for (const r of rec.file_refs) {\n      lines.push(`  ${r.path}${r.is_dir ? \"  (dir)\" : \"\"}`);\n    }\n  }\n  lines.push(\"wikilinks_out:\");\n  if (rec.wikilinks_out.length === 0) lines.push(\"  —\");\n  else for (const t of rec.wikilinks_out) lines.push(`  ${t}`);\n  lines.push(\"wikilinks_in:\");\n  if (rec.wikilinks_in.length === 0) lines.push(\"  —\");\n  else for (const s of rec.wikilinks_in) lines.push(`  ${s}`);\n  if (rec.cross_wiki_links.length > 0) {\n    lines.push(\"cross_wiki_links:\");\n    for (const x of rec.cross_wiki_links) {\n      lines.push(`  ${x.wiki}:${x.target}`);\n    }\n  }\n  return `${lines.join(\"\\n\")}\\n`;\n}\n","import { existsSync } from \"node:fs\";\n\nimport {\n  dropEntry,\n  readRegistry,\n  type RegistryEntry,\n} from \"../registry/index.js\";\n\nexport interface ListOptions {\n  json?: boolean;\n  drop?: string;\n}\n\nexport interface ListCommandOutput {\n  stdout: string;\n  exitCode: number;\n}\n\n/**\n * `almanac list` — the global discovery surface. Three modes:\n *\n *  - default: pretty table of reachable wikis\n *  - `--json`: structured output (reachable wikis only, by default)\n *  - `--drop <name>`: explicit removal, then exits\n *\n * **Unreachable paths are silently skipped in the default output**, but\n * never auto-dropped. This is the registry hygiene rule from the design —\n * branch switches, unmounted drives, and VM-offline repos should not cost\n * the user a registration. Only `--drop` removes entries.\n */\nexport async function listWikis(\n  options: ListOptions,\n): Promise<ListCommandOutput> {\n  if (options.drop !== undefined) {\n    return handleDrop(options.drop);\n  }\n\n  const entries = await readRegistry();\n  const reachable = entries.filter((e) => isReachable(e));\n\n  if (options.json === true) {\n    return { stdout: `${JSON.stringify(reachable, null, 2)}\\n`, exitCode: 0 };\n  }\n\n  return { stdout: formatPretty(reachable), exitCode: 0 };\n}\n\nasync function handleDrop(name: string): Promise<ListCommandOutput> {\n  const removed = await dropEntry(name);\n  if (removed === null) {\n    return {\n      stdout: `no registry entry named \"${name}\"\\n`,\n      exitCode: 1,\n    };\n  }\n  return {\n    stdout: `removed \"${removed.name}\" (${removed.path})\\n`,\n    exitCode: 0,\n  };\n}\n\n/**\n * A registry path is \"reachable\" if something still exists at that path.\n * We use `existsSync` rather than `stat` — we don't care whether the path\n * is a directory or has a `.almanac/` inside; we only hide it from default\n * output when the path itself is gone (e.g., repo deleted, drive\n * unmounted).\n */\nfunction isReachable(entry: RegistryEntry): boolean {\n  if (entry.path.length === 0) return false;\n  return existsSync(entry.path);\n}\n\n/**\n * Human-readable listing. Empty state prints a gentle hint rather than a\n * blank screen, and entries render in registration order (chronological,\n * since `addEntry` appends).\n */\nfunction formatPretty(entries: RegistryEntry[]): string {\n  if (entries.length === 0) {\n    return \"no wikis registered. run `almanac init` in a repo to create one.\\n\";\n  }\n\n  // Column-width the name for alignment; cap at 30 so absurd names don't\n  // stretch the whole table.\n  const nameWidth = Math.min(\n    30,\n    entries.reduce((w, e) => Math.max(w, e.name.length), 0),\n  );\n\n  const lines: string[] = [];\n  for (const entry of entries) {\n    const name = entry.name.padEnd(nameWidth);\n    const desc = entry.description.length > 0 ? entry.description : \"—\";\n    lines.push(`${name}  ${desc}`);\n    lines.push(`${\" \".repeat(nameWidth)}  ${entry.path}`);\n  }\n  return `${lines.join(\"\\n\")}\\n`;\n}\n","import { join } from \"node:path\";\n\nimport { ensureFreshIndex } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\n\nexport interface PathOptions {\n  cwd: string;\n  slug?: string;\n  stdin?: boolean;\n  stdinInput?: string;\n  wiki?: string;\n}\n\nexport interface PathCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * `almanac path <slug>` — slug → absolute file path.\n *\n * Pure scripting helper. With `--stdin` it maps each line of input to its\n * resolved path; unresolvable slugs go to stderr with a non-zero exit\n * while the resolvable ones still print on stdout.\n */\nexport async function runPath(\n  options: PathOptions,\n): Promise<PathCommandOutput> {\n  const repoRoot = await resolveWikiRoot({\n    cwd: options.cwd,\n    wiki: options.wiki,\n  });\n  await ensureFreshIndex({ repoRoot });\n\n  const dbPath = join(repoRoot, \".almanac\", \"index.db\");\n  const db = openIndex(dbPath);\n\n  try {\n    const slugs = collectSlugs(options);\n    if (slugs.length === 0) {\n      return {\n        stdout: \"\",\n        stderr: \"almanac: path requires a slug (or --stdin)\\n\",\n        exitCode: 1,\n      };\n    }\n\n    const stmt = db.prepare<[string], { file_path: string }>(\n      \"SELECT file_path FROM pages WHERE slug = ?\",\n    );\n    const resolved: string[] = [];\n    const missing: string[] = [];\n    for (const slug of slugs) {\n      const row = stmt.get(slug);\n      if (row === undefined) {\n        missing.push(slug);\n        continue;\n      }\n      resolved.push(row.file_path);\n    }\n\n    const stdout = resolved.length > 0 ? `${resolved.join(\"\\n\")}\\n` : \"\";\n    const stderr = missing\n      .map((s) => `almanac: no such page \"${s}\"\\n`)\n      .join(\"\");\n    return {\n      stdout,\n      stderr,\n      exitCode: missing.length > 0 ? 1 : 0,\n    };\n  } finally {\n    db.close();\n  }\n}\n\nfunction collectSlugs(options: PathOptions): string[] {\n  if (options.stdin === true && options.stdinInput !== undefined) {\n    return options.stdinInput\n      .split(/\\r?\\n/)\n      .map((s) => s.trim())\n      .filter((s) => s.length > 0);\n  }\n  if (options.slug !== undefined && options.slug.length > 0) {\n    return [options.slug];\n  }\n  return [];\n}\n","import { runIndexer, type IndexResult } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\n\nexport interface ReindexOptions {\n  cwd: string;\n  wiki?: string;\n}\n\nexport interface ReindexCommandOutput {\n  result: IndexResult;\n  stdout: string;\n  exitCode: number;\n}\n\n/**\n * `almanac reindex` — force a full rebuild.\n *\n * Unlike the implicit reindex every query command triggers, this one\n * prints a summary line so the user gets feedback for an explicitly\n * requested action. The summary is terse on purpose (one line, three\n * numbers) — verbose progress reporting would fight the design rule that\n * the CLI stays quiet by default.\n */\nexport async function runReindex(\n  options: ReindexOptions,\n): Promise<ReindexCommandOutput> {\n  const repoRoot = await resolveWikiRoot({\n    cwd: options.cwd,\n    wiki: options.wiki,\n  });\n  const result = await runIndexer({ repoRoot });\n  // Summary wording: \"reindexed: N pages (K updated, R removed)\". When\n  // some files were on disk but never made it into the index\n  // (slug collisions, ENOENT races, un-sluggable filenames), tack on a\n  // `; S skipped` suffix so the user notices. The per-file reason was\n  // already written to stderr at indexing time.\n  const skipSuffix =\n    result.filesSkipped > 0 ? `; ${result.filesSkipped} skipped` : \"\";\n  const stdout = `reindexed: ${result.pagesIndexed} page${result.pagesIndexed === 1 ? \"\" : \"s\"} (${result.changed} updated, ${result.removed} removed${skipSuffix})\\n`;\n  return { result, stdout, exitCode: 0 };\n}\n","import { join } from \"node:path\";\n\nimport type Database from \"better-sqlite3\";\n\nimport { parseDuration } from \"../indexer/duration.js\";\nimport { ensureFreshIndex } from \"../indexer/index.js\";\nimport { looksLikeDir, normalizePath } from \"../indexer/paths.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\n\nexport interface SearchOptions {\n  cwd: string;\n  query?: string;\n  topics: string[];\n  mentions?: string;\n  since?: string;\n  stale?: string;\n  orphan?: boolean;\n  includeArchive?: boolean;\n  archived?: boolean;\n  wiki?: string;\n  json?: boolean;\n  limit?: number;\n}\n\nexport interface SearchResult {\n  slug: string;\n  title: string | null;\n  updated_at: number;\n  archived_at: number | null;\n  superseded_by: string | null;\n  topics: string[];\n}\n\nexport interface SearchCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * `almanac search` — the core query surface.\n *\n * Filters compose with AND logic. The implementation is deliberately\n * pedestrian: build a list of clauses + params, join them with `AND`,\n * intersect topic filters by requiring one subquery per `--topic`. No\n * clever query-planner tricks needed for the sizes we handle (<10k pages).\n *\n * All output ordering is stable: `updated_at DESC, slug ASC`. FTS5 rank\n * is layered on top when the user passed a text query — we ORDER BY rank\n * first, then fall through to the default.\n */\nexport async function runSearch(\n  options: SearchOptions,\n): Promise<SearchCommandOutput> {\n  const repoRoot = await resolveWikiRoot({\n    cwd: options.cwd,\n    wiki: options.wiki,\n  });\n  await ensureFreshIndex({ repoRoot });\n\n  const dbPath = join(repoRoot, \".almanac\", \"index.db\");\n  const db = openIndex(dbPath);\n\n  try {\n    const rows = executeQuery(db, options);\n    const limited =\n      options.limit !== undefined && options.limit >= 0\n        ? rows.slice(0, options.limit)\n        : rows;\n\n    const stdout = formatResults(limited, options);\n    const stderr = buildStderr(limited, options);\n    return { stdout, stderr, exitCode: 0 };\n  } finally {\n    db.close();\n  }\n}\n\ninterface PageRow {\n  slug: string;\n  title: string | null;\n  updated_at: number;\n  archived_at: number | null;\n  superseded_by: string | null;\n}\n\nfunction executeQuery(\n  db: Database.Database,\n  options: SearchOptions,\n): SearchResult[] {\n  const whereClauses: string[] = [];\n  const params: (string | number)[] = [];\n\n  // Archive scope. Three modes, mutually exclusive in practice:\n  //   - default            → active only\n  //   - --include-archive  → active + archived\n  //   - --archived         → archived only\n  // `--archived` wins over `--include-archive` when both are passed —\n  // being explicit about \"only archived\" is strictly narrower than\n  // \"include archived\", so intersecting them yields \"only archived\".\n  if (options.archived === true) {\n    whereClauses.push(\"p.archived_at IS NOT NULL\");\n  } else if (options.includeArchive !== true) {\n    whereClauses.push(\"p.archived_at IS NULL\");\n  }\n\n  // --topic foo --topic bar → page must have BOTH. We add one EXISTS\n  // subquery per topic rather than grouping, which keeps param order\n  // simple and the plan readable.\n  for (const rawTopic of options.topics) {\n    const topicSlug = slugForTopic(rawTopic);\n    if (topicSlug.length === 0) continue;\n    whereClauses.push(\n      \"EXISTS (SELECT 1 FROM page_topics pt WHERE pt.page_slug = p.slug AND pt.topic_slug = ?)\",\n    );\n    params.push(topicSlug);\n  }\n\n  // --mentions: look for a file_refs row on this page that either\n  // matches exactly, OR is a containing folder (is_dir=1 and the query\n  // path starts with the row's path), OR the row itself lives inside\n  // the queried folder. See spec → \"Graph querying → Query examples\".\n  //\n  // We deliberately avoid GLOB on the RHS of the comparison with stored\n  // `r.path`, because stored paths can legitimately contain GLOB\n  // metacharacters — Next.js dynamic routes like `src/[id]/page.tsx`\n  // store a literal `[id]`, and `[abc]` is a SQL GLOB character class.\n  // Concatenating `r.path || '*'` into a GLOB pattern would make\n  // `src/[id]/page.tsx*` match `src/i/page.tsx` (spurious hit on the\n  // character class).\n  //\n  // Instead we enumerate the prefix folders in JS and use parameterized\n  // equality. For `src/checkout/handler.ts` the prefixes are\n  // `['src/', 'src/checkout/']`; any file_refs row with is_dir=1 and\n  // a path in that list is a containing folder of the queried file.\n  // This also lets SQLite use `idx_file_refs_path` as an equality\n  // probe rather than a range scan.\n  if (options.mentions !== undefined && options.mentions.length > 0) {\n    const isDir = looksLikeDir(options.mentions);\n    const norm = normalizePath(options.mentions, isDir);\n    if (isDir) {\n      // Query is a folder. Match: the exact folder, OR any file/sub-\n      // folder whose path starts with the folder prefix. The prefix\n      // match is the one place we still need GLOB — but we escape any\n      // wildcard metacharacters in `norm` first so a user-supplied\n      // `src/[id]/` query is treated as a literal. Note: the query\n      // path comes from the caller, not from stored data, but a user\n      // typing `--mentions src/[id]/` should get the literal folder,\n      // not a character class.\n      const escaped = escapeGlobMeta(norm);\n      whereClauses.push(\n        `EXISTS (\n           SELECT 1 FROM file_refs r\n           WHERE r.page_slug = p.slug\n             AND (r.path = ? OR r.path GLOB ?)\n         )`,\n      );\n      params.push(norm, `${escaped}*`);\n    } else {\n      // Query is a file. Match: the exact file, OR any folder whose\n      // path is a prefix of this file. Build the prefix list in JS and\n      // probe file_refs with equality — no GLOB on stored values.\n      const prefixes = parentFolderPrefixes(norm);\n      if (prefixes.length === 0) {\n        whereClauses.push(\n          `EXISTS (\n             SELECT 1 FROM file_refs r\n             WHERE r.page_slug = p.slug AND r.path = ?\n           )`,\n        );\n        params.push(norm);\n      } else {\n        const placeholders = prefixes.map(() => \"?\").join(\", \");\n        whereClauses.push(\n          `EXISTS (\n             SELECT 1 FROM file_refs r\n             WHERE r.page_slug = p.slug\n               AND (\n                 r.path = ?\n                 OR (r.is_dir = 1 AND r.path IN (${placeholders}))\n               )\n           )`,\n        );\n        params.push(norm, ...prefixes);\n      }\n    }\n  }\n\n  const now = Math.floor(Date.now() / 1000);\n\n  if (options.since !== undefined) {\n    const seconds = parseDuration(options.since);\n    whereClauses.push(\"p.updated_at >= ?\");\n    params.push(now - seconds);\n  }\n\n  if (options.stale !== undefined) {\n    const seconds = parseDuration(options.stale);\n    whereClauses.push(\"p.updated_at < ?\");\n    params.push(now - seconds);\n  }\n\n  if (options.orphan === true) {\n    whereClauses.push(\n      \"NOT EXISTS (SELECT 1 FROM page_topics pt WHERE pt.page_slug = p.slug)\",\n    );\n  }\n\n  // FTS5 text query. When a text query is supplied we JOIN against\n  // `fts_pages` so we can ORDER BY its `rank` column — lower (more\n  // negative) ranks are better matches. Without a query we skip the\n  // join entirely.\n  let sql: string;\n  if (options.query !== undefined && options.query.trim().length > 0) {\n    const ftsExpr = buildFtsQuery(options.query);\n    sql = `\n      SELECT p.slug, p.title, p.updated_at, p.archived_at, p.superseded_by\n      FROM pages p\n      JOIN fts_pages f ON f.slug = p.slug\n      WHERE fts_pages MATCH ?\n        ${whereClauses.length > 0 ? `AND ${whereClauses.join(\" AND \")}` : \"\"}\n      ORDER BY f.rank ASC, p.updated_at DESC, p.slug ASC\n    `;\n    // MATCH param goes first (it's the first `?` in the compiled SQL).\n    params.unshift(ftsExpr);\n  } else {\n    sql = buildSql(whereClauses);\n  }\n\n  const rows = db.prepare<unknown[], PageRow>(sql).all(...params);\n\n  // Attach topics in a second pass — simpler than a correlated\n  // `GROUP_CONCAT`, and the output rows are small enough that N+1 on a\n  // single prepared statement is fine.\n  const topicStmt = db.prepare<[string], { topic_slug: string }>(\n    \"SELECT topic_slug FROM page_topics WHERE page_slug = ? ORDER BY topic_slug\",\n  );\n  const out: SearchResult[] = rows.map((row) => ({\n    slug: row.slug,\n    title: row.title,\n    updated_at: row.updated_at,\n    archived_at: row.archived_at,\n    superseded_by: row.superseded_by,\n    topics: topicStmt.all(row.slug).map((t) => t.topic_slug),\n  }));\n\n  return out;\n}\n\nfunction buildSql(whereClauses: string[]): string {\n  const where =\n    whereClauses.length > 0 ? `WHERE ${whereClauses.join(\" AND \")}` : \"\";\n  return `\n    SELECT p.slug, p.title, p.updated_at, p.archived_at, p.superseded_by\n    FROM pages p\n    ${where}\n    ORDER BY p.updated_at DESC, p.slug ASC\n  `;\n}\n\n/**\n * Turn a user query into an FTS5 MATCH expression. FTS5's default\n * grammar gets unhappy with punctuation (hyphens, colons, slashes), so\n * we tokenize into alphanumeric runs and emit a conjunction of prefixed\n * tokens. Each token is suffixed with `*` so \"stri\" matches \"stripe\".\n *\n * Quoted input (`\"stripe webhook\"`) is treated as an FTS5 phrase query\n * — tokens must appear contiguously in that order. This matches shell\n * conventions where quoting something means \"match it literally\". We\n * strip the surrounding quotes, collapse inner punctuation to spaces,\n * and re-wrap in quotes for FTS5's phrase syntax. Any embedded `\"` in\n * the user input is dropped (FTS5 phrase syntax has no escape).\n *\n * Anything that tokenizes to empty (e.g. pure punctuation) falls back\n * to an empty MATCH, which yields no rows — which is the right answer.\n */\nfunction buildFtsQuery(raw: string): string {\n  const trimmed = raw.trim();\n  if (\n    trimmed.length >= 2 &&\n    trimmed.startsWith(\"\\\"\") &&\n    trimmed.endsWith(\"\\\"\")\n  ) {\n    // Phrase mode. Strip outer quotes, lowercase, collapse non-alnum\n    // runs to a single space, trim. Any surviving inner `\"` are\n    // removed since FTS5 phrase syntax has no escape mechanism.\n    const inner = trimmed\n      .slice(1, -1)\n      .toLowerCase()\n      .replace(/[^a-z0-9]+/g, \" \")\n      .trim();\n    if (inner.length === 0) return \"\\\"\\\"\";\n    return `\"${inner}\"`;\n  }\n  const tokens = trimmed\n    .toLowerCase()\n    .split(/[^a-z0-9]+/)\n    .filter((t) => t.length > 0);\n  if (tokens.length === 0) return \"\\\"\\\"\";\n  return tokens.map((t) => `${t}*`).join(\" AND \");\n}\n\nfunction slugForTopic(raw: string): string {\n  return raw\n    .toLowerCase()\n    .replace(/[^a-z0-9]+/g, \"-\")\n    .replace(/^-+|-+$/g, \"\");\n}\n\n/**\n * For a normalized file path like `src/checkout/handler.ts`, enumerate\n * every containing folder in the form those folders are stored (trailing\n * slash): `['src/', 'src/checkout/']`. Empty for paths with no folder\n * separator (e.g. `README.md`) — a top-level file has no parent folder\n * recorded in `file_refs`.\n *\n * Used by the `--mentions <file>` path to let us probe `file_refs` with\n * equality instead of GLOB, sidestepping wildcard-escape bugs entirely.\n */\nfunction parentFolderPrefixes(filePath: string): string[] {\n  const out: string[] = [];\n  let cursor = 0;\n  while (true) {\n    const next = filePath.indexOf(\"/\", cursor);\n    if (next === -1) break;\n    // Slice includes the slash — matches how directories are stored.\n    out.push(filePath.slice(0, next + 1));\n    cursor = next + 1;\n  }\n  return out;\n}\n\n/**\n * Escape SQLite GLOB metacharacters (`*`, `?`, `[`) by wrapping each in\n * a single-character class. SQLite GLOB has no backslash-escape, so the\n * idiomatic trick is `[*]` → literal `*`, `[?]` → literal `?`, `[[]` →\n * literal `[`. `]` doesn't need escaping outside a class.\n *\n * We only need this on the *query* side — stored paths aren't\n * concatenated into GLOB patterns anymore (see --mentions handling).\n * But a user-typed `--mentions src/[id]/` should still match a stored\n * `src/[id]/` literally, not as a character class over `i` or `d`.\n */\nfunction escapeGlobMeta(s: string): string {\n  return s.replace(/[\\*\\?\\[]/g, (ch) => `[${ch}]`);\n}\n\nfunction formatResults(\n  rows: SearchResult[],\n  options: SearchOptions,\n): string {\n  if (options.json === true) {\n    return `${JSON.stringify(rows, null, 2)}\\n`;\n  }\n  // Default output: one slug per line. Empty result = empty output (not\n  // \"no results found\") — makes piping into xargs / subsequent commands\n  // degrade gracefully.\n  if (rows.length === 0) return \"\";\n  return `${rows.map((r) => r.slug).join(\"\\n\")}\\n`;\n}\n\nfunction buildStderr(rows: SearchResult[], options: SearchOptions): string {\n  // Spec: \"print warns if >50 when not --json\". The warning goes to\n  // stderr so it doesn't corrupt pipelines that filter stdout.\n  if (options.json === true) return \"\";\n  if (options.limit !== undefined) return \"\";\n  if (rows.length > 50) {\n    return `almanac: ${rows.length} results — consider --limit or a narrower query\\n`;\n  }\n  return \"\";\n}\n","import { readFile } from \"node:fs/promises\";\nimport { join } from \"node:path\";\n\nimport { ensureFreshIndex } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\n\nexport interface ShowOptions {\n  cwd: string;\n  slug?: string;\n  stdin?: boolean;\n  stdinInput?: string; // injected by the CLI when --stdin is set; tests can pass directly\n  wiki?: string;\n}\n\nexport interface ShowCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * `almanac show <slug>` — cat the markdown file for a page.\n *\n * This is the one command that is allowed to read page file contents;\n * everything else operates on the index (per the spec's design\n * principles).\n *\n * Output shapes:\n *   - positional slug → raw markdown on stdout, unchanged (the cat case)\n *   - `--stdin`       → JSON Lines: one `{slug, content}` object per\n *                       successfully-read page, terminated by `\\n`. JSON\n *                       Lines is parseable, unlike the old `\\n---\\n`\n *                       separator which collided with YAML frontmatter\n *                       delimiters in the page bodies themselves.\n *\n * Unresolvable slugs go to stderr with a non-zero exit; we still print\n * whatever we could resolve on stdout so bulk runs don't have to fail\n * atomically.\n */\nexport async function runShow(\n  options: ShowOptions,\n): Promise<ShowCommandOutput> {\n  const repoRoot = await resolveWikiRoot({\n    cwd: options.cwd,\n    wiki: options.wiki,\n  });\n  await ensureFreshIndex({ repoRoot });\n\n  const dbPath = join(repoRoot, \".almanac\", \"index.db\");\n  const db = openIndex(dbPath);\n\n  try {\n    const slugs = collectSlugs(options);\n    if (slugs.length === 0) {\n      return {\n        stdout: \"\",\n        stderr: \"almanac: show requires a slug (or --stdin)\\n\",\n        exitCode: 1,\n      };\n    }\n\n    const stmt = db.prepare<[string], { file_path: string }>(\n      \"SELECT file_path FROM pages WHERE slug = ?\",\n    );\n\n    const records: Array<{ slug: string; content: string }> = [];\n    const missing: string[] = [];\n    for (const slug of slugs) {\n      const row = stmt.get(slug);\n      if (row === undefined) {\n        missing.push(slug);\n        continue;\n      }\n      try {\n        records.push({ slug, content: await readFile(row.file_path, \"utf8\") });\n      } catch (err: unknown) {\n        const message = err instanceof Error ? err.message : String(err);\n        missing.push(`${slug} (${message})`);\n      }\n    }\n\n    const bulk = options.stdin === true;\n    let stdout: string;\n    if (bulk) {\n      // JSON Lines: one object per line, trailing newline on the last.\n      // Consumers can split on `\\n` and `JSON.parse` each line.\n      stdout = records\n        .map((r) => JSON.stringify(r))\n        .join(\"\\n\");\n      if (stdout.length > 0) stdout += \"\\n\";\n    } else {\n      // Positional single-slug: just emit the raw markdown. No\n      // separator, no wrapping — this is the \"cat\" case.\n      stdout = records.map((r) => r.content).join(\"\");\n    }\n    const stderr = missing\n      .map((s) => `almanac: no such page \"${s}\"\\n`)\n      .join(\"\");\n    return {\n      stdout,\n      stderr,\n      exitCode: missing.length > 0 ? 1 : 0,\n    };\n  } finally {\n    db.close();\n  }\n}\n\nfunction collectSlugs(options: ShowOptions): string[] {\n  if (options.stdin === true && options.stdinInput !== undefined) {\n    return options.stdinInput\n      .split(/\\r?\\n/)\n      .map((s) => s.trim())\n      .filter((s) => s.length > 0);\n  }\n  if (options.slug !== undefined && options.slug.length > 0) {\n    return [options.slug];\n  }\n  return [];\n}\n","import { readFile, rename, writeFile } from \"node:fs/promises\";\n\nimport yaml from \"js-yaml\";\n\n/**\n * Rewrite the `topics:` field in a markdown file's YAML frontmatter.\n *\n * The absolute requirement is **body byte-preservation**. Tag/untag/\n * rename commands touch only the frontmatter; everything after the\n * closing `---` must be byte-identical to the input (same line endings,\n * same trailing whitespace, same final-newline-or-not). We lean on a\n * precise split rather than re-serializing the whole file so any\n * incidental bytes in the body (literal `\\r\\n`, unusual trailing\n * whitespace, triple-hyphen rulers) are left alone.\n *\n * For the frontmatter itself we do a **surgical rewrite of the `topics:`\n * field only** — not a full YAML roundtrip. Reasons:\n *   - `js-yaml` normalizes quoting, re-orders keys alphabetically by\n *     default, and can drop comments. Any of those would surprise a user\n *     who hand-edited their own frontmatter and expects their formatting\n *     preserved byte-for-byte.\n *   - We only care about one field. Replacing just that field lets the\n *     rest of the YAML survive verbatim.\n *\n * The strategy:\n *   1. Find the exact span of the `topics:` key (whether flow\n *      `topics: [a, b]` or block `topics:\\n  - a\\n  - b\\n`) using a\n *      small line scanner.\n *   2. Compute the new topics list from the caller's transform.\n *   3. Replace the span with a freshly-emitted `topics: [a, b, c]` line\n *      (flow style — compact, readable, and what most authors write).\n *   4. If no `topics:` key exists and the new list is non-empty, append\n *      a line to the end of the frontmatter block.\n *   5. If `topics:` exists but the new list is empty, drop the line\n *      entirely rather than leaving `topics: []` around.\n *\n * The transform function gets the current deduplicated topic list and\n * returns the new list. Returning an empty array means \"remove the\n * `topics:` key entirely\".\n */\n\nexport interface RewriteResult {\n  /** The page's topics before the rewrite (possibly empty). */\n  before: string[];\n  /** The page's topics after the rewrite (possibly empty). */\n  after: string[];\n  /** True iff the file content actually changed. */\n  changed: boolean;\n}\n\n/**\n * Read `filePath`, compute the new topics via `transform`, and\n * atomically rewrite if the result differs.\n *\n * Atomic per file: write to `<path>.tmp` then rename, same pattern as\n * the registry and topics.yaml writers. A half-written page would\n * corrupt committed user content, so this is non-negotiable.\n */\nexport async function rewritePageTopics(\n  filePath: string,\n  transform: (current: string[]) => string[],\n): Promise<RewriteResult> {\n  const raw = await readFile(filePath, \"utf8\");\n  const { before, after, output, changed } = applyTopicsTransform(\n    raw,\n    transform,\n  );\n  if (changed) {\n    const tmp = `${filePath}.tmp`;\n    await writeFile(tmp, output, \"utf8\");\n    await rename(tmp, filePath);\n  }\n  return { before, after, changed };\n}\n\ninterface TransformApplied {\n  before: string[];\n  after: string[];\n  output: string;\n  changed: boolean;\n}\n\n/**\n * Pure-string version of `rewritePageTopics`. Useful for tests and for\n * the few places (rename, delete) where we loop many files and want to\n * short-circuit no-op writes cheaply.\n */\nexport function applyTopicsTransform(\n  raw: string,\n  transform: (current: string[]) => string[],\n): TransformApplied {\n  const parsed = splitFrontmatter(raw);\n  if (parsed === null) {\n    // No frontmatter at all. Tagging a topic on such a page means\n    // creating a frontmatter block. We keep the body untouched and\n    // prepend `---\\ntopics: [...]\\n---\\n\\n`. If the transform yields\n    // an empty list, this is a no-op. Line endings: default to LF for a\n    // brand-new frontmatter — we can't infer intent from a file that\n    // doesn't have frontmatter yet, and LF is the committed default in\n    // most modern repos.\n    const next = dedupeSlugs(transform([]));\n    if (next.length === 0) {\n      return { before: [], after: [], output: raw, changed: false };\n    }\n    const fm = `---\\ntopics: ${flowList(next)}\\n---\\n\\n`;\n    return {\n      before: [],\n      after: next,\n      output: `${fm}${raw}`,\n      changed: true,\n    };\n  }\n\n  const { opener, fmLines, closer, body, eol } = parsed;\n  const { before, existingRange } = readTopicsFromLines(fmLines);\n  const beforeDeduped = dedupeSlugs(before);\n  const after = dedupeSlugs(transform(beforeDeduped));\n\n  if (arraysEqual(beforeDeduped, after)) {\n    return { before: beforeDeduped, after, output: raw, changed: false };\n  }\n\n  let nextFmLines: string[];\n  if (existingRange === null) {\n    // No `topics:` key currently present. Add one (only if non-empty).\n    if (after.length === 0) {\n      return { before: beforeDeduped, after, output: raw, changed: false };\n    }\n    nextFmLines = [...fmLines, `topics: ${flowList(after)}`];\n  } else {\n    const replacement =\n      after.length === 0 ? null : `topics: ${flowList(after)}`;\n    // Interleaved comments/blank lines from a block-style list are\n    // re-emitted BELOW the new flow-style `topics:` line so the\n    // author's commentary sticks around. Flow/scalar inputs produce an\n    // empty `preserved` array, so this collapses to the old behavior\n    // for the common case. When we fully delete the key (empty after)\n    // the preserved lines go too — without a `topics:` key to anchor\n    // them to, trailing \"# below the topics list\" comments become\n    // orphans that no longer mean what they said.\n    const preservedTail =\n      replacement === null ? [] : existingRange.preserved;\n    nextFmLines = [\n      ...fmLines.slice(0, existingRange.start),\n      ...(replacement === null ? [] : [replacement]),\n      ...preservedTail,\n      ...fmLines.slice(existingRange.end),\n    ];\n  }\n\n  // Rejoin with the same line ending the input frontmatter used so a\n  // CRLF-authored file comes out CRLF end-to-end. `splitFrontmatter`\n  // sniffed the dominant separator for us.\n  const fmBlock =\n    nextFmLines.length === 0 ? \"\" : `${nextFmLines.join(eol)}${eol}`;\n  const output = `${opener}${fmBlock}${closer}${body}`;\n  return {\n    before: beforeDeduped,\n    after,\n    output,\n    changed: true,\n  };\n}\n\ninterface SplitFrontmatter {\n  /** The opening `---\\n` or `---\\r\\n`. */\n  opener: string;\n  /** Frontmatter lines (no line-ending character included). */\n  fmLines: string[];\n  /** The closing `---\\n` (or `---\\r\\n`, possibly without trailing newline if EOF). */\n  closer: string;\n  /** Everything after the closing fence, byte-for-byte. */\n  body: string;\n  /**\n   * Dominant line ending inside the frontmatter block. CRLF-authored\n   * files stay CRLF on write; LF stays LF. We sniff once at split time\n   * so rewriting doesn't have to re-inspect every line.\n   */\n  eol: \"\\n\" | \"\\r\\n\";\n}\n\n/**\n * Split a file into (opener, frontmatter lines, closer, body). The\n * regex mirrors `parseFrontmatter` in `indexer/frontmatter.ts` so the\n * indexer and the rewriter agree on what \"has frontmatter\" means.\n *\n * Returns `null` when the file doesn't start with a `---` fence or\n * lacks a matching closer — both cases are legal (a page with only\n * body content) and the caller treats them as \"no frontmatter to\n * rewrite\".\n */\nfunction splitFrontmatter(raw: string): SplitFrontmatter | null {\n  if (!raw.startsWith(\"---\")) return null;\n  // Match the exact opener (with its line ending) so we can preserve\n  // it byte-for-byte.\n  const openerMatch = raw.match(/^---(\\r?\\n)/);\n  if (openerMatch === null) return null;\n  const opener = `---${openerMatch[1] ?? \"\\n\"}`;\n  const rest = raw.slice(opener.length);\n  // Find the closing `---` that begins at the start of a line. We\n  // also handle the edge case where the closer sits at position 0 of\n  // `rest` (frontmatter was empty).\n  let fenceIdx: number;\n  if (rest.startsWith(\"---\")) {\n    fenceIdx = 0;\n  } else {\n    const m = rest.match(/\\r?\\n---(\\r?\\n|$)/);\n    if (m === null || m.index === undefined) return null;\n    // `m.index` points at the `\\r?\\n` before `---`; skip that newline\n    // so fenceIdx lands exactly on the `-`.\n    const leadingNewlineLen = (m[0] ?? \"\").startsWith(\"\\r\\n\") ? 2 : 1;\n    fenceIdx = m.index + leadingNewlineLen;\n  }\n  const fmBlock = rest.slice(0, fenceIdx);\n  // Determine the closer's full span, including its trailing newline if any.\n  const afterDashes = rest.slice(fenceIdx + 3);\n  let closerTail = \"\";\n  if (afterDashes.startsWith(\"\\r\\n\")) {\n    closerTail = \"\\r\\n\";\n  } else if (afterDashes.startsWith(\"\\n\")) {\n    closerTail = \"\\n\";\n  }\n  const closer = `---${closerTail}`;\n  const body = afterDashes.slice(closerTail.length);\n  const fmLines =\n    fmBlock.length === 0 ? [] : fmBlock.replace(/\\r?\\n$/, \"\").split(/\\r?\\n/);\n  // Sniff the frontmatter's dominant line ending. We look at the\n  // opener first (most reliable signal — it's always present and\n  // always has an ending). Fall back to checking the fmBlock for any\n  // `\\r\\n` runs so a frontmatter with a single-line opener and\n  // multi-line body still gets classified right.\n  const eol: \"\\n\" | \"\\r\\n\" =\n    opener.endsWith(\"\\r\\n\") || /\\r\\n/.test(fmBlock) ? \"\\r\\n\" : \"\\n\";\n  return { opener, fmLines, closer, body, eol };\n}\n\ninterface ExistingRange {\n  /** Index in `fmLines` of the `topics:` key line (inclusive). */\n  start: number;\n  /** Index in `fmLines` one past the last line belonging to this key. */\n  end: number;\n  /**\n   * Lines inside `[start+1, end)` that aren't `- entry` lines — i.e.\n   * interleaved comments and blank lines a user wrote between entries.\n   * We preserve these verbatim when rewriting block-style lists to\n   * flow; otherwise a `tag` on a commented list would silently drop\n   * the commentary. Empty for flow/scalar shapes.\n   */\n  preserved: string[];\n}\n\n/**\n * Find `topics:` in a frontmatter-lines array and read the values.\n *\n * Handles three YAML shapes authors commonly write:\n *   - `topics: [a, b, c]`       (flow sequence, one line)\n *   - `topics:` followed by block entries like `  - a` (block sequence)\n *   - `topics: a` (a single scalar — treated as one element)\n *\n * Also handles the empty case `topics:` with nothing after it, and the\n * \"no topics key\" case (returns `existingRange: null`).\n *\n * This is NOT a general YAML parser — it's intentionally scoped to the\n * one key we mutate, because using `js-yaml` for a round-trip would\n * lose comments and re-quote strings the user picked a specific way.\n */\nfunction readTopicsFromLines(fmLines: string[]): {\n  before: string[];\n  existingRange: ExistingRange | null;\n} {\n  const keyLineIdx = findTopKey(fmLines, \"topics\");\n  if (keyLineIdx === -1) {\n    return { before: [], existingRange: null };\n  }\n  const keyLine = fmLines[keyLineIdx] ?? \"\";\n  const colonIdx = keyLine.indexOf(\":\");\n  // Everything to the right of the first colon, trimmed.\n  const after = keyLine.slice(colonIdx + 1).trim();\n  // Strip trailing `# ...` line-comment from a flow value so we don't\n  // parse comments as list contents. (A block list's sub-items have\n  // their own comments stripped in the block branch below.)\n  const afterNoComment = stripTrailingComment(after);\n\n  if (afterNoComment.length === 0) {\n    // Block sequence style: collect subsequent `- item` lines. Between\n    // entries a user may have written:\n    //   - interleaved `# comment` lines\n    //   - blank lines\n    // We must NOT break the scan on those — doing so would drop every\n    // entry after the first comment/blank when we rewrite (silent data\n    // loss: the original bug that triggered this fix). We skip them in\n    // the scan and stash them in `preserved` so the replacement step\n    // can re-emit them verbatim BETWEEN the new flow-style line and\n    // the rest of the frontmatter.\n    //\n    // Edge: comments/blanks that appear BEFORE the first `- entry` or\n    // AFTER the last `- entry` count as part of the block too — pulling\n    // them out keeps the author's commentary near the list it belongs\n    // to. We cap the scan when we hit a real non-entry line (e.g. the\n    // next top-level key), leaving everything from that line onward\n    // outside the range.\n    const values: string[] = [];\n    const preserved: string[] = [];\n    // Provisional scan cursor. `endIdx` only advances when we've seen\n    // something we're sure belongs to this block (an entry line), so\n    // trailing whitespace/comments that don't precede another entry\n    // stay OUTSIDE the range and aren't shuffled on rewrite.\n    let i = keyLineIdx + 1;\n    let endIdx = i;\n    // `pendingNonEntries` holds comments/blanks we've seen since the\n    // last confirmed entry. They're committed to `preserved` only\n    // when a subsequent `- entry` proves they live mid-list.\n    let pendingNonEntries: string[] = [];\n    while (i < fmLines.length) {\n      const line = fmLines[i] ?? \"\";\n      const trimmed = line.trim();\n      if (trimmed.length === 0 || trimmed.startsWith(\"#\")) {\n        pendingNonEntries.push(line);\n        i += 1;\n        continue;\n      }\n      const m = line.match(/^\\s*-\\s+(.*)$/);\n      if (m === null) break;\n      // Promote any pending comments/blanks — they're between entries\n      // (or before the first entry within the block).\n      if (pendingNonEntries.length > 0) {\n        preserved.push(...pendingNonEntries);\n        pendingNonEntries = [];\n      }\n      const raw = stripTrailingComment((m[1] ?? \"\").trim());\n      const parsed = parseScalar(raw);\n      if (parsed.length > 0) values.push(parsed);\n      i += 1;\n      endIdx = i;\n    }\n    return {\n      before: values,\n      existingRange: { start: keyLineIdx, end: endIdx, preserved },\n    };\n  }\n\n  // Flow / scalar shape on one line. Let js-yaml handle the value-parsing\n  // (quoting, escapes, etc.) for the RHS only.\n  let parsed: unknown;\n  try {\n    parsed = yaml.load(afterNoComment);\n  } catch {\n    parsed = null;\n  }\n  const values: string[] = [];\n  if (Array.isArray(parsed)) {\n    for (const v of parsed) {\n      if (typeof v === \"string\" && v.trim().length > 0) {\n        values.push(v.trim());\n      }\n    }\n  } else if (typeof parsed === \"string\" && parsed.trim().length > 0) {\n    values.push(parsed.trim());\n  }\n  return {\n    before: values,\n    existingRange: { start: keyLineIdx, end: keyLineIdx + 1, preserved: [] },\n  };\n}\n\n/**\n * Find a top-level key line. \"Top-level\" means no leading whitespace —\n * we don't walk into nested mappings. The indexer's frontmatter parser\n * only reads top-level keys too, so this matches.\n */\nfunction findTopKey(fmLines: string[], key: string): number {\n  const re = new RegExp(`^${escapeRegex(key)}\\\\s*:`);\n  for (let i = 0; i < fmLines.length; i += 1) {\n    if (re.test(fmLines[i] ?? \"\")) return i;\n  }\n  return -1;\n}\n\nfunction escapeRegex(s: string): string {\n  return s.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n}\n\nfunction stripTrailingComment(s: string): string {\n  // Only strip `#` outside of quotes. For the shapes we handle —\n  // slug-like kebab-case topics — quoted strings with `#` are rare, but\n  // be defensive.\n  let inSingle = false;\n  let inDouble = false;\n  for (let i = 0; i < s.length; i += 1) {\n    const ch = s[i];\n    if (ch === \"'\" && !inDouble) inSingle = !inSingle;\n    else if (ch === '\"' && !inSingle) inDouble = !inDouble;\n    else if (ch === \"#\" && !inSingle && !inDouble) {\n      return s.slice(0, i).trimEnd();\n    }\n  }\n  return s;\n}\n\n/**\n * Strip YAML quoting from a scalar. Block-sequence items might be\n * written as `- 'foo'` or `- \"foo\"` or bare `- foo`; we accept all\n * three and return the plain string.\n */\nfunction parseScalar(s: string): string {\n  if (s.length === 0) return s;\n  if (s.length >= 2 && s[0] === '\"' && s[s.length - 1] === '\"') {\n    return s.slice(1, -1);\n  }\n  if (s.length >= 2 && s[0] === \"'\" && s[s.length - 1] === \"'\") {\n    return s.slice(1, -1);\n  }\n  return s;\n}\n\n/**\n * Emit a flow-style YAML sequence like `[auth, jwt, security]`. We use\n * flow because it's the shape most authors write by hand and stays on\n * one line, which keeps diffs tight. Values are quoted only when\n * necessary — plain kebab-case slugs never need quoting.\n */\nfunction flowList(items: string[]): string {\n  return `[${items.map((t) => formatScalar(t)).join(\", \")}]`;\n}\n\nfunction formatScalar(s: string): string {\n  // If it's a bare kebab/alnum slug, no quotes. Otherwise fall back to\n  // js-yaml for correct escaping. We check against a conservative\n  // pattern — anything outside it gets YAML-quoted.\n  if (/^[a-z0-9][a-z0-9-]*$/.test(s)) return s;\n  return yaml\n    .dump(s, { flowLevel: 0, lineWidth: Number.MAX_SAFE_INTEGER })\n    .trimEnd();\n}\n\nfunction dedupeSlugs(list: string[]): string[] {\n  const seen = new Set<string>();\n  const out: string[] = [];\n  for (const raw of list) {\n    const s = raw.trim();\n    if (s.length === 0) continue;\n    if (seen.has(s)) continue;\n    seen.add(s);\n    out.push(s);\n  }\n  return out;\n}\n\nfunction arraysEqual(a: string[], b: string[]): boolean {\n  if (a.length !== b.length) return false;\n  for (let i = 0; i < a.length; i += 1) {\n    if (a[i] !== b[i]) return false;\n  }\n  return true;\n}\n","import { join } from \"node:path\";\n\n/**\n * `.almanac/topics.yaml` inside a given repo root. Single helper so no\n * caller has to remember where the file lives.\n */\nexport function topicsYamlPath(repoRoot: string): string {\n  return join(repoRoot, \".almanac\", \"topics.yaml\");\n}\n\n/**\n * `.almanac/index.db` inside a given repo root. Mirrors `topicsYamlPath`\n * so the topics commands don't have to import from scattered places.\n */\nexport function indexDbPath(repoRoot: string): string {\n  return join(repoRoot, \".almanac\", \"index.db\");\n}\n","import { ensureFreshIndex, runIndexer } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\nimport { toKebabCase } from \"../slug.js\";\nimport { rewritePageTopics } from \"../topics/frontmatterRewrite.js\";\nimport { indexDbPath, topicsYamlPath } from \"../topics/paths.js\";\nimport {\n  ensureTopic,\n  loadTopicsFile,\n  writeTopicsFile,\n} from \"../topics/yaml.js\";\n\n/**\n * `almanac tag <page> <topic>...` and `almanac untag <page> <topic>`.\n *\n * These are the page-side of the topics system — `topics ...` manages\n * the DAG and metadata; `tag`/`untag` wires concrete pages into\n * topics. Both commands mutate page frontmatter atomically per file\n * and leave body bytes untouched.\n *\n * Auto-creation policy: if a topic passed to `tag` doesn't yet exist\n * in `topics.yaml`, we create a minimal entry for it (title-cased\n * title, no description, no parents). This matches the spec: \"Ensure\n * topic exists in topics.yaml; if not, create a minimal entry.\" We\n * don't silently create topics on `untag` — you can only untag\n * something that was already a topic.\n */\n\nexport interface TagCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\nexport interface TagOptions {\n  cwd: string;\n  wiki?: string;\n  page?: string;\n  topics: string[];\n  stdin?: boolean;\n  stdinInput?: string;\n}\n\nexport interface UntagOptions {\n  cwd: string;\n  wiki?: string;\n  page: string;\n  topic: string;\n}\n\nexport async function runTag(options: TagOptions): Promise<TagCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n\n  const topics = options.topics\n    .map((t) => toKebabCase(t))\n    .filter((t) => t.length > 0);\n  if (topics.length === 0) {\n    return {\n      stdout: \"\",\n      stderr: \"almanac: tag requires at least one topic\\n\",\n      exitCode: 1,\n    };\n  }\n\n  // Bulk mode reads slugs from stdin; single mode uses the positional.\n  const pages: string[] = [];\n  if (options.stdin === true) {\n    if (options.stdinInput === undefined) {\n      return {\n        stdout: \"\",\n        stderr: \"almanac: tag --stdin called without stdin input\\n\",\n        exitCode: 1,\n      };\n    }\n    for (const line of options.stdinInput.split(/\\r?\\n/)) {\n      const s = line.trim();\n      if (s.length > 0) pages.push(s);\n    }\n  } else if (options.page !== undefined && options.page.length > 0) {\n    pages.push(options.page);\n  } else {\n    return {\n      stdout: \"\",\n      stderr: \"almanac: tag requires a page slug (or --stdin)\\n\",\n      exitCode: 1,\n    };\n  }\n\n  // Resolve slugs to file paths from the DB. A stale index is fine for\n  // `tag` — we just need to find each page's file; `ensureFreshIndex`\n  // runs first so the common path is consistent.\n  await ensureFreshIndex({ repoRoot });\n  const db = openIndex(indexDbPath(repoRoot));\n\n  // Validate every requested page exists BEFORE touching topics.yaml.\n  // Previously we auto-created topics first, which meant\n  // `almanac tag does-not-exist brand-new` left `brand-new` in\n  // topics.yaml as a state leak even though the tag itself errored. We\n  // resolve rows up front, then short-circuit with an error (and no\n  // mutations) if none of the pages are valid.\n  const stmt = db.prepare<[string], { file_path: string }>(\n    \"SELECT file_path FROM pages WHERE slug = ?\",\n  );\n  const resolved: { page: string; filePath: string }[] = [];\n  const missing: string[] = [];\n  try {\n    for (const page of pages) {\n      const row = stmt.get(toKebabCase(page));\n      if (row === undefined) {\n        missing.push(page);\n      } else {\n        resolved.push({ page, filePath: row.file_path });\n      }\n    }\n  } finally {\n    db.close();\n  }\n\n  // Hard-fail when NO page resolved. We deliberately don't mutate\n  // topics.yaml on this path — the user's intent (tag page X) is\n  // inarguably unsatisfiable, so we shouldn't leave breadcrumbs.\n  //\n  // In bulk mode (`--stdin`) some pages might resolve and others\n  // won't; keeping the original partial-progress behavior for that case\n  // (topics get created, resolved pages get tagged, `missing` are\n  // reported on stderr with exitCode 1). The state leak only matters\n  // when NOTHING succeeds, and that's the case we're fixing.\n  if (resolved.length === 0) {\n    const stderr = missing.map((p) => `almanac: no such page \"${p}\"\\n`).join(\"\");\n    return {\n      stdout: \"\",\n      stderr,\n      exitCode: 1,\n    };\n  }\n\n  // Auto-create missing topics in topics.yaml. Safe to do now — we have\n  // at least one page that will actually end up tagged with them.\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n  let fileChanged = false;\n  for (const t of topics) {\n    // ensureTopic mutates the file; we check presence beforehand so\n    // we only write when something actually changes (skip a redundant\n    // atomic rewrite + mtime bump).\n    const before = file.topics.length;\n    ensureTopic(file, t);\n    if (file.topics.length > before) fileChanged = true;\n  }\n  if (fileChanged) {\n    await writeTopicsFile(yamlPath, file);\n  }\n\n  const summary: string[] = [];\n  let taggedPages = 0;\n  for (const { page, filePath } of resolved) {\n    const result = await rewritePageTopics(filePath, (current) => {\n      // Preserve existing order; append new topics in the order\n      // the caller supplied them. `applyTopicsTransform` will\n      // dedupe for us, but we skip redundant work here too.\n      const out = [...current];\n      for (const t of topics) if (!current.includes(t)) out.push(t);\n      return out;\n    });\n    if (result.changed) {\n      taggedPages += 1;\n      // Only surface the NEWLY ADDED topics — not the full request.\n      // Reporting every requested topic (including ones the page\n      // already had) reads like false positives in commit diffs.\n      const added = result.after.filter((t) => !result.before.includes(t));\n      summary.push(`tagged ${page}: ${added.join(\", \")}`);\n    } else {\n      summary.push(\n        `no change ${page} (already tagged with ${topics.join(\", \")})`,\n      );\n    }\n  }\n\n  if (taggedPages > 0 || fileChanged) {\n    // Trigger a reindex so downstream queries see the new rows\n    // immediately. Writes to page files bumped their mtimes; writes to\n    // topics.yaml are caught by `topicsYamlNewerThan`.\n    await runIndexer({ repoRoot });\n  }\n\n  const stderr = missing.map((p) => `almanac: no such page \"${p}\"\\n`).join(\"\");\n  return {\n    stdout: summary.length > 0 ? `${summary.join(\"\\n\")}\\n` : \"\",\n    stderr,\n    exitCode: missing.length > 0 ? 1 : 0,\n  };\n}\n\nexport async function runUntag(\n  options: UntagOptions,\n): Promise<TagCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  const page = toKebabCase(options.page);\n  const topic = toKebabCase(options.topic);\n  if (page.length === 0) {\n    return {\n      stdout: \"\",\n      stderr: \"almanac: untag requires a page slug\\n\",\n      exitCode: 1,\n    };\n  }\n  if (topic.length === 0) {\n    return {\n      stdout: \"\",\n      stderr: \"almanac: untag requires a topic\\n\",\n      exitCode: 1,\n    };\n  }\n\n  await ensureFreshIndex({ repoRoot });\n  const db = openIndex(indexDbPath(repoRoot));\n  let filePath: string;\n  try {\n    const row = db\n      .prepare<[string], { file_path: string }>(\n        \"SELECT file_path FROM pages WHERE slug = ?\",\n      )\n      .get(page);\n    if (row === undefined) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: no such page \"${page}\"\\n`,\n        exitCode: 1,\n      };\n    }\n    filePath = row.file_path;\n  } finally {\n    db.close();\n  }\n\n  const result = await rewritePageTopics(filePath, (current) =>\n    current.filter((t) => t !== topic),\n  );\n  if (result.changed) {\n    await runIndexer({ repoRoot });\n  }\n\n  return {\n    stdout: result.changed\n      ? `untagged ${page}: ${topic}\\n`\n      : `no change ${page} (not tagged with ${topic})\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n","import { readFile } from \"node:fs/promises\";\nimport { join } from \"node:path\";\n\nimport fg from \"fast-glob\";\nimport type Database from \"better-sqlite3\";\n\nimport { ensureFreshIndex, runIndexer } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolveWiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\nimport { toKebabCase } from \"../slug.js\";\nimport { ancestorsInFile, descendantsInDb } from \"../topics/dag.js\";\nimport {\n  applyTopicsTransform,\n  rewritePageTopics,\n} from \"../topics/frontmatterRewrite.js\";\nimport { indexDbPath, topicsYamlPath } from \"../topics/paths.js\";\nimport {\n  ensureTopic,\n  findTopic,\n  loadTopicsFile,\n  titleCase,\n  writeTopicsFile,\n  type TopicEntry,\n  type TopicsFile,\n} from \"../topics/yaml.js\";\n\n/**\n * All `almanac topics <verb>` logic lives here. The CLI dispatches on\n * `verb` and forwards positionals/flags. One module per top-level\n * command group matches the pattern used by `search`, `info`, etc.\n *\n * Design notes:\n *   - The module is stateless; every entry function takes a `cwd` and\n *     optional `wiki` and is safe to call many times in a test suite.\n *   - Mutations go file → DB: write `.almanac/topics.yaml` atomically,\n *     then trigger a reindex so the DB reflects the new state by the\n *     time the command prints its summary. Reads run after a cheap\n *     `ensureFreshIndex` so they always see the latest committed data.\n *   - The command functions return a `TopicsCommandOutput`; the CLI\n *     layer in `cli.ts` decides how to print. This mirrors the shape of\n *     `runSearch`, `runInfo`, and friends.\n */\n\nexport interface TopicsCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\nexport interface TopicsBaseOptions {\n  cwd: string;\n  wiki?: string;\n  json?: boolean;\n}\n\nexport interface TopicsListOptions extends TopicsBaseOptions {}\n\nexport interface TopicsShowOptions extends TopicsBaseOptions {\n  slug: string;\n  descendants?: boolean;\n}\n\nexport interface TopicsCreateOptions extends TopicsBaseOptions {\n  name: string;\n  parents?: string[];\n}\n\nexport interface TopicsLinkOptions extends TopicsBaseOptions {\n  child: string;\n  parent: string;\n}\n\nexport interface TopicsUnlinkOptions extends TopicsLinkOptions {}\n\nexport interface TopicsRenameOptions extends TopicsBaseOptions {\n  oldSlug: string;\n  newSlug: string;\n}\n\nexport interface TopicsDeleteOptions extends TopicsBaseOptions {\n  slug: string;\n}\n\nexport interface TopicsDescribeOptions extends TopicsBaseOptions {\n  slug: string;\n  description: string;\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// list — `almanac topics`\n// ─────────────────────────────────────────────────────────────────────\n\n/**\n * `almanac topics` (and `almanac topics list`). Prints one line per\n * known topic — from the DB, which already unions topics.yaml with any\n * ad-hoc slugs found in page frontmatter. Page counts come straight\n * from `page_topics`, which the indexer rebuilt on entry.\n */\nexport async function runTopicsList(\n  options: TopicsListOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  await ensureFreshIndex({ repoRoot });\n\n  const db = openIndex(indexDbPath(repoRoot));\n  try {\n    const rows = db\n      .prepare<\n        [],\n        { slug: string; title: string | null; description: string | null; page_count: number }\n      >(\n        // page_count excludes archived pages — matches the policy used\n        // by `topics show` (see `pagesDirectlyTagged`) and by every\n        // page-scoped check in `health`. Pick one rule and apply it\n        // everywhere; a topic with \"5 pages\" in `topics list` and \"3\n        // pages\" in `topics show` is a trust-eroding inconsistency.\n        `SELECT t.slug, t.title, t.description,\n                (SELECT COUNT(*)\n                   FROM page_topics pt\n                   JOIN pages p ON p.slug = pt.page_slug\n                   WHERE pt.topic_slug = t.slug AND p.archived_at IS NULL\n                ) AS page_count\n         FROM topics t\n         ORDER BY t.slug`,\n      )\n      .all();\n\n    if (options.json === true) {\n      return {\n        stdout: `${JSON.stringify(rows, null, 2)}\\n`,\n        stderr: \"\",\n        exitCode: 0,\n      };\n    }\n\n    if (rows.length === 0) {\n      return {\n        stdout:\n          \"no topics. create one with `almanac topics create <name>` or tag a page.\\n\",\n        stderr: \"\",\n        exitCode: 0,\n      };\n    }\n\n    const slugWidth = rows.reduce((w, r) => Math.max(w, r.slug.length), 0);\n    const lines = rows.map((r) => {\n      const slug = r.slug.padEnd(slugWidth);\n      const count = `(${r.page_count} page${r.page_count === 1 ? \"\" : \"s\"})`;\n      return `${slug}  ${count}`;\n    });\n    return { stdout: `${lines.join(\"\\n\")}\\n`, stderr: \"\", exitCode: 0 };\n  } finally {\n    db.close();\n  }\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// show — `almanac topics show <slug>`\n// ─────────────────────────────────────────────────────────────────────\n\nexport interface TopicsShowRecord {\n  slug: string;\n  title: string | null;\n  description: string | null;\n  parents: string[];\n  children: string[];\n  pages: string[];\n  descendants_used?: boolean;\n}\n\n/**\n * `almanac topics show <slug>`. Prints metadata + parents, children,\n * and the page list. `--descendants` widens the page list to include\n * pages tagged with any descendant topic (via the DAG).\n */\nexport async function runTopicsShow(\n  options: TopicsShowOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  await ensureFreshIndex({ repoRoot });\n\n  const slug = toKebabCase(options.slug);\n  if (slug.length === 0) {\n    return {\n      stdout: \"\",\n      stderr: `almanac: empty topic slug\\n`,\n      exitCode: 1,\n    };\n  }\n\n  const db = openIndex(indexDbPath(repoRoot));\n  try {\n    const row = db\n      .prepare<\n        [string],\n        { slug: string; title: string | null; description: string | null }\n      >(\"SELECT slug, title, description FROM topics WHERE slug = ?\")\n      .get(slug);\n    if (row === undefined) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: no such topic \"${slug}\"\\n`,\n        exitCode: 1,\n      };\n    }\n\n    const parents = db\n      .prepare<[string], { parent_slug: string }>(\n        \"SELECT parent_slug FROM topic_parents WHERE child_slug = ? ORDER BY parent_slug\",\n      )\n      .all(slug)\n      .map((r) => r.parent_slug);\n\n    const children = db\n      .prepare<[string], { child_slug: string }>(\n        \"SELECT child_slug FROM topic_parents WHERE parent_slug = ? ORDER BY child_slug\",\n      )\n      .all(slug)\n      .map((r) => r.child_slug);\n\n    const pageSlugs = options.descendants === true\n      ? pagesForSubtree(db, slug)\n      : pagesDirectlyTagged(db, slug);\n\n    const record: TopicsShowRecord = {\n      slug: row.slug,\n      title: row.title,\n      description: row.description,\n      parents,\n      children,\n      pages: pageSlugs,\n      descendants_used: options.descendants === true,\n    };\n\n    if (options.json === true) {\n      return {\n        stdout: `${JSON.stringify(record, null, 2)}\\n`,\n        stderr: \"\",\n        exitCode: 0,\n      };\n    }\n    return { stdout: formatShow(record), stderr: \"\", exitCode: 0 };\n  } finally {\n    db.close();\n  }\n}\n\nfunction pagesDirectlyTagged(db: Database.Database, slug: string): string[] {\n  return db\n    .prepare<[string], { page_slug: string }>(\n      `SELECT pt.page_slug\n       FROM page_topics pt\n       JOIN pages p ON p.slug = pt.page_slug\n       WHERE pt.topic_slug = ? AND p.archived_at IS NULL\n       ORDER BY pt.page_slug`,\n    )\n    .all(slug)\n    .map((r) => r.page_slug);\n}\n\nfunction pagesForSubtree(db: Database.Database, slug: string): string[] {\n  const slugs = [slug, ...descendantsInDb(db, slug)];\n  // Deduplicate + preserve order via a Set — a page can belong to\n  // multiple topics in the subtree and we only want one row per page.\n  const placeholders = slugs.map(() => \"?\").join(\", \");\n  const rows = db\n    .prepare<unknown[], { page_slug: string }>(\n      `SELECT DISTINCT pt.page_slug\n       FROM page_topics pt\n       JOIN pages p ON p.slug = pt.page_slug\n       WHERE pt.topic_slug IN (${placeholders}) AND p.archived_at IS NULL\n       ORDER BY pt.page_slug`,\n    )\n    .all(...slugs);\n  return rows.map((r) => r.page_slug);\n}\n\nfunction formatShow(r: TopicsShowRecord): string {\n  const lines: string[] = [];\n  lines.push(`slug:         ${r.slug}`);\n  lines.push(`title:        ${r.title ?? titleCase(r.slug)}`);\n  lines.push(`description:  ${r.description ?? \"—\"}`);\n  lines.push(\n    `parents:      ${r.parents.length > 0 ? r.parents.join(\", \") : \"—\"}`,\n  );\n  lines.push(\n    `children:     ${r.children.length > 0 ? r.children.join(\", \") : \"—\"}`,\n  );\n  const pagesLabel = r.descendants_used === true ? \"pages (incl. descendants)\" : \"pages\";\n  lines.push(`${pagesLabel}:`);\n  if (r.pages.length === 0) {\n    lines.push(\"  —\");\n  } else {\n    for (const p of r.pages) lines.push(`  ${p}`);\n  }\n  return `${lines.join(\"\\n\")}\\n`;\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// create — `almanac topics create <name> [--parent <slug>]...`\n// ─────────────────────────────────────────────────────────────────────\n\n/**\n * `almanac topics create <name> [--parent <slug>]...`.\n *\n * Policy: `--parent <slug>` MUST refer to an existing topic (created\n * earlier in topics.yaml or indexed from page frontmatter). Auto-\n * creating parents silently would let typos cascade — `create JWT\n * --parent secuirty` would quietly spawn a \"secuirty\" topic. Better to\n * refuse and point the user at `almanac topics create <parent>` first.\n *\n * Already-exists is not an error if no new parents are being added —\n * rerunning the same `create` is a no-op. If new parents are introduced\n * we add them (respecting cycle prevention, just like `link`).\n */\nexport async function runTopicsCreate(\n  options: TopicsCreateOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n\n  const slug = toKebabCase(options.name);\n  if (slug.length === 0) {\n    return {\n      stdout: \"\",\n      stderr: `almanac: topic name \"${options.name}\" has no slug-able characters\\n`,\n      exitCode: 1,\n    };\n  }\n  const title = options.name.trim().length > 0 ? options.name.trim() : titleCase(slug);\n\n  // Reindex first so an ad-hoc `--parent <slug>` created by a\n  // just-written page is visible to `topicExists`. Every other topics\n  // command did this; `create` silently skipped the refresh which meant\n  // a brand-new page's `topics: [newparent]` couldn't be used as a\n  // parent until the next query touched the DB.\n  await ensureFreshIndex({ repoRoot });\n\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n\n  // Hoist the DB open out of the parents loop. We used to open + close\n  // the DB inside `isAdHocTopicInDb` for every parent; opening is\n  // cheap but not free, and the iteration pattern shows up in other\n  // topics commands too.\n  const db = openIndex(indexDbPath(repoRoot));\n  try {\n    // Resolve/validate parents BEFORE mutating the file. All-or-nothing.\n    const requestedParents = (options.parents ?? [])\n      .map((p) => toKebabCase(p))\n      .filter((p) => p.length > 0);\n    for (const p of requestedParents) {\n      if (p === slug) {\n        return {\n          stdout: \"\",\n          stderr: `almanac: topic cannot be its own parent\\n`,\n          exitCode: 1,\n        };\n      }\n      if (!topicExists(file, db, p)) {\n        return {\n          stdout: \"\",\n          stderr: `almanac: parent topic \"${p}\" does not exist; create it first with \\`almanac topics create ${p}\\`\\n`,\n          exitCode: 1,\n        };\n      }\n      if (findTopic(file, p) === null) {\n        // Topic exists only as an ad-hoc DB entry. Promote it into\n        // topics.yaml so it has a proper record. `ensureTopic` is\n        // idempotent so this is safe even if two loop iterations\n        // reference the same ad-hoc parent.\n        ensureTopic(file, p);\n      }\n    }\n\n    const existing = findTopic(file, slug);\n    if (existing === null) {\n      const entry: TopicEntry = {\n        slug,\n        title,\n        description: null,\n        parents: requestedParents,\n      };\n      file.topics.push(entry);\n    } else {\n      // Add any new parents, skipping ones that already exist or would\n      // create a cycle.\n      for (const p of requestedParents) {\n        if (existing.parents.includes(p)) continue;\n        const ancestors = ancestorsInFile(file, p);\n        if (ancestors.has(slug) || p === slug) {\n          return {\n            stdout: \"\",\n            stderr: `almanac: adding \"${p}\" as a parent of \"${slug}\" would create a cycle\\n`,\n            exitCode: 1,\n          };\n        }\n        existing.parents.push(p);\n      }\n      // Promote the user-supplied title only if the existing one was a\n      // title-cased default (i.e., they didn't describe it yet). Don't\n      // clobber a deliberate title silently.\n      if (\n        existing.title === titleCase(existing.slug) &&\n        title !== titleCase(slug) &&\n        title !== existing.title\n      ) {\n        existing.title = title;\n      }\n    }\n\n    await writeTopicsFile(yamlPath, file);\n    await runIndexer({ repoRoot });\n    return {\n      stdout: existing === null\n        ? `created topic \"${slug}\"\\n`\n        : `updated topic \"${slug}\"\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  } finally {\n    db.close();\n  }\n}\n\n/**\n * Is `slug` a known topic anywhere — in `topics.yaml`, or as an ad-hoc\n * slug that a page's frontmatter mentioned and the indexer seeded?\n *\n * Collapses the previous `findTopic(file, s) === null &&\n * !isAdHocTopicInDb(root, s)` duplication into one intent-revealing\n * helper. Takes an open `db` handle so the caller can hoist DB open\n * out of tight loops — every earlier call site created + destroyed a\n * new connection per iteration.\n */\nfunction topicExists(\n  file: TopicsFile,\n  db: Database.Database,\n  slug: string,\n): boolean {\n  if (findTopic(file, slug) !== null) return true;\n  const row = db\n    .prepare<[string], { slug: string }>(\n      \"SELECT slug FROM topics WHERE slug = ?\",\n    )\n    .get(slug);\n  return row !== undefined;\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// link / unlink\n// ─────────────────────────────────────────────────────────────────────\n\n/**\n * `almanac topics link <child> <parent>`. Adds a DAG edge after\n * checking that it wouldn't close a cycle. Both topics must exist.\n */\nexport async function runTopicsLink(\n  options: TopicsLinkOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  const child = toKebabCase(options.child);\n  const parent = toKebabCase(options.parent);\n  if (child.length === 0 || parent.length === 0) {\n    return { stdout: \"\", stderr: `almanac: empty topic slug\\n`, exitCode: 1 };\n  }\n  if (child === parent) {\n    return {\n      stdout: \"\",\n      stderr: `almanac: topic cannot be its own parent\\n`,\n      exitCode: 1,\n    };\n  }\n\n  // Refresh the index so ad-hoc topics (ones the user tagged pages\n  // with but never formally `topics create`d) are visible to\n  // `topicExists` below.\n  await ensureFreshIndex({ repoRoot });\n\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n\n  const db = openIndex(indexDbPath(repoRoot));\n  try {\n    for (const slug of [child, parent]) {\n      if (!topicExists(file, db, slug)) {\n        return {\n          stdout: \"\",\n          stderr: `almanac: topic \"${slug}\" does not exist\\n`,\n          exitCode: 1,\n        };\n      }\n      if (findTopic(file, slug) === null) {\n        // DB-only ad-hoc topic → promote it into topics.yaml so the\n        // new DAG edge has a concrete home.\n        ensureTopic(file, slug);\n      }\n    }\n\n    const childEntry = findTopic(file, child);\n    if (childEntry === null) {\n      // Shouldn't happen after ensureTopic above — defensive.\n      return {\n        stdout: \"\",\n        stderr: `almanac: topic \"${child}\" not found\\n`,\n        exitCode: 1,\n      };\n    }\n\n    if (childEntry.parents.includes(parent)) {\n      return {\n        stdout: `edge ${child} → ${parent} already exists\\n`,\n        stderr: \"\",\n        exitCode: 0,\n      };\n    }\n\n    // Cycle check BEFORE mutation. Uses the in-memory file so the check\n    // operates on the state we're about to write — no DB round-trip needed.\n    const parentAncestors = ancestorsInFile(file, parent);\n    if (parentAncestors.has(child) || parent === child) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: adding ${parent} as parent of ${child} would create a cycle\\n`,\n        exitCode: 1,\n      };\n    }\n\n    childEntry.parents.push(parent);\n    await writeTopicsFile(yamlPath, file);\n    await runIndexer({ repoRoot });\n    return {\n      stdout: `linked ${child} → ${parent}\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  } finally {\n    db.close();\n  }\n}\n\n/**\n * `almanac topics unlink <child> <parent>`. Removes a DAG edge if it\n * exists. No-op (exit 0) if not. Never deletes topics.\n */\nexport async function runTopicsUnlink(\n  options: TopicsUnlinkOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  const child = toKebabCase(options.child);\n  const parent = toKebabCase(options.parent);\n  if (child.length === 0 || parent.length === 0) {\n    return { stdout: \"\", stderr: `almanac: empty topic slug\\n`, exitCode: 1 };\n  }\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n  const childEntry = findTopic(file, child);\n  if (childEntry === null || !childEntry.parents.includes(parent)) {\n    return {\n      stdout: `no edge ${child} → ${parent}\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n  childEntry.parents = childEntry.parents.filter((p) => p !== parent);\n  await writeTopicsFile(yamlPath, file);\n  await runIndexer({ repoRoot });\n  return {\n    stdout: `unlinked ${child} → ${parent}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// rename — `almanac topics rename <old> <new>`\n// ─────────────────────────────────────────────────────────────────────\n\n/**\n * `almanac topics rename <old> <new>`. Rewrites the slug both in\n * `topics.yaml` (as an entry key and in anyone who declared it as a\n * parent) and in every affected page's frontmatter.\n *\n * Refuses if `<new>` is already a distinct topic — \"merging\" two topics\n * should be explicit, not a silent side effect of a rename.\n */\nexport async function runTopicsRename(\n  options: TopicsRenameOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  const oldSlug = toKebabCase(options.oldSlug);\n  const newSlug = toKebabCase(options.newSlug);\n  if (oldSlug.length === 0 || newSlug.length === 0) {\n    return { stdout: \"\", stderr: `almanac: empty topic slug\\n`, exitCode: 1 };\n  }\n  if (oldSlug === newSlug) {\n    return {\n      stdout: `topic \"${oldSlug}\" unchanged\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  await ensureFreshIndex({ repoRoot });\n\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n\n  // Hoist the DB handle so the existence checks below don't reopen\n  // the index per-slug.\n  const db = openIndex(indexDbPath(repoRoot));\n  let pagesUpdated: number;\n  try {\n    // Fetch existence info. `oldInYaml` is kept as a direct reference\n    // because we mutate the entry; the DB check is only needed when\n    // the slug isn't in the file (ad-hoc-only).\n    const oldInYaml = findTopic(file, oldSlug);\n    if (!topicExists(file, db, oldSlug)) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: no such topic \"${oldSlug}\"\\n`,\n        exitCode: 1,\n      };\n    }\n\n    if (topicExists(file, db, newSlug)) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: topic \"${newSlug}\" already exists; delete it first if you intend to merge\\n`,\n        exitCode: 1,\n      };\n    }\n\n    // Rewrite `topics.yaml`: the entry itself (if present) plus any\n    // parent reference to `oldSlug`.\n    if (oldInYaml !== null) {\n      oldInYaml.slug = newSlug;\n      if (oldInYaml.title === titleCase(oldSlug)) {\n        // Title was the auto-generated default — refresh it to the new\n        // slug's title-case. A custom title stays as-is.\n        oldInYaml.title = titleCase(newSlug);\n      }\n    }\n    for (const t of file.topics) {\n      t.parents = t.parents.map((p) => (p === oldSlug ? newSlug : p));\n    }\n\n    // Write ordering matters: topics.yaml FIRST (atomic tmp+rename), THEN\n    // the page rewrites. If topics.yaml write fails, no page was touched.\n    // If a page rewrite fails midway, topics.yaml already reflects the\n    // rename so the next reindex picks up the ad-hoc state and the user\n    // can re-run to finish the remaining pages. The opposite ordering\n    // would leave half-rewritten pages referencing a slug that\n    // topics.yaml doesn't know about.\n    await writeTopicsFile(yamlPath, file);\n\n    // Rewrite every page that has `oldSlug` in `topics:` frontmatter.\n    pagesUpdated = await rewriteTopicOnPages(repoRoot, (topics) =>\n      topics.map((t) => (t === oldSlug ? newSlug : t)),\n    );\n  } finally {\n    db.close();\n  }\n\n  await runIndexer({ repoRoot });\n  return {\n    stdout: `renamed ${oldSlug} → ${newSlug} (${pagesUpdated} page${pagesUpdated === 1 ? \"\" : \"s\"} updated)\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// delete — `almanac topics delete <slug>`\n// ─────────────────────────────────────────────────────────────────────\n\n/**\n * `almanac topics delete <slug>`. Removes the topic from `topics.yaml`\n * (if present), scrubs any parent edges pointing at it, and untags\n * every page that had it. Pages themselves are left alone — deleting a\n * topic doesn't delete pages, just the relationship.\n */\nexport async function runTopicsDelete(\n  options: TopicsDeleteOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  const slug = toKebabCase(options.slug);\n  if (slug.length === 0) {\n    return { stdout: \"\", stderr: `almanac: empty topic slug\\n`, exitCode: 1 };\n  }\n\n  await ensureFreshIndex({ repoRoot });\n\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n  const db = openIndex(indexDbPath(repoRoot));\n  let pagesUpdated: number;\n  try {\n    if (!topicExists(file, db, slug)) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: no such topic \"${slug}\"\\n`,\n        exitCode: 1,\n      };\n    }\n\n    // Remove the entry and strip it from everyone else's `parents` list.\n    file.topics = file.topics.filter((t) => t.slug !== slug);\n    for (const t of file.topics) {\n      t.parents = t.parents.filter((p) => p !== slug);\n    }\n\n    // Same write ordering as rename: topics.yaml first (atomic), then\n    // pages. A crash between the two leaves topics.yaml already scrubbed\n    // and any remaining in-page references become ad-hoc topics — which\n    // the reindex will pick up as empty-topics on next health, and the\n    // user can re-run to finish untagging.\n    await writeTopicsFile(yamlPath, file);\n\n    pagesUpdated = await rewriteTopicOnPages(repoRoot, (topics) =>\n      topics.filter((t) => t !== slug),\n    );\n  } finally {\n    db.close();\n  }\n\n  await runIndexer({ repoRoot });\n  return {\n    stdout: `deleted topic \"${slug}\" (${pagesUpdated} page${pagesUpdated === 1 ? \"\" : \"s\"} untagged)\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// describe — `almanac topics describe <slug> \"<text>\"`\n// ─────────────────────────────────────────────────────────────────────\n\n/**\n * `almanac topics describe <slug> \"<text>\"`. Sets or updates the\n * one-liner description. An empty string clears it.\n */\nexport async function runTopicsDescribe(\n  options: TopicsDescribeOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  const slug = toKebabCase(options.slug);\n  if (slug.length === 0) {\n    return { stdout: \"\", stderr: `almanac: empty topic slug\\n`, exitCode: 1 };\n  }\n\n  await ensureFreshIndex({ repoRoot });\n\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n  const db = openIndex(indexDbPath(repoRoot));\n  try {\n    if (!topicExists(file, db, slug)) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: no such topic \"${slug}\"\\n`,\n        exitCode: 1,\n      };\n    }\n    // `ensureTopic` is idempotent — if the topic was DB-only it\n    // promotes into `file`; if already in `file` it returns the\n    // existing entry. Either way we get a concrete entry to mutate.\n    const entry = ensureTopic(file, slug);\n\n    const text = options.description.trim();\n    entry.description = text.length === 0 ? null : text;\n\n    await writeTopicsFile(yamlPath, file);\n  } finally {\n    db.close();\n  }\n\n  await runIndexer({ repoRoot });\n  return {\n    stdout: `described ${slug}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// Shared helpers\n// ─────────────────────────────────────────────────────────────────────\n\n/**\n * Apply a `topic-list transform` to every `.almanac/pages/*.md` file\n * whose frontmatter contains a relevant topic. Returns the number of\n * files actually changed.\n *\n * We glob page files ourselves (not the DB) so this works even on a\n * stale index — `rename` and `delete` run the indexer AFTER mutation,\n * and we don't want the scan to miss a page that was just modified.\n *\n * `transform` operates on the full topic list of each page; returning\n * the same list = no-op (no write). We short-circuit cheaply via\n * `applyTopicsTransform` before touching the file.\n */\nasync function rewriteTopicOnPages(\n  repoRoot: string,\n  transform: (topics: string[]) => string[],\n): Promise<number> {\n  const pagesDir = join(repoRoot, \".almanac\", \"pages\");\n  const files = await fg(\"**/*.md\", {\n    cwd: pagesDir,\n    absolute: true,\n    onlyFiles: true,\n  });\n  let changed = 0;\n  for (const filePath of files) {\n    // Cheap read → in-memory check. Skip files that wouldn't be\n    // changed so we don't bump their mtime.\n    const raw = await readFile(filePath, \"utf8\");\n    const applied = applyTopicsTransform(raw, transform);\n    if (!applied.changed) continue;\n    await rewritePageTopics(filePath, transform);\n    changed += 1;\n  }\n  return changed;\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// dispatch helpers (used by cli.ts)\n// ─────────────────────────────────────────────────────────────────────\n\nexport {\n  ensureTopic,\n  findTopic,\n  loadTopicsFile,\n  writeTopicsFile,\n  type TopicEntry,\n  type TopicsFile,\n};\n","import { existsSync } from \"node:fs\";\nimport { basename } from \"node:path\";\n\nimport { findNearestAlmanacDir } from \"../paths.js\";\nimport { toKebabCase } from \"../slug.js\";\nimport {\n  addEntry,\n  readRegistry,\n  type RegistryEntry,\n} from \"./index.js\";\n\n/**\n * If the current working directory (or any parent) has a `.almanac/` that\n * isn't in the registry, silently add it. Runs as a side effect of every\n * command except `init` (which does its own registration) and `list --drop`\n * (which shouldn't resurrect the entry the user just removed).\n *\n * The contract is \"silent\" for environmental problems — missing home dir,\n * unreadable registry file, permission errors. Those shouldn't block the\n * real command from running. 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If the dir name is\n    // somehow empty (e.g. repo is at filesystem root), skip — we don't\n    // want to register a nameless entry.\n    const name = toKebabCase(basename(repoRoot));\n    if (name.length === 0) return null;\n\n    // Resolve collisions on name by falling back to a disambiguated form.\n    // Auto-registration should never overwrite an existing named entry\n    // that points elsewhere.\n    const finalName = resolveNameCollision(entries, name, repoRoot);\n    if (finalName === null) return null;\n\n    const entry: RegistryEntry = {\n      name: finalName,\n      description: \"\",\n      path: repoRoot,\n      registered_at: new Date().toISOString(),\n    };\n    await addEntry(entry);\n    return entry;\n  } catch (err: unknown) {\n    // Only swallow errors that mean \"registry state isn't readable right\n    // now\" — everything else (malformed JSON, programmer errors, bugs)\n    // should propagate so the user can see it.\n    if (\n      err instanceof Error &&\n      \"code\" in err &&\n      (err.code === \"ENOENT\" ||\n        err.code === \"EACCES\" ||\n        err.code === \"EPERM\")\n    ) {\n      return null;\n    }\n    throw err;\n  }\n}\n\n/**\n * If another repo already claims `name`, append `-2`, `-3`, ... until we\n * find an unused slug. Only relevant for auto-registration — `init` with\n * `--name` lets the user resolve collisions explicitly.\n *\n * Takes a snapshot of registry entries instead of re-reading the file per\n * iteration. Caps at 1000 attempts to prevent pathological loops if the\n * registry somehow contains every suffix (it can't, but we'd rather fail\n * explicitly than spin).\n */\nfunction resolveNameCollision(\n  entries: RegistryEntry[],\n  baseName: string,\n  repoPath: string,\n): string | null {\n  const owner = entries.find((e) => e.name === baseName);\n  if (owner === undefined || samePath(owner.path, repoPath)) {\n    return baseName;\n  }\n  const taken = new Set(entries.map((e) => e.name));\n  const MAX_ATTEMPTS = 1000;\n  for (let suffix = 2; suffix < MAX_ATTEMPTS + 2; suffix += 1) {\n    const candidate = `${baseName}-${suffix}`;\n    if (!taken.has(candidate)) return candidate;\n  }\n  return null;\n}\n\n/**\n * Mirror `pathsEqual` in `registry/index.ts` — case-insensitive on\n * macOS/Windows, case-sensitive on Linux. Duplicated here rather than\n * exported to keep the registry module's public surface small.\n */\nfunction samePath(a: string, b: string): boolean {\n  if (process.platform === \"darwin\" || process.platform === \"win32\") {\n    return a.toLowerCase() === b.toLowerCase();\n  }\n  return a === b;\n}\n","import { run } from \"../src/cli.js\";\n\nrun(process.argv).catch((err: unknown) => {\n  const message = err instanceof Error ? err.message : String(err);\n  process.stderr.write(`almanac: ${message}\\n`);\n  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