codealmanac 0.1.5 → 0.1.6

package/dist/cli-GTEC5PC7.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli.ts","../src/commands/setup.ts","../src/agent/auth.ts","../src/commands/hook.ts","../src/commands/hook/script.ts","../src/commands/setup/install-path.ts","../src/commands/setup/next-steps.ts","../src/ansi.ts","../src/cli/help.ts","../src/cli/helpers.ts","../src/indexer/index.ts","../src/slug.ts","../src/topics/yaml.ts","../src/indexer/frontmatter.ts","../src/indexer/freshness.ts","../src/indexer/paths.ts","../src/indexer/schema.ts","../src/indexer/topics-yaml.ts","../src/indexer/wikilinks.ts","../src/indexer/resolve-wiki.ts","../src/paths.ts","../src/registry/index.ts","../src/topics/frontmatter-rewrite.ts","../src/topics/paths.ts","../src/commands/tag.ts","../src/topics/dag.ts","../src/commands/topics/workspace.ts","../src/commands/topics/create.ts","../src/commands/topics/page-rewrite.ts","../src/commands/topics/delete.ts","../src/commands/topics/describe.ts","../src/commands/topics/link.ts","../src/commands/topics/list.ts","../src/commands/topics/rename.ts","../src/commands/topics/read.ts","../src/commands/topics/show.ts","../src/commands/topics/unlink.ts","../src/registry/autoregister.ts","../src/cli/register-edit-commands.ts","../src/commands/health.ts","../src/indexer/duration.ts","../src/commands/list.ts","../src/commands/search.ts","../src/commands/show.ts","../src/cli/register-query-commands.ts","../src/commands/doctor-checks/format.ts","../src/commands/doctor-checks/install.ts","../src/commands/doctor-checks/probes.ts","../src/update/config.ts","../src/update/schedule.ts","../src/update/check.ts","../src/update/state.ts","../src/update/semver.ts","../src/commands/doctor-checks/duration.ts","../src/commands/doctor-checks/updates.ts","../src/commands/doctor-checks/wiki.ts","../src/commands/doctor.ts","../src/commands/uninstall.ts","../src/commands/update.ts","../src/cli/register-setup-commands.ts","../src/commands/bootstrap.ts","../src/agent/prompts.ts","../src/agent/sdk.ts","../src/commands/init.ts","../src/commands/capture.ts","../src/commands/reindex.ts","../src/cli/register-wiki-lifecycle-commands.ts","../src/cli/register-commands.ts","../src/update/announce.ts"],"sourcesContent":["import { createRequire } from \"node:module\";\nimport { basename } from \"node:path\";\n\nimport { Command } from \"commander\";\n\nimport { runSetup } from \"./commands/setup.js\";\nimport { configureGroupedHelp } from \"./cli/help.js\";\nimport { emit } from \"./cli/helpers.js\";\nimport { registerCommands } from \"./cli/register-commands.js\";\nimport { announceUpdateIfAvailable } from \"./update/announce.js\";\nimport {\n  runInternalUpdateCheck,\n  scheduleBackgroundUpdateCheck,\n} from \"./update/schedule.js\";\n\n/**\n * Optional dependency overrides for `run`. Tests use these to avoid\n * spawning the real setup wizard, the real update background check,\n * and the real update banner. Production callers pass nothing.\n */\nexport interface RunDeps {\n  /** Replace the setup wizard (bare `codealmanac` / `almanac setup`). */\n  runSetup?: typeof runSetup;\n  /** Replace the pre-command update-nag banner. */\n  announceUpdate?: (stderr: NodeJS.WritableStream) => void;\n  /** Replace the post-command background update check scheduler. */\n  scheduleUpdateCheck?: (argv: string[]) => void;\n  /** Replace the internal update-check worker (run on --internal-check-updates). */\n  runInternalUpdateCheck?: () => Promise<void>;\n}\n\n/**\n * Process-level CLI entrypoint. This owns invocation-level behavior:\n * update checks, bare `codealmanac` setup routing, Commander creation,\n * grouped help, and parsing. Individual command wiring lives in\n * `src/cli/register-commands.ts`.\n */\nexport async function run(argv: string[], deps: RunDeps = {}): Promise<void> {\n  const runSetupFn = deps.runSetup ?? runSetup;\n  const announceUpdateFn = deps.announceUpdate ?? announceUpdateIfAvailable;\n  const scheduleUpdateCheckFn =\n    deps.scheduleUpdateCheck ?? scheduleBackgroundUpdateCheck;\n  const runInternalUpdateCheckFn =\n    deps.runInternalUpdateCheck ?? runInternalUpdateCheck;\n\n  if (argv.slice(2).includes(\"--internal-check-updates\")) {\n    await runInternalUpdateCheckFn();\n    return;\n  }\n\n  const programName = getProgramName(argv);\n\n  announceUpdateFn(process.stderr);\n  scheduleUpdateCheckFn(argv);\n\n  const program = new Command();\n  program\n    .name(programName)\n    .description(\n      \"codealmanac — a living wiki for codebases, maintained by AI agents\",\n    )\n    .version(readPackageVersion(), \"-v, --version\", \"print version\");\n\n  if (programName === \"codealmanac\") {\n    const setupInvocation = tryParseSetupShortcut(argv.slice(2));\n    if (setupInvocation !== null) {\n      emit(await runSetupFn(setupInvocation));\n      return;\n    }\n  }\n\n  registerCommands(program);\n  configureGroupedHelp(program);\n\n  await program.parseAsync(argv);\n}\n\nfunction getProgramName(argv: string[]): \"almanac\" | \"codealmanac\" {\n  const invoked = argv[1] !== undefined ? basename(argv[1]) : \"almanac\";\n  return invoked === \"codealmanac\" ? \"codealmanac\" : \"almanac\";\n}\n\nfunction readPackageVersion(): string {\n  try {\n    const require = createRequire(import.meta.url);\n    const pkg = require(\"../package.json\") as { version?: unknown };\n    if (typeof pkg.version === \"string\" && pkg.version.length > 0) {\n      return pkg.version;\n    }\n  } catch {\n    // Fall back to \"unknown\" rather than crashing the CLI on a broken install.\n  }\n  return \"unknown\";\n}\n\nexport interface SetupShortcutOptions {\n  yes?: boolean;\n  skipHook?: boolean;\n  skipGuides?: boolean;\n}\n\n/**\n * Decide whether a bare `codealmanac [...args]` invocation should route\n * straight to `runSetup` (and if so, with which flags). Returns the\n * options object when it's a setup shortcut, or `null` when Commander\n * should parse the invocation normally.\n */\nexport function tryParseSetupShortcut(args: string[]): SetupShortcutOptions | null {\n  if (args.length === 0) return {};\n\n  const opts: SetupShortcutOptions = {};\n  for (const arg of args) {\n    if (arg === \"--yes\" || arg === \"-y\") {\n      opts.yes = true;\n      continue;\n    }\n    if (arg === \"--skip-hook\") {\n      opts.skipHook = true;\n      continue;\n    }\n    if (arg === \"--skip-guides\") {\n      opts.skipGuides = true;\n      continue;\n    }\n    return null;\n  }\n  return opts;\n}\n","import { existsSync } from \"node:fs\";\nimport {\n  copyFile,\n  mkdir,\n  readFile,\n  writeFile,\n} from \"node:fs/promises\";\nimport { createRequire } from \"node:module\";\nimport { homedir } from \"node:os\";\nimport path from \"node:path\";\nimport { fileURLToPath } from \"node:url\";\n\nimport {\n  checkClaudeAuth,\n  type ClaudeAuthStatus,\n  type SpawnCliFn,\n  UNAUTHENTICATED_MESSAGE,\n} from \"../agent/auth.js\";\nimport { runHookInstall } from \"./hook.js\";\nimport {\n  detectCurrentInstallPath,\n  detectEphemeral,\n  spawnGlobalInstall,\n} from \"./setup/install-path.js\";\nimport {\n  countExistingPages,\n  printNextSteps,\n} from \"./setup/next-steps.js\";\n\n/**\n * `codealmanac setup` — the MCP-style branded TUI that runs when a user\n * invokes the bare `codealmanac` binary (or `almanac setup` / `codealmanac\n * setup` explicitly).\n *\n * Model: `mcp-ts/src/setup.ts` from openalmanac. Same ASCII banner + badge\n * + step-indicator style, same interactive + `--yes` + non-interactive\n * modes.\n *\n * Three things get installed:\n *\n *   1. The `SessionEnd` hook in `~/.claude/settings.json` (delegated to\n *      `runHookInstall` from `./hook.ts`).\n *   2. The short \"how to use codealmanac\" guide at\n *      `~/.claude/codealmanac.md`, sourced from `guides/mini.md` in the\n *      package.\n *   3. The full reference at `~/.claude/codealmanac-reference.md`,\n *      sourced from `guides/reference.md`.\n *   4. An `@~/.claude/codealmanac.md` import line in `~/.claude/CLAUDE.md`\n *      so Claude Code picks up the short guide globally.\n *\n * Everything is idempotent — running setup again is safe. `--skip-hook`\n * and `--skip-guides` opt out of the individual installs. `--yes` or a\n * non-TTY stdin skips all prompts and installs everything.\n */\n\nexport interface SetupOptions {\n  /** Install everything without prompting. */\n  yes?: boolean;\n  /** Don't install the SessionEnd hook. */\n  skipHook?: boolean;\n  /** Don't install the CLAUDE.md guides. */\n  skipGuides?: boolean;\n\n  // ─── Injection points (tests only) ────────────────────────────────\n  /** Override the subprocess spawner for `claude auth status`. */\n  spawnCli?: SpawnCliFn;\n  /** Override `~/.claude/settings.json` path. */\n  settingsPath?: string;\n  /** Override the bundled hook script path. */\n  hookScriptPath?: string;\n  /** Override the stable hooks directory for the hook script copy. */\n  stableHooksDir?: string;\n  /** Override `~/.claude/` dir for guide install. */\n  claudeDir?: string;\n  /** Override the directory containing `mini.md` / `reference.md`. */\n  guidesDir?: string;\n  /** Override interactivity; defaults to `process.stdin.isTTY`. */\n  isTTY?: boolean;\n  /** Stdout sink; defaults to `process.stdout`. */\n  stdout?: NodeJS.WritableStream;\n  /**\n   * Override the install-path probe result. When `null` the probe is\n   * bypassed (tests that don't care about the ephemeral-path step).\n   * When a string it's treated as the detected install path.\n   */\n  installPath?: string | null;\n  /**\n   * Override the npm global install spawner (tests inject a no-op to\n   * avoid actually spawning npm during CI).\n   */\n  spawnGlobalInstall?: () => Promise<void>;\n}\n\nexport interface SetupResult {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n// ─── ANSI helpers ────────────────────────────────────────────────────\n\nconst RST = \"\\x1b[0m\";\nconst DIM = \"\\x1b[2m\";\nconst WHITE_BOLD = \"\\x1b[1;37m\";\nconst BLUE = \"\\x1b[38;5;75m\";\nconst ACCENT_BG = \"\\x1b[48;5;252m\\x1b[38;5;16m\";\n\nconst GRADIENT = [\n  \"\\x1b[38;5;255m\",\n  \"\\x1b[38;5;253m\",\n  \"\\x1b[38;5;251m\",\n  \"\\x1b[38;5;249m\",\n  \"\\x1b[38;5;246m\",\n  \"\\x1b[38;5;243m\",\n];\n\n// `codealmanac` 11-letter ASCII banner. Chosen for tasteful rendering —\n// same banner used in the MCP setup wizard design, retooled letters for\n// the word \"codealmanac\". Each glyph is 6 lines tall.\n//\n// If you tweak this, keep it to ≤80 visual columns wide so it fits in\n// narrow terminals (80 cols is the classic default).\nconst LOGO_LINES = [\n  \"  ___ ___  ___  ___   _   _    __  __   _   _  _   _   ___ \",\n  \" / __/ _ \\\\|   \\\\| __| /_\\\\ | |  |  \\\\/  | /_\\\\ | \\\\| | /_\\\\ / __|\",\n  \"| (_| (_) | |) | _| / _ \\\\| |__| |\\\\/| |/ _ \\\\| .` |/ _ \\\\ (__ \",\n  \" \\\\___\\\\___/|___/|___/_/ \\\\_\\\\____|_|  |_/_/ \\\\_\\\\_|\\\\_/_/ \\\\_\\\\___|\",\n  \"                                                           \",\n  \"        a living wiki for codebases, for your agent         \",\n];\n\nconst BAR = `  ${DIM}\\u2502${RST}`;\n\nfunction printBanner(out: NodeJS.WritableStream): void {\n  out.write(\"\\n\");\n  for (let i = 0; i < LOGO_LINES.length; i++) {\n    const color = GRADIENT[Math.min(i, GRADIENT.length - 1)] ?? \"\";\n    out.write(`${color}${LOGO_LINES[i]}${RST}\\n`);\n  }\n  out.write(`\\n${WHITE_BOLD}  Install the hook + agent guides${RST}\\n`);\n}\n\nfunction printBadge(out: NodeJS.WritableStream): void {\n  out.write(`\\n   ${ACCENT_BG} codealmanac ${RST}\\n\\n`);\n}\n\nfunction stepDone(out: NodeJS.WritableStream, msg: string): void {\n  out.write(`  ${BLUE}\\u25c7${RST}  ${msg}\\n`);\n}\n\nfunction stepActive(out: NodeJS.WritableStream, msg: string): void {\n  out.write(`  ${BLUE}\\u25c6${RST}  ${msg}\\n`);\n}\n\nfunction stepSkipped(out: NodeJS.WritableStream, msg: string): void {\n  out.write(`  ${DIM}\\u25cb  ${msg}${RST}\\n`);\n}\n\n// ─── Entry point ─────────────────────────────────────────────────────\n\nexport async function runSetup(\n  options: SetupOptions = {},\n): Promise<SetupResult> {\n  const out = options.stdout ?? process.stdout;\n  const isTTY =\n    options.isTTY ?? (process.stdin.isTTY === true);\n  const interactive = isTTY && options.yes !== true;\n\n  // No-op fast path. When the caller explicitly skipped every install\n  // step, rendering the full banner + step markers + \"Setup complete\"\n  // box is actively misleading — nothing was actually set up. Emit a\n  // single terse line and exit so the user gets honest feedback and\n  // piped callers (CI, scripts) don't parse through nine lines of ANSI\n  // to conclude nothing happened.\n  if (options.skipHook === true && options.skipGuides === true) {\n    out.write(\n      \"codealmanac: nothing to install — use --help to see what setup does\\n\",\n    );\n    return { stdout: \"\", stderr: \"\", exitCode: 0 };\n  }\n\n  printBanner(out);\n  printBadge(out);\n\n  // Step 1: auth status. We report what we find; we don't block. The user\n  // can still install the hook + guides without being logged in — they'll\n  // hit the auth wall on first `capture`, not on setup.\n  const auth = await safeCheckAuth(options.spawnCli);\n  reportAuth(out, auth);\n  out.write(BAR + \"\\n\");\n\n  // Step 1b: ephemeral install detection. When codealmanac was invoked via\n  // `npx codealmanac` (no prior `npm i -g`), the binary lives inside an\n  // npx cache directory or pnpm store that can be evicted at any time.\n  // `almanac` is also not on PATH, so the user can't use it after setup.\n  //\n  // When we detect an ephemeral location, we offer (or, on --yes, perform)\n  // a `npm install -g codealmanac` to make the install permanent.\n  //\n  // This is Bug #2 from codealmanac-known-bugs.md.\n  const ephem = options.installPath !== undefined\n    ? (options.installPath !== null\n        ? detectEphemeral(options.installPath)\n        : false)\n    : detectEphemeral(detectCurrentInstallPath());\n  if (ephem) {\n    let globalAction: InstallDecision = \"install\";\n    if (interactive) {\n      globalAction = await confirm(\n        out,\n        `Running from an ephemeral npx location. Install globally so 'almanac' stays on PATH?`,\n        true,\n      );\n    }\n    if (globalAction === \"install\") {\n      stepActive(out, \"Installing codealmanac globally…\");\n      try {\n        await (options.spawnGlobalInstall ?? spawnGlobalInstall)();\n        stepDone(out, \"codealmanac installed globally (almanac now on PATH)\");\n      } catch (err: unknown) {\n        const msg = err instanceof Error ? err.message : String(err);\n        stepActive(out, `Global install failed: ${msg}`);\n        out.write(\n          `  ${DIM}You can retry manually: npm install -g codealmanac${RST}\\n`,\n        );\n      }\n    } else {\n      stepSkipped(\n        out,\n        `Global install ${DIM}skipped — almanac will not be on PATH after this session${RST}`,\n      );\n    }\n    out.write(BAR + \"\\n\");\n  }\n\n  // Step 2: install the hook (default yes).\n  let hookAction: InstallDecision = \"install\";\n  if (options.skipHook === true) {\n    hookAction = \"skip\";\n  } else if (interactive) {\n    hookAction = await confirm(\n      out,\n      \"Install the SessionEnd hook so capture runs at the end of every Claude Code session?\",\n      true,\n    );\n  }\n\n  let hookResultLine = \"\";\n  if (hookAction === \"install\") {\n    const res = await runHookInstall({\n      settingsPath: options.settingsPath,\n      hookScriptPath: options.hookScriptPath,\n      stableHooksDir: options.stableHooksDir,\n    });\n    if (res.exitCode !== 0) {\n      stepActive(out, `SessionEnd hook: ${res.stderr.trim()}`);\n      return {\n        stdout: \"\",\n        stderr: res.stderr,\n        exitCode: res.exitCode,\n      };\n    }\n    hookResultLine = res.stdout.includes(\"already installed\")\n      ? `SessionEnd hook ${DIM}already installed${RST}`\n      : `SessionEnd hook installed`;\n    stepDone(out, hookResultLine);\n  } else {\n    stepSkipped(out, `SessionEnd hook ${DIM}skipped${RST}`);\n  }\n  out.write(BAR + \"\\n\");\n\n  // Step 3: install the guides.\n  let guidesAction: InstallDecision = \"install\";\n  if (options.skipGuides === true) {\n    guidesAction = \"skip\";\n  } else if (interactive) {\n    guidesAction = await confirm(\n      out,\n      \"Install the codealmanac usage guides into ~/.claude/ and import them from CLAUDE.md?\",\n      true,\n    );\n  }\n\n  let guidesSummary: string;\n  if (guidesAction === \"install\") {\n    try {\n      const summary = await installGuides({\n        claudeDir: options.claudeDir ?? path.join(homedir(), \".claude\"),\n        guidesDir: options.guidesDir ?? resolveGuidesDir(),\n      });\n      guidesSummary = summary.anyChanges\n        ? `Guides installed (${summary.filesWritten.join(\", \")})`\n        : `Guides ${DIM}already installed${RST}`;\n      stepDone(out, guidesSummary);\n    } catch (err: unknown) {\n      const msg = err instanceof Error ? err.message : String(err);\n      return {\n        stdout: \"\",\n        stderr: `almanac: guide install failed: ${msg}\\n`,\n        exitCode: 1,\n      };\n    }\n  } else {\n    stepSkipped(out, `Guides ${DIM}skipped${RST}`);\n  }\n  out.write(BAR + \"\\n\");\n\n  stepDone(out, `${BLUE}Setup complete${RST}`);\n  out.write(\"\\n\");\n\n  // Detect whether the current working directory is inside a repo that\n  // already has a wiki with pages. This fixes Bug #6 from\n  // codealmanac-known-bugs.md: Engineer B clones a repo that already has\n  // `.almanac/pages/` (committed by Engineer A) and gets told to run\n  // `almanac bootstrap`, which is wrong — the wiki already exists.\n  const existingPageCount = countExistingPages(process.cwd());\n  printNextSteps(out, existingPageCount);\n\n  return { stdout: \"\", stderr: \"\", exitCode: 0 };\n}\n\n// ─── Auth reporting ──────────────────────────────────────────────────\n\nasync function safeCheckAuth(\n  spawnCli?: SpawnCliFn,\n): Promise<ClaudeAuthStatus> {\n  try {\n    return await checkClaudeAuth(spawnCli);\n  } catch {\n    return { loggedIn: false };\n  }\n}\n\nfunction reportAuth(\n  out: NodeJS.WritableStream,\n  auth: ClaudeAuthStatus,\n): void {\n  if (auth.loggedIn) {\n    const who = auth.email ?? \"Claude account\";\n    const plan =\n      auth.subscriptionType !== undefined\n        ? ` ${DIM}(${auth.subscriptionType})${RST}`\n        : \"\";\n    stepDone(out, `Claude auth: ${WHITE_BOLD}${who}${RST}${plan}`);\n    return;\n  }\n  if (\n    process.env.ANTHROPIC_API_KEY !== undefined &&\n    process.env.ANTHROPIC_API_KEY.length > 0\n  ) {\n    stepDone(out, `Claude auth: ${WHITE_BOLD}ANTHROPIC_API_KEY${RST} set`);\n    return;\n  }\n  // Not blocking — just report and show the two paths.\n  stepActive(out, `Claude auth: ${DIM}not signed in${RST}`);\n  for (const line of UNAUTHENTICATED_MESSAGE.split(\"\\n\")) {\n    out.write(`  ${DIM}\\u2502   ${line}${RST}\\n`);\n  }\n}\n\n// ─── Guide installation ──────────────────────────────────────────────\n\ninterface InstallGuidesOptions {\n  claudeDir: string;\n  guidesDir: string;\n}\n\ninterface InstallGuidesResult {\n  anyChanges: boolean;\n  filesWritten: string[];\n}\n\n/**\n * Copy the two guide files into `~/.claude/` and append an `@import`\n * line to `~/.claude/CLAUDE.md`. Every step is idempotent:\n *\n *   - Guide files are compared by bytes before we write. If the content\n *     matches the bundled version, we skip (so `setup` doesn't cause a\n *     spurious mtime bump on every invocation).\n *   - The import line is appended only if `CLAUDE.md` doesn't already\n *     contain the exact `@~/.claude/codealmanac.md` token on a line by\n *     itself. We don't try to parse the file — any mention of the token\n *     on a non-comment line is treated as \"already present\".\n *\n * Returns a summary the caller uses to decide whether to say \"installed\"\n * or \"already installed\" in the TUI.\n */\nasync function installGuides(\n  options: InstallGuidesOptions,\n): Promise<InstallGuidesResult> {\n  await mkdir(options.claudeDir, { recursive: true });\n\n  const srcMini = path.join(options.guidesDir, \"mini.md\");\n  const srcRef = path.join(options.guidesDir, \"reference.md\");\n  if (!existsSync(srcMini)) {\n    throw new Error(`missing bundled guide: ${srcMini}`);\n  }\n  if (!existsSync(srcRef)) {\n    throw new Error(`missing bundled guide: ${srcRef}`);\n  }\n\n  const destMini = path.join(options.claudeDir, \"codealmanac.md\");\n  const destRef = path.join(options.claudeDir, \"codealmanac-reference.md\");\n\n  const miniChanged = await copyIfChanged(srcMini, destMini);\n  const refChanged = await copyIfChanged(srcRef, destRef);\n\n  const claudeMd = path.join(options.claudeDir, \"CLAUDE.md\");\n  const importChanged = await ensureImport(claudeMd);\n\n  const filesWritten: string[] = [];\n  if (miniChanged) filesWritten.push(\"codealmanac.md\");\n  if (refChanged) filesWritten.push(\"codealmanac-reference.md\");\n  if (importChanged) filesWritten.push(\"CLAUDE.md\");\n\n  return { anyChanges: filesWritten.length > 0, filesWritten };\n}\n\nasync function copyIfChanged(src: string, dest: string): Promise<boolean> {\n  const srcBytes = await readFile(src);\n  if (existsSync(dest)) {\n    try {\n      const destBytes = await readFile(dest);\n      if (srcBytes.equals(destBytes)) return false;\n    } catch {\n      // Fall through to write.\n    }\n  }\n  await copyFile(src, dest);\n  return true;\n}\n\n/** The exact import line we manage. Changing this requires updating\n * uninstall too. */\nexport const IMPORT_LINE = \"@~/.claude/codealmanac.md\";\n\n/**\n * Append the import line to `~/.claude/CLAUDE.md` if it isn't already\n * present. Creates the file if absent. Returns true when we wrote, false\n * when the line was already there.\n *\n * We match on `@~/.claude/codealmanac.md` appearing on any non-empty\n * line (trimmed). This catches both the bare line we write and any\n * user-edited variant (comments, trailing whitespace). We deliberately\n * do NOT try to repair a user who deleted the newline — that's their\n * file to shape.\n */\nasync function ensureImport(claudeMdPath: string): Promise<boolean> {\n  let existing = \"\";\n  if (existsSync(claudeMdPath)) {\n    existing = await readFile(claudeMdPath, \"utf8\");\n  }\n  if (hasImportLine(existing)) return false;\n\n  const sep =\n    existing.length === 0 ? \"\" : existing.endsWith(\"\\n\") ? \"\\n\" : \"\\n\\n\";\n  const body = `${existing}${sep}${IMPORT_LINE}\\n`;\n  await writeFile(claudeMdPath, body, \"utf8\");\n  return true;\n}\n\nexport function hasImportLine(contents: string): boolean {\n  // Match line-starts-with-token rather than exact-line equality so a\n  // user who annotated the import line (`@~/.claude/codealmanac.md #\n  // codealmanac`) doesn't cause us to re-append a duplicate below.\n  // The trailing-character check rules out accidental matches on a\n  // longer line like `@~/.claude/codealmanac.md-extra`.\n  const lines = contents.split(/\\r?\\n/).map((l) => l.trim());\n  return lines.some((line) => {\n    if (line === IMPORT_LINE) return true;\n    if (!line.startsWith(IMPORT_LINE)) return false;\n    const next = line[IMPORT_LINE.length];\n    return next === \" \" || next === \"\\t\";\n  });\n}\n\n// ─── Interactive prompt ──────────────────────────────────────────────\n\ntype InstallDecision = \"install\" | \"skip\";\n\n/**\n * Minimal `[Y/n]` prompt. No raw mode, no cursor — just readline. The\n * MCP setup uses a fancy arrow-key TUI for multi-choice; we only have\n * binary decisions here, so a line-reader prompt is clearer and doesn't\n * fight with the step-indicator rendering above it.\n */\nfunction confirm(\n  out: NodeJS.WritableStream,\n  question: string,\n  defaultYes: boolean,\n): Promise<InstallDecision> {\n  return new Promise((resolve) => {\n    const hint = defaultYes ? \"[Y/n]\" : \"[y/N]\";\n    out.write(`  ${BLUE}\\u25c6${RST}  ${question} ${DIM}${hint}${RST} `);\n\n    let buf = \"\";\n    const onData = (chunk: Buffer): void => {\n      buf += chunk.toString(\"utf8\");\n      const nl = buf.indexOf(\"\\n\");\n      if (nl === -1) return;\n      process.stdin.removeListener(\"data\", onData);\n      process.stdin.pause();\n\n      const answer = buf.slice(0, nl).trim().toLowerCase();\n      const accepted =\n        answer.length === 0\n          ? defaultYes\n          : answer === \"y\" || answer === \"yes\";\n      resolve(accepted ? \"install\" : \"skip\");\n    };\n\n    process.stdin.resume();\n    process.stdin.on(\"data\", onData);\n  });\n}\n\n// ─── Guides path resolution ──────────────────────────────────────────\n\n/**\n * Locate `guides/` relative to the installed package. Mirrors\n * `resolvePromptsDir` from `src/agent/prompts.ts`.\n *\n * Two runtime layouts to handle:\n *\n *   1. **Bundled dist.** `dist/codealmanac.js` → walk one level up →\n *      `guides/`.\n *   2. **Source (tests / tsx).** `src/commands/setup.ts` → walk two\n *      levels up → `guides/`.\n *\n * We also try `createRequire` to resolve the package root from the\n * `codealmanac/package.json` manifest, as a belt-and-suspenders fallback\n * for unusual install layouts (monorepo hoisting, etc.). That path is\n * only exercised when the direct walk-up fails.\n */\nexport function resolveGuidesDir(): string {\n  const here = path.dirname(fileURLToPath(import.meta.url));\n  const candidates = [\n    path.resolve(here, \"..\", \"guides\"), // dist layout\n    path.resolve(here, \"..\", \"..\", \"guides\"), // src layout\n    path.resolve(here, \"..\", \"..\", \"..\", \"guides\"),\n  ];\n  for (const dir of candidates) {\n    if (looksLikeGuidesDir(dir)) return dir;\n  }\n  // Fallback: resolve via the package.json of the currently-running\n  // codealmanac. createRequire lets us ask Node's resolver rather than\n  // guessing at directory layouts.\n  try {\n    const require = createRequire(import.meta.url);\n    const pkgJson = require.resolve(\"codealmanac/package.json\");\n    const guides = path.join(path.dirname(pkgJson), \"guides\");\n    if (looksLikeGuidesDir(guides)) return guides;\n  } catch {\n    // Ignore — we'll throw with the candidate list below.\n  }\n  throw new Error(\n    \"could not locate bundled guides/ directory. Tried:\\n\" +\n      candidates.map((c) => `  - ${c}`).join(\"\\n\"),\n  );\n}\n\nfunction looksLikeGuidesDir(dir: string): boolean {\n  return existsSync(path.join(dir, \"mini.md\"));\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 { mkdir, readFile, rename, writeFile } from \"node:fs/promises\";\nimport path from \"node:path\";\n\nimport {\n  copyToStableHooksDir,\n  resolveHookScriptPath,\n  resolveSettingsPath,\n  type ScriptResolution,\n} from \"./hook/script.js\";\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 * - **Schema.** Claude Code validates `settings.json` against a strict\n *   schema: each entry in an event array (like `SessionEnd`) is a\n *   `{matcher, hooks: [...]}` container, and the actual command objects\n *   live in the nested `hooks` array. v0.1.0–v0.1.4 wrote command objects\n *   directly at the event-array level; newer Claude Code versions now\n *   reject that shape. We produce the wrapped form on install, and when\n *   encountering a legacy unwrapped entry that we recognize as ours (by\n *   `command` ending in `almanac-capture.sh`) we migrate it on next\n *   install. `SessionEnd` never uses the `matcher` field to discriminate\n *   anything — we always emit an empty `matcher: \"\"` (matches\n *   everything, which is what session-end lifecycle hooks want).\n *\n * - **Idempotent.** `install` twice leaves one entry, not two. We match by\n *   `command` string equality on the inner `hooks[]` entries. If the user\n *   replaces our absolute path with a symlink pointing at the same\n *   script, we'll treat it as foreign. That's acceptable; the `status`\n *   output shows the path we'd use, so the 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. Foreign wrapped containers that don't reference our script are\n *   preserved byte-for-byte.\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   * Override the stable hooks directory where we copy the script.\n   * Defaults to `~/.claude/hooks/`. Tests sandbox this to a tmpdir.\n   *\n   * Bug #1 fix: we always copy the bundled script to this stable path\n   * before writing it into settings.json. This way the settings entry\n   * points at a user-owned location that survives npm version bumps,\n   * npx cache evictions, and nvm version switches — instead of an\n   * ephemeral path inside ~/.npm/_npx/<sha>/... or the nvm-versioned\n   * node_modules/.\n   */\n  stableHooksDir?: string;\n}\n\nexport interface HookCommandResult {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\nconst HOOK_TIMEOUT_SECONDS = 10;\n\n/** A single command invocation inside a wrapper's `hooks[]` array. */\ninterface HookCommand {\n  type: \"command\";\n  command: string;\n  timeout?: number;\n}\n\n/** A wrapped SessionEnd entry per Claude Code's schema. */\ninterface WrappedEntry {\n  matcher: string;\n  hooks: HookCommand[];\n}\n\n/**\n * What we read from `settings.hooks.SessionEnd`. During a read we may\n * encounter the legacy unwrapped shape (`HookCommand` directly) written\n * by v0.1.0–v0.1.4 — we recognize and migrate it. Unknown entries we\n * can't classify are preserved as-is via `unknown`.\n */\ntype RawEntry = WrappedEntry | HookCommand | unknown;\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\n * so we don't drop user settings when we write the file back.\n */\ntype SettingsJson = Record<string, unknown> & {\n  hooks?: Record<string, RawEntry[] | undefined>;\n};\n\n/**\n * Heuristic: does this command path look like one we installed?\n *\n * We match on the filename `almanac-capture.sh` regardless of the parent\n * directory. This covers:\n *   - the stable path: `~/.claude/hooks/almanac-capture.sh`\n *   - legacy paths from v0.1.0–v0.1.5: inside the nvm node_modules or\n *     npx cache\n * The stable path is what new installs produce; legacy paths are what\n * we migrate when the user runs `almanac hook install` again.\n */\nfunction isOurCommandPath(command: string): boolean {\n  return command.endsWith(\"almanac-capture.sh\");\n}\n\n/**\n * Classify a raw SessionEnd entry. Wrapped entries are the canonical\n * shape; unwrapped-command entries are legacy output from v0.1.0–v0.1.4.\n * Anything else (random user JSON) is `unknown` and we leave it alone.\n */\ntype Classified =\n  | { kind: \"wrapped\"; entry: WrappedEntry }\n  | { kind: \"legacy\"; entry: HookCommand }\n  | { kind: \"unknown\"; entry: unknown };\n\nfunction classifyEntry(raw: RawEntry): Classified {\n  if (raw === null || typeof raw !== \"object\") {\n    return { kind: \"unknown\", entry: raw };\n  }\n  const obj = raw as Record<string, unknown>;\n  if (Array.isArray(obj.hooks)) {\n    // Wrapped shape. `matcher` may be absent in hand-edited files; treat\n    // absent as \"\" so we don't throw on slightly malformed input.\n    const matcher = typeof obj.matcher === \"string\" ? obj.matcher : \"\";\n    const hooks: HookCommand[] = [];\n    for (const h of obj.hooks as unknown[]) {\n      if (h !== null && typeof h === \"object\") {\n        const ho = h as Record<string, unknown>;\n        if (ho.type === \"command\" && typeof ho.command === \"string\") {\n          const cmd: HookCommand = {\n            type: \"command\",\n            command: ho.command,\n          };\n          if (typeof ho.timeout === \"number\") cmd.timeout = ho.timeout;\n          hooks.push(cmd);\n        }\n      }\n    }\n    return { kind: \"wrapped\", entry: { matcher, hooks } };\n  }\n  if (obj.type === \"command\" && typeof obj.command === \"string\") {\n    // Legacy unwrapped shape — v0.1.0–v0.1.4 wrote this form.\n    const cmd: HookCommand = {\n      type: \"command\",\n      command: obj.command as string,\n    };\n    if (typeof obj.timeout === \"number\") cmd.timeout = obj.timeout;\n    return { kind: \"legacy\", entry: cmd };\n  }\n  return { kind: \"unknown\", entry: raw };\n}\n\n/** True when the entry references our script and is safely ours to manage. */\nfunction isOurWrapped(entry: WrappedEntry): boolean {\n  return entry.hooks.some((h) => isOurCommandPath(h.command));\n}\n\nexport async function runHookInstall(\n  options: HookCommandOptions = {},\n): Promise<HookCommandResult> {\n  const bundled = resolveHookScriptPath(options);\n  if (!bundled.ok) {\n    return { stdout: \"\", stderr: `almanac: ${bundled.error}\\n`, exitCode: 1 };\n  }\n\n  // Copy the bundled hook script to a stable user-owned location before\n  // writing that path into settings.json. This is the Bug #1 fix:\n  //\n  //   OLD behavior: settings.json pointed at the bundled path (inside\n  //   ~/.nvm/versions/node/<ver>/lib/node_modules/codealmanac/hooks/... or\n  //   ~/.npm/_npx/<sha>/node_modules/codealmanac/hooks/...). When the user\n  //   switches Node versions or the npx cache is evicted, the path breaks\n  //   silently and captures stop firing.\n  //\n  //   NEW behavior: we copy almanac-capture.sh to ~/.claude/hooks/ (same\n  //   directory Claude Code uses for its own built-in hooks, always present)\n  //   and point settings.json there. The stable path is independent of\n  //   Node version and npm cache state. When the user upgrades codealmanac,\n  //   `almanac hook install` copies a fresh script and updates settings.json\n  //   if the path changed.\n  //\n  // When `hookScriptPath` is explicitly provided (test injection), the\n  // caller has already specified the destination path — skip the copy and\n  // use that path directly. The stable-copy concern only applies to the\n  // production flow where we resolved from the bundled package layout.\n  const script: ScriptResolution = options.hookScriptPath !== undefined\n    ? bundled // already the caller-provided path, no copy needed\n    : await copyToStableHooksDir(bundled.path, 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  // Walk existing entries and split them into buckets:\n  //   - `preserved`  — foreign wrapped/unknown entries we leave alone.\n  //   - `oursAlready` — a wrapped entry that already points at OUR exact\n  //                     script path (makes install a no-op).\n  //   - `oursStale`   — a wrapped or legacy entry that references our\n  //                     capture script but at a different absolute path\n  //                     (old install, `npm i` moved us) or in the legacy\n  //                     unwrapped shape. We'll collapse these into a\n  //                     single fresh entry at the new path.\n  const preserved: RawEntry[] = [];\n  let oursAlready: WrappedEntry | null = null;\n  const staleCount = { n: 0 };\n\n  for (const raw of existing) {\n    const c = classifyEntry(raw);\n    if (c.kind === \"wrapped\") {\n      if (!isOurWrapped(c.entry)) {\n        preserved.push(raw);\n        continue;\n      }\n      // Entry belongs to us. Does it already point at the exact script\n      // path? If every command in its `hooks[]` that looks like ours is\n      // already at `script.path`, it's up to date.\n      const exactMatch = c.entry.hooks.some(\n        (h) => h.command === script.path,\n      );\n      if (exactMatch && oursAlready === null) {\n        oursAlready = c.entry;\n      } else {\n        staleCount.n += 1;\n      }\n    } else if (c.kind === \"legacy\") {\n      if (isOurCommandPath(c.entry.command)) {\n        // Legacy unwrapped entry of ours — always migrate to wrapped.\n        staleCount.n += 1;\n      } else {\n        // Foreign legacy entry (user had their own script before\n        // settings.json required wrapping). Leave it alone.\n        preserved.push(raw);\n      }\n    } else {\n      // Unknown shape — we can't classify it. Preserve verbatim.\n      preserved.push(raw);\n    }\n  }\n\n  // If every non-ours entry is a foreign unwrapped command (not a\n  // wrapped one) we refuse to touch the file — Claude Code's newer\n  // schema will already reject such files, but surfacing it here lets\n  // the user clean up before we stack our entry on top. Wrapped foreign\n  // entries are fine to leave alongside ours.\n  const foreignLegacy = preserved.filter((raw) => {\n    const c = classifyEntry(raw);\n    return c.kind === \"legacy\";\n  });\n  if (foreignLegacy.length > 0) {\n    const lines = foreignLegacy\n      .map((raw) => {\n        const c = classifyEntry(raw);\n        if (c.kind === \"legacy\") return `  - ${c.entry.command}`;\n        return \"  - <unrecognized>\";\n      })\n      .join(\"\\n\");\n    return {\n      stdout: \"\",\n      stderr:\n        `almanac: SessionEnd has a foreign legacy entry:\\n${lines}\\n` +\n        `Remove or rewrap it manually in ${settingsPath} before installing.\\n`,\n      exitCode: 1,\n    };\n  }\n\n  if (oursAlready !== null && staleCount.n === 0) {\n    return {\n      stdout: `almanac: SessionEnd hook already installed at ${script.path}\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  // Build the fresh wrapped entry and append to preserved foreign\n  // entries. Stale entries of ours are dropped (we only ever want a\n  // single active entry; multiple copies of the capture hook would\n  // double-fire on session end).\n  const fresh: WrappedEntry = {\n    matcher: \"\",\n    hooks: [\n      {\n        type: \"command\",\n        command: script.path,\n        timeout: HOOK_TIMEOUT_SECONDS,\n      },\n    ],\n  };\n\n  const newEntries: RawEntry[] = [...preserved, fresh];\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  const kept: RawEntry[] = [];\n  let removed = 0;\n\n  for (const raw of existing) {\n    const c = classifyEntry(raw);\n    if (c.kind === \"wrapped\") {\n      // Filter out our command(s) from the inner hooks array. Keep\n      // anything else in the array intact — a foreign wrapper that\n      // happened to include our script alongside its own commands\n      // (unusual, but survivable) loses our entry and keeps theirs.\n      const innerKept = c.entry.hooks.filter(\n        (h) => !isOurCommandPath(h.command),\n      );\n      const innerRemoved = c.entry.hooks.length - innerKept.length;\n      removed += innerRemoved;\n      if (innerKept.length === 0) {\n        // Only drop the outer wrapper when it was entirely ours. A\n        // foreign wrapper that never contained our script stays verbatim\n        // below (handled by `innerRemoved === 0`, which leaves\n        // `innerKept.length === c.entry.hooks.length`, hence we fall\n        // through to the else-branch).\n        if (innerRemoved === 0) kept.push(raw);\n        // else: fully owned by us, drop the container.\n      } else if (innerRemoved === 0) {\n        // Untouched foreign wrapper — preserve the raw object to keep\n        // any fields (like matcher) byte-for-byte.\n        kept.push(raw);\n      } else {\n        // Partial: rebuild with just the kept inner entries, preserving\n        // the original matcher string.\n        kept.push({ matcher: c.entry.matcher, hooks: innerKept });\n      }\n    } else if (c.kind === \"legacy\") {\n      if (isOurCommandPath(c.entry.command)) {\n        removed += 1;\n      } else {\n        kept.push(raw);\n      }\n    } else {\n      kept.push(raw);\n    }\n  }\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\n  // Walk the array looking for any entry (wrapped or legacy) that\n  // references our capture script. Gathering foreign entries separately\n  // lets us show them to the user if nothing of ours was found.\n  let ourCommand: string | null = null;\n  const foreignSummary: string[] = [];\n  for (const raw of existing) {\n    const c = classifyEntry(raw);\n    if (c.kind === \"wrapped\") {\n      for (const h of c.entry.hooks) {\n        if (isOurCommandPath(h.command)) {\n          ourCommand ??= h.command;\n        } else {\n          foreignSummary.push(h.command);\n        }\n      }\n    } else if (c.kind === \"legacy\") {\n      if (isOurCommandPath(c.entry.command)) {\n        ourCommand ??= c.entry.command;\n      } else {\n        foreignSummary.push(c.entry.command);\n      }\n    }\n  }\n\n  if (ourCommand === null) {\n    const foreignLines = foreignSummary\n      .map((c) => `  - ${c}`)\n      .join(\"\\n\");\n    return {\n      stdout:\n        `SessionEnd hook: not installed\\n` +\n        `settings: ${settingsPath}\\n` +\n        (foreignSummary.length > 0\n          ? `(${foreignSummary.length} foreign entr${foreignSummary.length === 1 ? \"y\" : \"ies\"} present:\\n${foreignLines})\\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: ${ourCommand}\\n` +\n      `settings: ${settingsPath}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\n// ─── Settings JSON helpers ───────────────────────────────────────────\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 { copyFile, mkdir, readFile } from \"node:fs/promises\";\nimport { homedir } from \"node:os\";\nimport path from \"node:path\";\nimport { fileURLToPath } from \"node:url\";\n\nexport interface HookPathOptions {\n  hookScriptPath?: string;\n  settingsPath?: string;\n  stableHooksDir?: string;\n}\n\nexport type ScriptResolution =\n  | { ok: true; path: string }\n  | { ok: false; error: string };\n\nexport function resolveSettingsPath(options: HookPathOptions): string {\n  if (options.settingsPath !== undefined) return options.settingsPath;\n  return path.join(homedir(), \".claude\", \"settings.json\");\n}\n\n/**\n * Copy the bundled hook script to `~/.claude/hooks/almanac-capture.sh`.\n *\n * This stable, user-owned destination survives Node version switches and\n * npm/npx cache evictions. The copy is idempotent: if bytes already match\n * we skip writing so repeated setup runs do not bump mtimes.\n */\nexport async function copyToStableHooksDir(\n  bundledPath: string,\n  options: HookPathOptions,\n): Promise<ScriptResolution> {\n  const stableHooksDir =\n    options.stableHooksDir ?? path.join(homedir(), \".claude\", \"hooks\");\n  const dest = path.join(stableHooksDir, \"almanac-capture.sh\");\n\n  try {\n    await mkdir(stableHooksDir, { recursive: true });\n    const srcBytes = await readFile(bundledPath);\n    let needsCopy = true;\n    if (existsSync(dest)) {\n      try {\n        const destBytes = await readFile(dest);\n        if (srcBytes.equals(destBytes)) needsCopy = false;\n      } catch {\n        // Can't read dest — overwrite.\n      }\n    }\n    if (needsCopy) {\n      await copyFile(bundledPath, dest);\n    }\n    return { ok: true, path: dest };\n  } catch (err: unknown) {\n    const msg = err instanceof Error ? err.message : String(err);\n    return {\n      ok: false,\n      error: `could not copy hook script to ${dest}: ${msg}`,\n    };\n  }\n}\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 */\nexport function resolveHookScriptPath(\n  options: HookPathOptions,\n): 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 after ts-node-style module layout or nested dist helpers.\n    path.resolve(here, \"..\", \"..\", \"hooks\", \"almanac-capture.sh\"),\n    // Source: `.../codealmanac/src/commands/hook/script.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","import { execFile } from \"node:child_process\";\nimport { createRequire } from \"node:module\";\nimport { homedir } from \"node:os\";\nimport path from \"node:path\";\nimport { fileURLToPath } from \"node:url\";\n\n/**\n * Return the directory of the currently-running codealmanac install by\n * walking up from this module's file to the nearest `package.json` whose\n * `name` is `codealmanac`. Returns the empty string when the walk fails.\n */\nexport function detectCurrentInstallPath(): string {\n  try {\n    const req = createRequire(import.meta.url);\n    const here = fileURLToPath(import.meta.url);\n    let dir = path.dirname(here);\n    for (let i = 0; i < 6; i++) {\n      const pkgPath = path.join(dir, \"package.json\");\n      try {\n        const raw = req(\"fs\").readFileSync(pkgPath, \"utf-8\") as string;\n        const pkg = JSON.parse(raw) as { name?: unknown };\n        if (pkg.name === \"codealmanac\") return dir;\n      } catch {\n        // keep walking\n      }\n      const parent = path.dirname(dir);\n      if (parent === dir) break;\n      dir = parent;\n    }\n  } catch {\n    // import.meta.url unavailable — not ephemeral for our purposes.\n  }\n  return \"\";\n}\n\n/**\n * Return true when the given install path looks ephemeral.\n *\n * Ephemeral locations we recognize:\n *   - `~/.npm/_npx/` — npm's npx cache (GC'd on version bumps or\n *     `npm cache clean`)\n *   - `~/.local/share/pnpm/dlx/` — pnpm's dlx (like npx) cache\n *   - `/tmp/` or `/var/folders/` — common CI / temp paths\n *\n * A global install (`~/.nvm/.../lib/node_modules/`, `/usr/local/lib/...`,\n * `~/.local/lib/node_modules/`) is NOT ephemeral.\n */\nexport function detectEphemeral(installPath: string): boolean {\n  if (installPath.length === 0) return false;\n  const home = homedir();\n  if (installPath.startsWith(path.join(home, \".npm\", \"_npx\"))) return true;\n  if (\n    installPath.startsWith(path.join(home, \".local\", \"share\", \"pnpm\", \"dlx\"))\n  ) return true;\n  if (installPath.startsWith(\"/tmp/\")) return true;\n  if (installPath.startsWith(\"/var/folders/\")) return true;\n  return false;\n}\n\n/**\n * Spawn `npm install -g codealmanac@latest` in a child process and wait\n * for it to finish. Rejects on non-zero exit or spawn error.\n */\nexport function spawnGlobalInstall(): Promise<void> {\n  return new Promise((resolve, reject) => {\n    execFile(\n      \"npm\",\n      [\"install\", \"-g\", \"codealmanac@latest\"],\n      { shell: false },\n      (err, _stdout, stderr) => {\n        if (err !== null) {\n          reject(\n            new Error(\n              stderr.length > 0\n                ? stderr.trim().split(\"\\n\")[0] ?? err.message\n                : err.message,\n            ),\n          );\n        } else {\n          resolve();\n        }\n      },\n    );\n  });\n}\n","import { existsSync, readdirSync } from \"node:fs\";\nimport path from \"node:path\";\n\nconst RST = \"\\x1b[0m\";\nconst BOLD = \"\\x1b[1m\";\nconst DIM = \"\\x1b[2m\";\nconst WHITE_BOLD = \"\\x1b[1;37m\";\nconst BLUE = \"\\x1b[38;5;75m\";\nconst BLUE_DIM = \"\\x1b[38;5;69m\";\n\n/**\n * Print the \"Next steps\" box. When `existingPageCount` is greater than 0,\n * the current working directory already has a wiki with committed pages.\n * In that case we skip the `almanac bootstrap` step and tell the user to\n * start querying.\n */\nexport function printNextSteps(\n  out: NodeJS.WritableStream,\n  existingPageCount: number,\n): void {\n  const innerW = 62;\n  const vis = (s: string): number =>\n    s.replace(/\\x1b\\[[0-9;]*m/g, \"\").length;\n  const row = (content: string): string => {\n    const padding = Math.max(0, innerW - vis(content));\n    return `  ${BLUE_DIM}\\u2502${RST}${content}${\" \".repeat(padding)}${BLUE_DIM}\\u2502${RST}\\n`;\n  };\n  const empty = row(\"\");\n\n  out.write(`  ${BLUE_DIM}\\u256d${\"─\".repeat(innerW)}\\u256e${RST}\\n`);\n  out.write(empty);\n  out.write(row(`  ${WHITE_BOLD}Next steps${RST}`));\n  out.write(empty);\n\n  if (existingPageCount > 0) {\n    out.write(\n      row(\n        `  ${BLUE}\\u25c7${RST}  This repo already has a wiki ${DIM}(${existingPageCount} page${existingPageCount === 1 ? \"\" : \"s\"})${RST}`,\n      ),\n    );\n    out.write(empty);\n    out.write(row(`  ${BLUE}1.${RST}  Start querying your wiki:`));\n    out.write(row(`       ${BOLD}almanac search --mentions <file>${RST}`));\n    out.write(\n      row(`  ${BLUE}2.${RST}  Work normally — capture runs on session end`),\n    );\n  } else {\n    out.write(\n      row(`  ${BLUE}1.${RST}  ${BOLD}cd${RST} into a repo you want to document`),\n    );\n    out.write(\n      row(\n        `  ${BLUE}2.${RST}  ${BOLD}almanac bootstrap${RST}  ${DIM}# scaffold the wiki${RST}`,\n      ),\n    );\n    out.write(\n      row(`  ${BLUE}3.${RST}  Work normally — capture runs on session end`),\n    );\n  }\n\n  out.write(empty);\n  out.write(`  ${BLUE_DIM}\\u2570${\"─\".repeat(innerW)}\\u256f${RST}\\n\\n`);\n}\n\n/**\n * Count `.md` files in `.almanac/pages/` under the current working\n * directory or any parent. Returns 0 when no wiki is found or the pages\n * directory is empty.\n */\nexport function countExistingPages(cwd: string): number {\n  try {\n    let dir = cwd;\n    for (let i = 0; i < 10; i++) {\n      const pagesDir = path.join(dir, \".almanac\", \"pages\");\n      if (existsSync(pagesDir)) {\n        try {\n          const entries = readdirSync(pagesDir);\n          return entries.filter((e) => e.endsWith(\".md\")).length;\n        } catch {\n          return 0;\n        }\n      }\n      const parent = path.dirname(dir);\n      if (parent === dir) break;\n      dir = parent;\n    }\n  } catch {\n    // Swallow — never crash setup because of this.\n  }\n  return 0;\n}\n","/**\n * Shared ANSI escape-code constants. TTY-aware: when stdout is not a\n * terminal or `NO_COLOR` is set, every constant resolves to the empty\n * string so formatted output degrades to plain text without per-call\n * checks at every use site.\n *\n * See https://no-color.org/ for the `NO_COLOR` convention.\n */\n\nconst useColor =\n  (process.stdout.isTTY ?? false) && !(\"NO_COLOR\" in process.env);\n\nexport const RST = useColor ? \"\\x1b[0m\" : \"\";\nexport const BOLD = useColor ? \"\\x1b[1m\" : \"\";\nexport const DIM = useColor ? \"\\x1b[2m\" : \"\";\nexport const GREEN = useColor ? \"\\x1b[38;5;35m\" : \"\";\nexport const RED = useColor ? \"\\x1b[38;5;167m\" : \"\";\nexport const BLUE = useColor ? \"\\x1b[38;5;75m\" : \"\";\nexport const YELLOW = useColor ? \"\\x1b[33m\" : \"\";\nexport const WHITE_BOLD = useColor ? \"\\x1b[1;37m\" : \"\";\nexport const BLUE_DIM = useColor ? \"\\x1b[38;5;69m\" : \"\";\nexport const ACCENT_BG = useColor\n  ? \"\\x1b[48;5;252m\\x1b[38;5;16m\"\n  : \"\";\n","import { Command, type Help } from \"commander\";\n\nimport { BLUE, BOLD, DIM, RST } from \"../ansi.js\";\n\nconst HELP_GROUPS: Array<{ title: string; commands: string[] }> = [\n  {\n    title: \"Query\",\n    commands: [\"search\", \"show\", \"health\", \"list\"],\n  },\n  {\n    title: \"Edit\",\n    commands: [\"tag\", \"untag\", \"topics\"],\n  },\n  {\n    title: \"Wiki lifecycle\",\n    commands: [\"bootstrap\", \"capture\", \"hook\", \"reindex\"],\n  },\n  {\n    title: \"Setup\",\n    commands: [\"setup\", \"uninstall\", \"doctor\", \"update\"],\n  },\n];\n\n/**\n * Install a custom `formatHelp` that replaces commander's flat\n * \"Commands:\" section with grouped headings. Keeps usage + options +\n * per-command short descriptions; only the commands section changes.\n */\nexport function configureGroupedHelp(program: Command): void {\n  program.configureHelp({\n    formatHelp(cmd, helper): string {\n      if (cmd.parent !== null) {\n        return renderDefault(cmd, helper);\n      }\n\n      const termWidth = helper.padWidth(cmd, helper);\n      const helpWidth =\n        helper.helpWidth ?? process.stdout.columns ?? 80;\n      const itemSepWidth = 2;\n\n      const out: string[] = [];\n      out.push(`${BOLD}Usage:${RST} ${helper.commandUsage(cmd)}\\n`);\n\n      const description = helper.commandDescription(cmd);\n      if (description.length > 0) {\n        out.push(\n          helper.wrap(description, helpWidth, 0) + \"\\n\",\n        );\n      }\n\n      const optionList = helper\n        .visibleOptions(cmd)\n        .map((o) => {\n          const term = helper.optionTerm(o);\n          const pad = \" \".repeat(Math.max(0, termWidth - term.length) + itemSepWidth);\n          return `${BLUE}${term}${RST}${pad}${DIM}${helper.optionDescription(o)}${RST}`;\n        });\n      if (optionList.length > 0) {\n        out.push(`${BOLD}Options:${RST}`);\n        for (const l of optionList) out.push(`  ${l}`);\n        out.push(\"\");\n      }\n\n      const visible = helper.visibleCommands(cmd);\n      const byName = new Map<string, (typeof visible)[number]>();\n      for (const c of visible) byName.set(c.name(), c);\n\n      for (const group of HELP_GROUPS) {\n        const members = group.commands\n          .map((n) => byName.get(n))\n          .filter((c): c is (typeof visible)[number] => c !== undefined);\n        if (members.length === 0) continue;\n        out.push(`${BOLD}${group.title}:${RST}`);\n        for (const c of members) {\n          const term = helper.subcommandTerm(c);\n          const desc = helper.subcommandDescription(c);\n          const padding = Math.max(\n            0,\n            termWidth - term.length + itemSepWidth,\n          );\n          out.push(`  ${BLUE}${term}${RST}${\" \".repeat(padding)}${DIM}${desc}${RST}`);\n          byName.delete(c.name());\n        }\n        out.push(\"\");\n      }\n\n      byName.delete(\"help\");\n      if (byName.size > 0) {\n        out.push(`${BOLD}Other:${RST}`);\n        for (const c of byName.values()) {\n          const term = helper.subcommandTerm(c);\n          const desc = helper.subcommandDescription(c);\n          const padding = Math.max(\n            0,\n            termWidth - term.length + itemSepWidth,\n          );\n          out.push(`  ${BLUE}${term}${RST}${\" \".repeat(padding)}${DIM}${desc}${RST}`);\n        }\n        out.push(\"\");\n      }\n\n      return out.join(\"\\n\");\n    },\n  });\n}\n\nfunction renderDefault(cmd: Command, helper: Help): string {\n  const termWidth = helper.padWidth(cmd, helper);\n  const helpWidth = helper.helpWidth ?? process.stdout.columns ?? 80;\n  const itemSepWidth = 2;\n\n  const lines: string[] = [`${BOLD}Usage:${RST} ${helper.commandUsage(cmd)}\\n`];\n  const description = helper.commandDescription(cmd);\n  if (description.length > 0) {\n    lines.push(helper.wrap(description, helpWidth, 0) + \"\\n\");\n  }\n\n  const args = helper.visibleArguments(cmd).map((a) => {\n    const term = helper.argumentTerm(a);\n    const pad = \" \".repeat(Math.max(0, termWidth - term.length) + itemSepWidth);\n    return `${BLUE}${term}${RST}${pad}${DIM}${helper.argumentDescription(a)}${RST}`;\n  });\n  if (args.length > 0) {\n    lines.push(`${BOLD}Arguments:${RST}`);\n    for (const a of args) lines.push(`  ${a}`);\n    lines.push(\"\");\n  }\n\n  const opts = helper.visibleOptions(cmd).map((o) => {\n    const term = helper.optionTerm(o);\n    const pad = \" \".repeat(Math.max(0, termWidth - term.length) + itemSepWidth);\n    return `${BLUE}${term}${RST}${pad}${DIM}${helper.optionDescription(o)}${RST}`;\n  });\n  if (opts.length > 0) {\n    lines.push(`${BOLD}Options:${RST}`);\n    for (const o of opts) lines.push(`  ${o}`);\n    lines.push(\"\");\n  }\n\n  const subs = helper.visibleCommands(cmd).map((c) => {\n    const term = helper.subcommandTerm(c);\n    const pad = \" \".repeat(Math.max(0, termWidth - term.length) + itemSepWidth);\n    return `${BLUE}${term}${RST}${pad}${DIM}${helper.subcommandDescription(c)}${RST}`;\n  });\n  if (subs.length > 0) {\n    lines.push(`${BOLD}Commands:${RST}`);\n    for (const s of subs) lines.push(`  ${s}`);\n    lines.push(\"\");\n  }\n\n  return lines.join(\"\\n\");\n}\n","export interface CommandResult {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\nexport function emit(result: CommandResult): void {\n  if (result.stderr.length > 0) process.stderr.write(result.stderr);\n  if (result.stdout.length > 0) process.stdout.write(result.stdout);\n  if (result.exitCode !== 0) process.exitCode = result.exitCode;\n}\n\nexport function collectOption(value: string, previous: string[]): string[] {\n  return [...previous, value];\n}\n\nexport function parsePositiveInt(value: string): number {\n  const n = Number.parseInt(value, 10);\n  if (!Number.isFinite(n) || n < 0) {\n    throw new Error(`invalid --limit \"${value}\" (expected a non-negative integer)`);\n  }\n  return n;\n}\n\nexport async 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 { createHash } from \"node:crypto\";\nimport { existsSync, statSync } from \"node:fs\";\nimport { readFile, utimes } from \"node:fs/promises\";\nimport { basename, join } from \"node:path\";\n\nimport fg from \"fast-glob\";\nimport type Database from \"better-sqlite3\";\n\nimport { toKebabCase } from \"../slug.js\";\nimport { titleCase } from \"../topics/yaml.js\";\nimport { firstH1, parseFrontmatter } from \"./frontmatter.js\";\nimport {\n  PAGES_GLOB,\n  pagesNewerThan,\n  topicsYamlNewerThan,\n} from \"./freshness.js\";\nimport {\n  normalizePath,\n  normalizePathPreservingCase,\n  looksLikeDir,\n} from \"./paths.js\";\nimport { openIndex } from \"./schema.js\";\nimport { applyTopicsYaml, TOPICS_YAML_FILENAME } from \"./topics-yaml.js\";\nimport { extractWikilinks } from \"./wikilinks.js\";\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/**\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  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\nfunction hashContent(raw: string): string {\n  return createHash(\"sha256\").update(raw).digest(\"hex\");\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 { 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","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, statSync } from \"node:fs\";\nimport { join } from \"node:path\";\n\nimport fg from \"fast-glob\";\n\n// Glob is relative to `.almanac/pages/`, so this is every markdown page\n// beneath pages without repeating the `pages/` prefix.\nexport const PAGES_GLOB = \"**/*.md\";\n\n/**\n * Return true if any page file has an mtime strictly greater than the\n * index DB's mtime. This is intentionally cheap: `fast-glob` with\n * `stats: true` gives us mtimes without a second `stat` round-trip, and\n * the synchronous walk keeps the decision path simple for CLI entrypoints.\n */\nexport function 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  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\n/**\n * Return true if `topics.yaml` has an mtime strictly greater than the\n * index DB's mtime. Missing `topics.yaml` is legal: it means \"no topic\n * metadata yet\", not \"the index is stale\".\n */\nexport function topicsYamlNewerThan(\n  almanacDir: string,\n  dbPath: string,\n): 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 * 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 { existsSync } from \"node:fs\";\n\nimport type Database from \"better-sqlite3\";\n\nimport { loadTopicsFile } from \"../topics/yaml.js\";\n\nexport const TOPICS_YAML_FILENAME = \"topics.yaml\";\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` and rewrite that topic's parent edges.\n *\n * Important invariants:\n * - Missing `topics.yaml` is a no-op. Absence is legal and means \"no\n *   topic metadata yet\".\n * - Topics mentioned only in page frontmatter are legal ad-hoc topics.\n *   Do not delete them just because they are absent from `topics.yaml`.\n * - Stale topic rows are pruned only after upserting declared topics and\n *   collecting current `page_topics`, so `health` does not flag topics\n *   that were removed from every page after a rename/delete.\n */\nexport async 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  // Declared means either explicitly present in topics.yaml or currently\n  // referenced by page frontmatter. Anything outside this set is stale.\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 last, after\n    // the upserts above have 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 { 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 bootstrap` first\",\n    );\n  }\n  return nearest;\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 { 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 { 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/resolve-wiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\nimport { toKebabCase } from \"../slug.js\";\nimport { rewritePageTopics } from \"../topics/frontmatter-rewrite.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 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 type Database from \"better-sqlite3\";\n\nimport { ensureFreshIndex } from \"../../indexer/index.js\";\nimport { resolveWikiRoot } from \"../../indexer/resolve-wiki.js\";\nimport { openIndex } from \"../../indexer/schema.js\";\nimport { indexDbPath, topicsYamlPath } from \"../../topics/paths.js\";\nimport {\n  findTopic,\n  loadTopicsFile,\n  type TopicsFile,\n} from \"../../topics/yaml.js\";\n\ninterface TopicsRepoOptions {\n  cwd: string;\n  wiki?: string;\n}\n\nexport interface TopicsWorkspace {\n  repoRoot: string;\n  yamlPath: string;\n  file: TopicsFile;\n  db: Database.Database;\n}\n\nexport function resolveTopicsRepo(options: TopicsRepoOptions): Promise<string> {\n  return resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n}\n\n/**\n * Shared setup path for mutating topic commands. These commands all need\n * a fresh DB view so ad-hoc topics from page frontmatter can be promoted\n * into `topics.yaml` before mutation.\n */\nexport async function openFreshTopicsWorkspace(\n  repoRoot: string,\n): Promise<TopicsWorkspace> {\n  await ensureFreshIndex({ repoRoot });\n\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n  const db = openIndex(indexDbPath(repoRoot));\n  return { repoRoot, yamlPath, file, db };\n}\n\nexport function closeWorkspace(workspace: TopicsWorkspace): void {\n  workspace.db.close();\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 */\nexport function 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","import { runIndexer } from \"../../indexer/index.js\";\nimport { toKebabCase } from \"../../slug.js\";\nimport { ancestorsInFile } from \"../../topics/dag.js\";\nimport {\n  ensureTopic,\n  findTopic,\n  titleCase,\n  writeTopicsFile,\n  type TopicEntry,\n} from \"../../topics/yaml.js\";\nimport type { TopicsCommandOutput, TopicsCreateOptions } from \"./types.js\";\nimport {\n  closeWorkspace,\n  openFreshTopicsWorkspace,\n  resolveTopicsRepo,\n  topicExists,\n} from \"./workspace.js\";\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 resolveTopicsRepo(options);\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  const workspace = await openFreshTopicsWorkspace(repoRoot);\n  try {\n    const { repoRoot, yamlPath, file, db } = workspace;\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    closeWorkspace(workspace);\n  }\n}\n","import { readFile } from \"node:fs/promises\";\nimport { join } from \"node:path\";\n\nimport fg from \"fast-glob\";\n\nimport {\n  applyTopicsTransform,\n  rewritePageTopics,\n} from \"../../topics/frontmatter-rewrite.js\";\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 */\nexport async 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","import { runIndexer } from \"../../indexer/index.js\";\nimport { toKebabCase } from \"../../slug.js\";\nimport { writeTopicsFile } from \"../../topics/yaml.js\";\nimport { rewriteTopicOnPages } from \"./page-rewrite.js\";\nimport type { TopicsCommandOutput, TopicsDeleteOptions } from \"./types.js\";\nimport {\n  closeWorkspace,\n  openFreshTopicsWorkspace,\n  resolveTopicsRepo,\n  topicExists,\n} from \"./workspace.js\";\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 resolveTopicsRepo(options);\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  const workspace = await openFreshTopicsWorkspace(repoRoot);\n  let pagesUpdated: number;\n  try {\n    const { repoRoot, yamlPath, file, db } = workspace;\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    closeWorkspace(workspace);\n  }\n\n  await runIndexer({ repoRoot: workspace.repoRoot });\n  return {\n    stdout: `deleted topic \"${slug}\" (${pagesUpdated} page${pagesUpdated === 1 ? \"\" : \"s\"} untagged)\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n","import { runIndexer } from \"../../indexer/index.js\";\nimport { toKebabCase } from \"../../slug.js\";\nimport { ensureTopic, writeTopicsFile } from \"../../topics/yaml.js\";\nimport type { TopicsCommandOutput, TopicsDescribeOptions } from \"./types.js\";\nimport {\n  closeWorkspace,\n  openFreshTopicsWorkspace,\n  resolveTopicsRepo,\n  topicExists,\n} from \"./workspace.js\";\n\n/**\n * `almanac topics describe <slug> \"<text>\"`. Sets or updates the\n * one-liner description. An empty string clears it.\n */\nexport async function runTopicsDescribe(\n  options: TopicsDescribeOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveTopicsRepo(options);\n  const slug = toKebabCase(options.slug);\n  if (slug.length === 0) {\n    return { stdout: \"\", stderr: `almanac: empty topic slug\\n`, exitCode: 1 };\n  }\n\n  const workspace = await openFreshTopicsWorkspace(repoRoot);\n  try {\n    const { yamlPath, file, db } = workspace;\n    if (!topicExists(file, db, slug)) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: no such topic \"${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    closeWorkspace(workspace);\n  }\n\n  await runIndexer({ repoRoot: workspace.repoRoot });\n  return {\n    stdout: `described ${slug}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n","import { runIndexer } from \"../../indexer/index.js\";\nimport { toKebabCase } from \"../../slug.js\";\nimport { ancestorsInFile } from \"../../topics/dag.js\";\nimport {\n  ensureTopic,\n  findTopic,\n  writeTopicsFile,\n} from \"../../topics/yaml.js\";\nimport type { TopicsCommandOutput, TopicsLinkOptions } from \"./types.js\";\nimport {\n  closeWorkspace,\n  openFreshTopicsWorkspace,\n  resolveTopicsRepo,\n  topicExists,\n} from \"./workspace.js\";\n\n/**\n * `almanac topics link <child> <parent>`. Adds a DAG edge after\n * checking that it wouldn't close a cycle. Both topics must exist.\n */\nexport async function runTopicsLink(\n  options: TopicsLinkOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveTopicsRepo(options);\n  const child = toKebabCase(options.child);\n  const parent = toKebabCase(options.parent);\n  if (child.length === 0 || parent.length === 0) {\n    return { stdout: \"\", stderr: `almanac: empty topic slug\\n`, exitCode: 1 };\n  }\n  if (child === parent) {\n    return {\n      stdout: \"\",\n      stderr: `almanac: topic cannot be its own parent\\n`,\n      exitCode: 1,\n    };\n  }\n\n  const workspace = await openFreshTopicsWorkspace(repoRoot);\n  try {\n    const { repoRoot, yamlPath, file, db } = workspace;\n    for (const slug of [child, parent]) {\n      if (!topicExists(file, db, slug)) {\n        return {\n          stdout: \"\",\n          stderr: `almanac: topic \"${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    closeWorkspace(workspace);\n  }\n}\n","import { BLUE, DIM, RST } from \"../../ansi.js\";\nimport { ensureFreshIndex } from \"../../indexer/index.js\";\nimport { resolveWikiRoot } from \"../../indexer/resolve-wiki.js\";\nimport { openIndex } from \"../../indexer/schema.js\";\nimport { indexDbPath } from \"../../topics/paths.js\";\nimport type { TopicsCommandOutput, TopicsListOptions } from \"./types.js\";\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 `${BLUE}${slug}${RST}  ${DIM}${count}${RST}`;\n    });\n    return { stdout: `${lines.join(\"\\n\")}\\n`, stderr: \"\", exitCode: 0 };\n  } finally {\n    db.close();\n  }\n}\n","import { runIndexer } from \"../../indexer/index.js\";\nimport { toKebabCase } from \"../../slug.js\";\nimport {\n  findTopic,\n  titleCase,\n  writeTopicsFile,\n} from \"../../topics/yaml.js\";\nimport { rewriteTopicOnPages } from \"./page-rewrite.js\";\nimport type { TopicsCommandOutput, TopicsRenameOptions } from \"./types.js\";\nimport {\n  closeWorkspace,\n  openFreshTopicsWorkspace,\n  resolveTopicsRepo,\n  topicExists,\n} from \"./workspace.js\";\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 resolveTopicsRepo(options);\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 \"${oldSlug}\" unchanged\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  const workspace = await openFreshTopicsWorkspace(repoRoot);\n  let pagesUpdated: number;\n  try {\n    const { repoRoot, yamlPath, file, db } = workspace;\n    // Fetch existence info. `oldInYaml` is kept as a direct reference\n    // because we mutate the entry; the DB check is only needed when\n    // the slug isn't in the file (ad-hoc-only).\n    const oldInYaml = findTopic(file, oldSlug);\n    if (!topicExists(file, db, oldSlug)) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: no such topic \"${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    closeWorkspace(workspace);\n  }\n\n  await runIndexer({ repoRoot: workspace.repoRoot });\n  return {\n    stdout: `renamed ${oldSlug} → ${newSlug} (${pagesUpdated} page${pagesUpdated === 1 ? \"\" : \"s\"} updated)\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n","import type Database from \"better-sqlite3\";\n\nimport { BLUE, DIM, RST } from \"../../ansi.js\";\nimport { descendantsInDb } from \"../../topics/dag.js\";\nimport { titleCase } from \"../../topics/yaml.js\";\n\nexport interface TopicsShowRecord {\n  slug: string;\n  title: string | null;\n  description: string | null;\n  parents: string[];\n  children: string[];\n  pages: string[];\n  descendants_used?: boolean;\n}\n\nexport function pagesDirectlyTagged(\n  db: Database.Database,\n  slug: string,\n): string[] {\n  return db\n    .prepare<[string], { page_slug: string }>(\n      `SELECT pt.page_slug\n       FROM page_topics pt\n       JOIN pages p ON p.slug = pt.page_slug\n       WHERE pt.topic_slug = ? AND p.archived_at IS NULL\n       ORDER BY pt.page_slug`,\n    )\n    .all(slug)\n    .map((r) => r.page_slug);\n}\n\nexport function pagesForSubtree(\n  db: Database.Database,\n  slug: string,\n): string[] {\n  const slugs = [slug, ...descendantsInDb(db, slug)];\n  // Deduplicate + preserve order via a Set — a page can belong to\n  // multiple topics in the subtree and we only want one row per page.\n  const placeholders = slugs.map(() => \"?\").join(\", \");\n  const rows = db\n    .prepare<unknown[], { page_slug: string }>(\n      `SELECT DISTINCT pt.page_slug\n       FROM page_topics pt\n       JOIN pages p ON p.slug = pt.page_slug\n       WHERE pt.topic_slug IN (${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\nexport function formatShow(r: TopicsShowRecord): string {\n  const lines: string[] = [];\n  lines.push(`${DIM}slug:${RST}         ${BLUE}${r.slug}${RST}`);\n  lines.push(`${DIM}title:${RST}        ${r.title ?? titleCase(r.slug)}`);\n  lines.push(`${DIM}description:${RST}  ${r.description ?? \"—\"}`);\n  lines.push(\n    `${DIM}parents:${RST}      ${r.parents.length > 0 ? r.parents.join(\", \") : \"—\"}`,\n  );\n  lines.push(\n    `${DIM}children:${RST}     ${r.children.length > 0 ? r.children.join(\", \") : \"—\"}`,\n  );\n  const pagesLabel = r.descendants_used === true\n    ? \"pages (incl. descendants)\"\n    : \"pages\";\n  lines.push(`${DIM}${pagesLabel}:${RST}`);\n  if (r.pages.length === 0) {\n    lines.push(\"  —\");\n  } else {\n    for (const p of r.pages) lines.push(`  ${BLUE}${p}${RST}`);\n  }\n  return `${lines.join(\"\\n\")}\\n`;\n}\n","import { ensureFreshIndex } from \"../../indexer/index.js\";\nimport { resolveWikiRoot } from \"../../indexer/resolve-wiki.js\";\nimport { openIndex } from \"../../indexer/schema.js\";\nimport { toKebabCase } from \"../../slug.js\";\nimport { indexDbPath } from \"../../topics/paths.js\";\nimport {\n  formatShow,\n  pagesDirectlyTagged,\n  pagesForSubtree,\n  type TopicsShowRecord,\n} from \"./read.js\";\nimport type { TopicsCommandOutput, TopicsShowOptions } from \"./types.js\";\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","import { runIndexer } from \"../../indexer/index.js\";\nimport { resolveWikiRoot } from \"../../indexer/resolve-wiki.js\";\nimport { toKebabCase } from \"../../slug.js\";\nimport { topicsYamlPath } from \"../../topics/paths.js\";\nimport {\n  findTopic,\n  loadTopicsFile,\n  writeTopicsFile,\n} from \"../../topics/yaml.js\";\nimport type { TopicsCommandOutput, TopicsUnlinkOptions } from \"./types.js\";\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","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. But a **malformed** registry IS surfaced: if\n * the JSON is corrupt, the user needs to know, not have auto-register\n * quietly pretend the registry was empty and start overwriting entries.\n */\nexport async function autoRegisterIfNeeded(\n  cwd: string,\n): Promise<RegistryEntry | null> {\n  try {\n    const repoRoot = findNearestAlmanacDir(cwd);\n    if (repoRoot === null) return null;\n\n    // Double-check the directory still exists — `findNearestAlmanacDir`\n    // already confirms this, but we're explicit about the precondition.\n    if (!existsSync(repoRoot)) return null;\n\n    // Read the registry ONCE. `resolveNameCollision` scans this snapshot\n    // in memory; re-reading per iteration would be O(N²) in collision\n    // count and needlessly hit the filesystem.\n    const entries = await readRegistry();\n\n    const existing = entries.find((e) => samePath(e.path, repoRoot));\n    if (existing !== undefined) return existing;\n\n    // Derive a kebab-case name from the directory. 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 { Command } from \"commander\";\n\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\";\nimport { collectOption, emit, readStdin } from \"./helpers.js\";\n\nexport function registerEditCommands(program: Command): void {\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        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  const topics = program\n    .command(\"topics\")\n    .description(\"manage the topic DAG\");\n\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(\"--parent <slug>\", \"parent topic slug (repeat for multiple parents)\", collectOption, [] as string[])\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (name: string, opts: { parent?: string[]; wiki?: string }) => {\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(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  topics\n    .command(\"unlink <child> <parent>\")\n    .description(\"remove a DAG edge\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(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  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(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  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(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","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 { BLUE, BOLD, DIM, GREEN, RED, RST } from \"../ansi.js\";\nimport { parseDuration } from \"../indexer/duration.js\";\nimport { ensureFreshIndex } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolve-wiki.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) => `  ${BLUE}${o.slug}${RST}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"stale\",\n      r.stale.length,\n      r.stale.map((s) => `  ${BLUE}${s.slug}${RST}     ${DIM}(${s.days_since_update} days)${RST}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"dead-refs\",\n      r.dead_refs.length,\n      r.dead_refs.map((d) => `  ${BLUE}${d.slug}${RST}  references ${d.path} ${DIM}(missing)${RST}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"broken-links\",\n      r.broken_links.length,\n      r.broken_links.map(\n        (b) => `  ${BLUE}${b.source_slug}${RST} → ${b.target_slug} ${DIM}(target does not exist)${RST}`,\n      ),\n    ),\n  );\n  sections.push(\n    section(\n      \"broken-xwiki\",\n      r.broken_xwiki.length,\n      r.broken_xwiki.map(\n        (b) =>\n          `  ${BLUE}${b.source_slug}${RST} → ${b.target_wiki}:${b.target_slug} ${DIM}(wiki unregistered or unreachable)${RST}`,\n      ),\n    ),\n  );\n  sections.push(\n    section(\n      \"empty-topics\",\n      r.empty_topics.length,\n      r.empty_topics.map((e) => `  ${BLUE}${e.slug}${RST}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"empty-pages\",\n      r.empty_pages.length,\n      r.empty_pages.map((e) => `  ${BLUE}${e.slug}${RST}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"slug-collisions\",\n      r.slug_collisions.length,\n      r.slug_collisions.map((c) => `  ${BLUE}${c.slug}${RST}: ${c.paths.join(\", \")}`),\n    ),\n  );\n  return `${sections.join(\"\\n\\n\")}\\n`;\n}\n\nfunction section(label: string, count: number, lines: string[]): string {\n  if (count === 0) return `${BOLD}${label}${RST} ${GREEN}(0): (ok)${RST}`;\n  return `${BOLD}${label}${RST} ${RED}(${count})${RST}:\\n${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 \"${unit ?? \"\"}\"`);\n  }\n}\n","import { existsSync } from \"node:fs\";\n\nimport { BLUE, BOLD, DIM, RST } from \"../ansi.js\";\nimport {\n  dropEntry,\n  readRegistry,\n  type RegistryEntry,\n} from \"../registry/index.js\";\n\nexport interface ListOptions {\n  json?: boolean;\n  drop?: string;\n}\n\nexport interface ListCommandOutput {\n  stdout: string;\n  exitCode: number;\n}\n\n/**\n * `almanac list` — the global discovery surface. Three modes:\n *\n *  - default: pretty table of reachable wikis\n *  - `--json`: structured output (reachable wikis only, by default)\n *  - `--drop <name>`: explicit removal, then exits\n *\n * **Unreachable paths are silently skipped in the default output**, but\n * never auto-dropped. This is the registry hygiene rule from the design —\n * branch switches, unmounted drives, and VM-offline repos should not cost\n * the user a registration. Only `--drop` removes entries.\n */\nexport async function listWikis(\n  options: ListOptions,\n): Promise<ListCommandOutput> {\n  if (options.drop !== undefined) {\n    return handleDrop(options.drop);\n  }\n\n  const entries = await readRegistry();\n  const reachable = entries.filter((e) => isReachable(e));\n\n  if (options.json === true) {\n    return { stdout: `${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}\" (${removed.path})\\n`,\n    exitCode: 0,\n  };\n}\n\n/**\n * A registry path is \"reachable\" if something still exists at that path.\n * We use `existsSync` rather than `stat` — we don't care whether the path\n * is a directory or has a `.almanac/` inside; we only hide it from default\n * output when the path itself is gone (e.g., repo deleted, drive\n * unmounted).\n */\nfunction isReachable(entry: RegistryEntry): boolean {\n  if (entry.path.length === 0) return false;\n  return existsSync(entry.path);\n}\n\n/**\n * Human-readable listing. Empty state prints a gentle hint rather than a\n * blank screen, and entries render in registration order (chronological,\n * since `addEntry` appends).\n */\nfunction formatPretty(entries: RegistryEntry[]): string {\n  if (entries.length === 0) {\n    return `${DIM}no wikis registered. run \\`almanac bootstrap\\` in a repo to create one.${RST}\\n`;\n  }\n\n  // Column-width the name for alignment; cap at 30 so absurd names don't\n  // stretch the whole table.\n  const nameWidth = Math.min(\n    30,\n    entries.reduce((w, e) => Math.max(w, e.name.length), 0),\n  );\n\n  const lines: string[] = [];\n  for (const entry of entries) {\n    const name = entry.name.padEnd(nameWidth);\n    const desc = entry.description.length > 0 ? entry.description : \"—\";\n    lines.push(`${BLUE}${BOLD}${name}${RST}  ${desc}`);\n    lines.push(`${\" \".repeat(nameWidth)}  ${DIM}${entry.path}${RST}`);\n  }\n  return `${lines.join(\"\\n\")}\\n`;\n}\n","import { join } from \"node:path\";\n\nimport type Database from \"better-sqlite3\";\n\nimport { BLUE, RST } from \"../ansi.js\";\nimport { parseDuration } from \"../indexer/duration.js\";\nimport { ensureFreshIndex } from \"../indexer/index.js\";\nimport { looksLikeDir, normalizePath } from \"../indexer/paths.js\";\nimport { resolveWikiRoot } from \"../indexer/resolve-wiki.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 `${rows.map((r) => `${BLUE}${r.slug}${RST}`).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  // Empty-result breadcrumb (v0.1.3). Interviews showed users saw blank\n  // stdout and concluded the wiki was broken rather than the query\n  // genuinely matched nothing. A single `# 0 results` line to stderr\n  // makes the outcome legible without corrupting stdout pipelines (the\n  // downstream command still sees zero lines). `--json` mode is silent\n  // because `[]` is the unambiguous empty signal there.\n  if (rows.length === 0) {\n    return \"# 0 results\\n\";\n  }\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 type Database from \"better-sqlite3\";\n\nimport { BLUE, DIM, RST } from \"../ansi.js\";\nimport { ensureFreshIndex } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolve-wiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\n\n/**\n * `almanac show <slug>` — structured view of a page.\n *\n * This file absorbs what used to be split across `show` (body), `info`\n * (metadata), and `path` (file path resolution). One command, multiple\n * view flags.\n *\n * Three output \"shapes\":\n *\n *   1. **Default** — metadata header + `\\n---\\n` separator + body. Useful\n *      to skim a page and still see its topics/files/links at a glance.\n *   2. **View flags** (mutually exclusive-ish):\n *        --json   structured JSON, overrides everything else\n *        --raw    body only (alias --body; the old `show` behavior)\n *        --meta   metadata only, no body\n *        --lead   first paragraph of body only (cheap preview)\n *   3. **Field flags** (composable). Each selects one \"field\" of the page:\n *        --title / --topics / --files / --links / --backlinks / --xwiki\n *        --lineage / --updated / --path\n *      A single field → bare, pipe-friendly output (one item per line).\n *      Multiple fields → labeled sections, one per flag.\n *\n * `--stdin` is always JSON Lines (one record per line). This avoids the\n * separator ambiguity with markdown `---` in bulk output: the old `info`\n * used a human-readable array; the old `show` used `\\n---\\n` which\n * collided with page frontmatter delimiters.\n */\nexport interface ShowOptions {\n  cwd: string;\n  slug?: string;\n  stdin?: boolean;\n  stdinInput?: string;\n  wiki?: string;\n\n  // View modes (mutually exclusive-ish — precedence: json > raw > meta > lead > default).\n  json?: boolean;\n  raw?: boolean; // alias: body\n  meta?: boolean;\n  lead?: boolean;\n\n  // Composable field flags.\n  title?: boolean;\n  topics?: boolean;\n  files?: boolean;\n  links?: boolean;\n  backlinks?: boolean;\n  xwiki?: boolean;\n  lineage?: boolean;\n  updated?: boolean;\n  path?: boolean;\n}\n\nexport interface ShowCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * The structured record emitted by `--json`. Also the shape we read into\n * in order to compose any other output. Keeping this a plain flat object\n * means callers can JSON.parse downstream tooling without chasing nested\n * subschemas.\n */\nexport interface ShowRecord {\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[];\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  body: string;\n}\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 records: ShowRecord[] = [];\n    const missing: string[] = [];\n    for (const slug of slugs) {\n      const rec = await fetchRecord(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 stdout = bulk\n      ? formatBulk(records)\n      : formatSingle(records, options);\n\n    const stderr = missing\n      .map((s) => `almanac: no such page \"${s}\"\\n`)\n      .join(\"\");\n\n    return {\n      stdout,\n      stderr,\n      exitCode: missing.length > 0 ? 1 : 0,\n    };\n  } finally {\n    db.close();\n  }\n}\n\n// ─── Record fetch ────────────────────────────────────────────────────\n\nasync function fetchRecord(\n  db: Database.Database,\n  slug: string,\n): Promise<ShowRecord | 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      \"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  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  // Read body (strip YAML frontmatter). `show` is the only command\n  // permitted to read page content, per the spec.\n  let body = \"\";\n  try {\n    body = stripFrontmatter(await readFile(pageRow.file_path, \"utf8\"));\n  } catch {\n    // If the page row exists but the file is unreadable (race with `git\n    // mv`, permission change, …) we keep the record — everything else we\n    // have is sourced from the index. Body renders as empty. The missing\n    // view flags still work.\n  }\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    body,\n  };\n}\n\n// ─── Formatting ──────────────────────────────────────────────────────\n\nfunction formatBulk(records: ShowRecord[]): string {\n  // JSON Lines. One record per line, trailing newline when non-empty.\n  // Consumers split on `\\n` and `JSON.parse` each line.\n  if (records.length === 0) return \"\";\n  return records.map((r) => JSON.stringify(r)).join(\"\\n\") + \"\\n\";\n}\n\nfunction formatSingle(\n  records: ShowRecord[],\n  options: ShowOptions,\n): string {\n  if (options.json === true) {\n    // JSON always wins. Positional mode emits a single object (never an\n    // array) for a found page, `null` for a missing one — matches the\n    // shape contract from the old `info --json`.\n    const only = records[0] ?? null;\n    return `${JSON.stringify(only, null, 2)}\\n`;\n  }\n  return records.map((r) => formatRecord(r, options)).join(\"\");\n}\n\n/**\n * Figure out which fields the user asked for. Precedence:\n *   1. `--raw` / `--body` — body only. Everything else is ignored.\n *   2. `--meta` — metadata only, no body. Ignores `--lead`.\n *   3. `--lead` — first paragraph only.\n *   4. Any field flag (`--title`, `--topics`, …) set → those fields only.\n *   5. Nothing set → full view (metadata header + body).\n */\ntype FieldName =\n  | \"title\"\n  | \"topics\"\n  | \"files\"\n  | \"links\"\n  | \"backlinks\"\n  | \"xwiki\"\n  | \"lineage\"\n  | \"updated\"\n  | \"path\";\n\nconst FIELD_ORDER: FieldName[] = [\n  \"title\",\n  \"topics\",\n  \"files\",\n  \"links\",\n  \"backlinks\",\n  \"xwiki\",\n  \"lineage\",\n  \"updated\",\n  \"path\",\n];\n\nfunction selectedFields(options: ShowOptions): FieldName[] {\n  const selected: FieldName[] = [];\n  for (const f of FIELD_ORDER) {\n    if (options[f] === true) selected.push(f);\n  }\n  return selected;\n}\n\nfunction formatRecord(rec: ShowRecord, options: ShowOptions): string {\n  // 1. raw / body\n  if (options.raw === true) {\n    // Guarantee exactly one trailing newline. Without it, shell redirects\n    // (`almanac show foo --raw > foo.md`) produce files missing a final\n    // newline, which confuses concatenation and diff tools. We don't\n    // collapse multiple trailing newlines — a page that ends with a\n    // blank line is intentional.\n    if (rec.body.length === 0) return \"\";\n    return rec.body.endsWith(\"\\n\") ? rec.body : `${rec.body}\\n`;\n  }\n\n  // 4. Field flags (check before meta/lead so --meta + --title is unambiguous).\n  const fields = selectedFields(options);\n  if (fields.length > 0) {\n    if (fields.length === 1) {\n      return bareField(rec, fields[0]!);\n    }\n    return labeledFields(rec, fields);\n  }\n\n  // 2. meta only\n  if (options.meta === true) {\n    return metadataHeader(rec) + \"\\n\";\n  }\n\n  // 3. lead only\n  if (options.lead === true) {\n    return firstParagraph(rec.body) + \"\\n\";\n  }\n\n  // 5. Default — metadata header + separator + body.\n  const header = metadataHeader(rec);\n  const body = rec.body;\n  const sep = body.length > 0 ? `\\n\\n${DIM}---${RST}\\n\\n` : \"\\n\";\n  return header + sep + body;\n}\n\n/**\n * Single-field bare output. One item per line, no labels, no colons —\n * designed to be piped directly into another command. The exact format\n * per field tries to preserve \"scriptable by default\":\n *\n *   --title      → the title (or empty if null)\n *   --topics     → one topic slug per line\n *   --files      → one file ref per line; trailing slash for folders\n *   --links      → one outgoing slug per line\n *   --backlinks  → one incoming slug per line\n *   --xwiki      → one `wiki:slug` per line\n *   --lineage    → archived_at / supersedes / superseded_by, one per line\n *                  (only the ones that exist — silent when all absent)\n *   --updated    → ISO-8601 UTC timestamp\n *   --path       → absolute file path (replaces the old `almanac path`)\n */\nfunction bareField(rec: ShowRecord, field: FieldName): string {\n  switch (field) {\n    case \"title\":\n      return (rec.title ?? \"\") + \"\\n\";\n    case \"topics\":\n      return rec.topics.map((t) => `${t}\\n`).join(\"\");\n    case \"files\":\n      return rec.file_refs\n        .map((r) => `${r.path}\\n`)\n        .join(\"\");\n    case \"links\":\n      return rec.wikilinks_out.map((t) => `${t}\\n`).join(\"\");\n    case \"backlinks\":\n      return rec.wikilinks_in.map((t) => `${t}\\n`).join(\"\");\n    case \"xwiki\":\n      return rec.cross_wiki_links\n        .map((x) => `${x.wiki}:${x.target}\\n`)\n        .join(\"\");\n    case \"lineage\": {\n      const lines: string[] = [];\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: ${rec.supersedes.join(\", \")}`);\n      }\n      return lines.length > 0 ? `${lines.join(\"\\n\")}\\n` : \"\";\n    }\n    case \"updated\":\n      return `${new Date(rec.updated_at * 1000).toISOString()}\\n`;\n    case \"path\":\n      return `${rec.file_path}\\n`;\n  }\n}\n\n/**\n * Multi-field labeled output. Each requested field renders as a labeled\n * section, in canonical order (the order of `FIELD_ORDER`, not the order\n * flags appeared on the command line). Sections are separated by blank\n * lines to make grep-by-label reliable.\n */\nfunction labeledFields(rec: ShowRecord, fields: FieldName[]): string {\n  const parts: string[] = [];\n  for (const f of fields) {\n    parts.push(labeledSection(rec, f));\n  }\n  return parts.join(\"\\n\");\n}\n\nfunction labeledSection(rec: ShowRecord, field: FieldName): string {\n  switch (field) {\n    case \"title\":\n      return `${DIM}title:${RST} ${rec.title ?? \"—\"}\\n`;\n    case \"topics\":\n      return rec.topics.length > 0\n        ? `${DIM}topics:${RST} ${rec.topics.join(\", \")}\\n`\n        : `${DIM}topics:${RST} —\\n`;\n    case \"files\":\n      return formatListSection(\n        \"files\",\n        rec.file_refs.map((r) => `${r.path}`),\n      );\n    case \"links\":\n      return formatListSection(\"links\", rec.wikilinks_out);\n    case \"backlinks\":\n      return formatListSection(\"backlinks\", rec.wikilinks_in);\n    case \"xwiki\":\n      return formatListSection(\n        \"xwiki\",\n        rec.cross_wiki_links.map((x) => `${x.wiki}:${x.target}`),\n      );\n    case \"lineage\": {\n      const lines: string[] = [`${DIM}lineage:${RST}`];\n      if (rec.archived_at !== null) {\n        lines.push(\n          `  ${DIM}archived_at:${RST} ${new Date(rec.archived_at * 1000).toISOString()}`,\n        );\n      }\n      if (rec.superseded_by !== null) {\n        lines.push(`  ${DIM}superseded_by:${RST} ${rec.superseded_by}`);\n      }\n      if (rec.supersedes.length > 0) {\n        lines.push(`  ${DIM}supersedes:${RST} ${rec.supersedes.join(\", \")}`);\n      }\n      if (lines.length === 1) lines.push(\"  —\");\n      return lines.join(\"\\n\") + \"\\n\";\n    }\n    case \"updated\":\n      return `${DIM}updated:${RST} ${new Date(rec.updated_at * 1000).toISOString()}\\n`;\n    case \"path\":\n      return `${DIM}path:${RST} ${rec.file_path}\\n`;\n  }\n}\n\nfunction formatListSection(label: string, items: string[]): string {\n  if (items.length === 0) return `${DIM}${label}:${RST} —\\n`;\n  if (items.length <= 3) return `${DIM}${label}:${RST} ${items.join(\", \")}\\n`;\n  return `${DIM}${label}:${RST}\\n${items.map((i) => `  ${i}`).join(\"\\n\")}\\n`;\n}\n\n/**\n * Metadata header rendered for default and `--meta` views. Single-line\n * fields for short lists; indented block form for long lists. This is\n * the human-readable counterpart to the JSON dump — labeled, column-\n * aligned, skimmable.\n */\nfunction metadataHeader(rec: ShowRecord): string {\n  const lines: string[] = [];\n  lines.push(`${DIM}slug:${RST}       ${BLUE}${rec.slug}${RST}`);\n  lines.push(`${DIM}title:${RST}      ${rec.title ?? \"—\"}`);\n  lines.push(\n    `${DIM}topics:${RST}     ${rec.topics.length > 0 ? rec.topics.join(\", \") : \"—\"}`,\n  );\n\n  if (rec.file_refs.length > 0) {\n    const parts = rec.file_refs.map(\n      (r) => `${r.path}`,\n    );\n    lines.push(`${DIM}files:${RST}      ${parts.join(\", \")}`);\n  }\n\n  lines.push(\n    `${DIM}updated:${RST}    ${new Date(rec.updated_at * 1000).toISOString()}`,\n  );\n\n  if (rec.wikilinks_out.length > 0) {\n    lines.push(`${DIM}links:${RST}      ${rec.wikilinks_out.join(\", \")}`);\n  }\n  if (rec.wikilinks_in.length > 0) {\n    lines.push(`${DIM}backlinks:${RST}  ${rec.wikilinks_in.join(\", \")}`);\n  }\n  if (rec.cross_wiki_links.length > 0) {\n    lines.push(\n      `${DIM}xwiki:${RST}      ${rec.cross_wiki_links\n        .map((x) => `${x.wiki}:${x.target}`)\n        .join(\", \")}`,\n    );\n  }\n  if (rec.archived_at !== null) {\n    lines.push(\n      `${DIM}archived:${RST}   ${new Date(rec.archived_at * 1000).toISOString()}`,\n    );\n  }\n  if (rec.superseded_by !== null) {\n    lines.push(`${DIM}superseded_by:${RST} ${rec.superseded_by}`);\n  }\n  if (rec.supersedes.length > 0) {\n    lines.push(`${DIM}supersedes:${RST} ${rec.supersedes.join(\", \")}`);\n  }\n\n  return lines.join(\"\\n\");\n}\n\n// ─── Helpers ─────────────────────────────────────────────────────────\n\n/**\n * Strip a leading YAML frontmatter block (fenced by `---` on its own\n * lines). Everything between the opening `---\\n` and the next `---\\n` is\n * dropped, along with the surrounding fence. If no opening fence is\n * present we return the source unchanged.\n *\n * Hand-rolled rather than pulling in gray-matter because the CLI's only\n * goal here is \"show the body without the YAML header\" — we don't need\n * the parsed fields, the indexer already has them.\n */\nfunction stripFrontmatter(src: string): string {\n  if (!src.startsWith(\"---\\n\") && !src.startsWith(\"---\\r\\n\")) return src;\n  // Strip the opening fence. A regex replace handles both LF and CRLF\n  // line endings without the off-by-one that `src.indexOf(\"\\n\") + 1`\n  // suffered on CRLF files — `indexOf(\"\\n\")` landed AFTER the `\\r`, so\n  // the `\\r` survived as a prefix on the first body byte.\n  const afterOpen = src.replace(/^---\\r?\\n/, \"\");\n  const endMatch = afterOpen.match(/^---[ \\t]*\\r?\\n/m);\n  if (endMatch === null || endMatch.index === undefined) return src;\n  // Slice after the closing fence's line.\n  return afterOpen.slice(endMatch.index + endMatch[0].length);\n}\n\n/**\n * First paragraph of the body, where \"paragraph\" is everything up to (but\n * not including) the first blank line. Skips a leading `# Title` line if\n * present so `--lead` previews the first real sentence, not the heading.\n */\nfunction firstParagraph(body: string): string {\n  let src = body.trimStart();\n  if (src.startsWith(\"# \")) {\n    const nl = src.indexOf(\"\\n\");\n    src = nl === -1 ? \"\" : src.slice(nl + 1).trimStart();\n  }\n  const blank = src.search(/\\n[ \\t]*\\n/);\n  if (blank === -1) return src.trimEnd();\n  return src.slice(0, blank).trimEnd();\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 { Command } from \"commander\";\n\nimport { runHealth } from \"../commands/health.js\";\nimport { listWikis } from \"../commands/list.js\";\nimport { runSearch } from \"../commands/search.js\";\nimport { runShow } from \"../commands/show.js\";\nimport { autoRegisterIfNeeded } from \"../registry/autoregister.js\";\nimport {\n  collectOption,\n  emit,\n  parsePositiveInt,\n  readStdin,\n} from \"./helpers.js\";\n\nexport function registerQueryCommands(program: Command): void {\n  program\n    .command(\"search [query]\")\n    .description(\"find pages by text, topic, file mentions, 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 path; matches exact file, trailing-slash folders, and any file under a folder prefix\",\n    )\n    .option(\"--since <duration>\", \"updated within duration, by file mtime (e.g. 2w, 30d)\")\n    .option(\"--stale <duration>\", \"NOT updated within duration, by file mtime\")\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        emit(result);\n      },\n    );\n\n  program\n    .command(\"show [slug]\")\n    .description(\"print a page (metadata + body; flags to narrow)\")\n    .option(\"--stdin\", \"read slugs from stdin (one per line)\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .option(\"--json\", \"structured JSON (overrides other view/field flags)\")\n    .option(\"--raw\", \"body only (alias: --body)\")\n    .option(\"--body\", \"body only (alias: --raw)\")\n    .option(\"--meta\", \"metadata only, no body\")\n    .option(\"--lead\", \"first paragraph of the body only\")\n    .option(\"--title\", \"print title\")\n    .option(\"--topics\", \"print topics\")\n    .option(\"--files\", \"print file refs\")\n    .option(\"--links\", \"print outgoing wikilinks\")\n    .option(\"--backlinks\", \"print incoming wikilinks\")\n    .option(\"--xwiki\", \"print cross-wiki links\")\n    .option(\"--lineage\", \"print archived_at / supersedes / superseded_by\")\n    .option(\"--updated\", \"print updated timestamp\")\n    .option(\"--path\", \"print absolute file path\")\n    .action(\n      async (\n        slug: string | undefined,\n        opts: {\n          stdin?: boolean;\n          wiki?: string;\n          json?: boolean;\n          raw?: boolean;\n          body?: boolean;\n          meta?: boolean;\n          lead?: boolean;\n          title?: boolean;\n          topics?: boolean;\n          files?: boolean;\n          links?: boolean;\n          backlinks?: boolean;\n          xwiki?: boolean;\n          lineage?: boolean;\n          updated?: boolean;\n          path?: boolean;\n        },\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          json: opts.json,\n          raw: opts.raw === true || opts.body === true,\n          meta: opts.meta,\n          lead: opts.lead,\n          title: opts.title,\n          topics: opts.topics,\n          files: opts.files,\n          links: opts.links,\n          backlinks: opts.backlinks,\n          xwiki: opts.xwiki,\n          lineage: opts.lineage,\n          updated: opts.updated,\n          path: opts.path,\n        });\n        emit(result);\n      },\n    );\n\n  program\n    .command(\"health\")\n    .description(\"report graph integrity problems\")\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  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      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","import { BLUE, BOLD, DIM, GREEN, RED, RST } from \"../../ansi.js\";\nimport type { Check, CheckStatus, DoctorOptions, DoctorReport } from \"./types.js\";\n\nexport function formatReport(\n  report: DoctorReport,\n  options: DoctorOptions,\n): string {\n  const color = options.stdout === undefined && process.stdout.isTTY === true;\n  const lines: string[] = [];\n  lines.push(`codealmanac v${report.version}`);\n  lines.push(\"\");\n  if (report.install.length > 0) {\n    lines.push(color ? `${BOLD}## Install${RST}` : \"## Install\");\n    for (const c of report.install) {\n      lines.push(formatCheck(c, color));\n    }\n    lines.push(\"\");\n  }\n  if (report.updates.length > 0) {\n    lines.push(color ? `${BOLD}## Updates${RST}` : \"## Updates\");\n    for (const c of report.updates) {\n      lines.push(formatCheck(c, color));\n    }\n    lines.push(\"\");\n  }\n  if (report.wiki.length > 0) {\n    lines.push(color ? `${BOLD}## Current wiki${RST}` : \"## Current wiki\");\n    for (const c of report.wiki) {\n      lines.push(formatCheck(c, color));\n    }\n    lines.push(\"\");\n  }\n  return `${lines.join(\"\\n\")}\\n`;\n}\n\nfunction formatCheck(c: Check, color: boolean): string {\n  const { icon, tint } = iconFor(c.status, color);\n  const head = `  ${tint}${icon}${color ? RST : \"\"} ${c.message}`;\n  if (c.fix === undefined) return head;\n  const fixLine = color\n    ? `    ${DIM}${c.fix}${RST}`\n    : `    ${c.fix}`;\n  return `${head}\\n${fixLine}`;\n}\n\nfunction iconFor(\n  status: CheckStatus,\n  color: boolean,\n): { icon: string; tint: string } {\n  switch (status) {\n    case \"ok\":\n      return { icon: \"\\u2713\", tint: color ? GREEN : \"\" };\n    case \"problem\":\n      return { icon: \"\\u2717\", tint: color ? RED : \"\" };\n    case \"info\":\n      return { icon: \"\\u25c7\", tint: color ? BLUE : \"\" };\n  }\n}\n","import { existsSync } from \"node:fs\";\nimport { readFile } from \"node:fs/promises\";\nimport { homedir } from \"node:os\";\nimport path from \"node:path\";\n\nimport type { ClaudeAuthStatus } from \"../../agent/auth.js\";\nimport { IMPORT_LINE } from \"../setup.js\";\nimport {\n  classifyInstallPath,\n  detectInstallPath,\n  probeBetterSqlite3,\n  safeCheckAuth,\n} from \"./probes.js\";\nimport type { Check, DoctorOptions } from \"./types.js\";\n\nexport async function gatherInstallChecks(\n  options: DoctorOptions,\n): Promise<Check[]> {\n  const checks: Check[] = [];\n\n  const rawPath = options.installPath ?? detectInstallPath();\n  const { installPath, isEphemeral } = classifyInstallPath(rawPath);\n  checks.push(describeInstallPath(installPath, isEphemeral));\n\n  const nodeVersion = options.nodeVersion ?? process.version;\n  const sqlite = options.sqliteProbe ?? probeBetterSqlite3();\n  checks.push({\n    status: sqlite.ok ? \"ok\" : \"problem\",\n    key: \"install.sqlite\",\n    message: sqlite.ok\n      ? `better-sqlite3 native binding OK (Node ${nodeVersion})`\n      : `better-sqlite3 native binding failed: ${sqlite.summary}`,\n    fix: sqlite.ok\n      ? undefined\n      : \"run: npm rebuild better-sqlite3 (in the install directory)\",\n  });\n\n  const auth = await safeCheckAuth(options.spawnCli);\n  checks.push(describeAuth(auth));\n\n  const settingsPath =\n    options.settingsPath ?? path.join(homedir(), \".claude\", \"settings.json\");\n  checks.push(await describeHook(settingsPath));\n\n  const claudeDir = options.claudeDir ?? path.join(homedir(), \".claude\");\n  checks.push(describeGuides(claudeDir));\n  checks.push(await describeImportLine(claudeDir));\n\n  return checks;\n}\n\nfunction describeInstallPath(\n  installPath: string | null,\n  isEphemeral: boolean,\n): Check {\n  if (installPath === null) {\n    return {\n      status: \"problem\",\n      key: \"install.path\",\n      message: \"could not detect codealmanac install path\",\n      fix: \"reinstall with: npm install -g codealmanac\",\n    };\n  }\n  return {\n    status: isEphemeral ? \"info\" : \"ok\",\n    key: \"install.path\",\n    message: isEphemeral\n      ? `codealmanac running from ephemeral npx location: ${installPath}`\n      : `codealmanac installed at ${installPath}`,\n    fix: isEphemeral\n      ? \"run: npm install -g codealmanac  (to make the install permanent)\"\n      : undefined,\n  };\n}\n\nfunction describeAuth(auth: ClaudeAuthStatus): Check {\n  if (auth.loggedIn) {\n    if (auth.authMethod === \"apiKey\") {\n      return {\n        status: \"ok\",\n        key: \"install.auth\",\n        message: \"claude auth: ANTHROPIC_API_KEY set\",\n      };\n    }\n    const who = auth.email ?? \"Claude account\";\n    const plan =\n      auth.subscriptionType !== undefined\n        ? ` (${auth.subscriptionType} subscription)`\n        : \"\";\n    return {\n      status: \"ok\",\n      key: \"install.auth\",\n      message: `claude auth: ${who}${plan}`,\n    };\n  }\n  if (\n    process.env.ANTHROPIC_API_KEY !== undefined &&\n    process.env.ANTHROPIC_API_KEY.length > 0\n  ) {\n    return {\n      status: \"ok\",\n      key: \"install.auth\",\n      message: \"claude auth: ANTHROPIC_API_KEY set\",\n    };\n  }\n  return {\n    status: \"problem\",\n    key: \"install.auth\",\n    message: \"claude auth: not signed in\",\n    fix: \"run: claude auth login --claudeai  (or export ANTHROPIC_API_KEY)\",\n  };\n}\n\nasync function describeHook(settingsPath: string): Promise<Check> {\n  if (!existsSync(settingsPath)) {\n    return {\n      status: \"problem\",\n      key: \"install.hook\",\n      message: \"SessionEnd hook not installed\",\n      fix: \"run: almanac setup --yes\",\n    };\n  }\n  try {\n    const raw = await readFile(settingsPath, \"utf8\");\n    const parsed = JSON.parse(raw) as {\n      hooks?: {\n        SessionEnd?: {\n          command?: string;\n          hooks?: { command?: string }[];\n        }[];\n      };\n    };\n    const entries = parsed.hooks?.SessionEnd ?? [];\n    const found = entries.some((e) => {\n      if (\n        typeof e?.command === \"string\" &&\n        e.command.endsWith(\"almanac-capture.sh\")\n      ) {\n        return true;\n      }\n      if (Array.isArray(e?.hooks)) {\n        return e.hooks.some(\n          (h) =>\n            typeof h?.command === \"string\" &&\n            h.command.endsWith(\"almanac-capture.sh\"),\n        );\n      }\n      return false;\n    });\n    if (!found) {\n      return {\n        status: \"problem\",\n        key: \"install.hook\",\n        message: \"SessionEnd hook not installed\",\n        fix: \"run: almanac setup --yes\",\n      };\n    }\n    return {\n      status: \"ok\",\n      key: \"install.hook\",\n      message: `SessionEnd hook installed at ${settingsPath}`,\n    };\n  } catch (err: unknown) {\n    const msg = err instanceof Error ? err.message : String(err);\n    return {\n      status: \"problem\",\n      key: \"install.hook\",\n      message: `could not read ${settingsPath}: ${msg}`,\n      fix: \"check the file for malformed JSON\",\n    };\n  }\n}\n\nfunction describeGuides(claudeDir: string): Check {\n  const mini = path.join(claudeDir, \"codealmanac.md\");\n  const ref = path.join(claudeDir, \"codealmanac-reference.md\");\n  const haveMini = existsSync(mini);\n  const haveRef = existsSync(ref);\n  if (haveMini && haveRef) {\n    return {\n      status: \"ok\",\n      key: \"install.guides\",\n      message: `Agent guides installed (${path.basename(mini)}, ${path.basename(ref)})`,\n    };\n  }\n  const missing = [\n    haveMini ? null : \"codealmanac.md\",\n    haveRef ? null : \"codealmanac-reference.md\",\n  ].filter((s): s is string => s !== null);\n  return {\n    status: \"problem\",\n    key: \"install.guides\",\n    message: `Agent guides missing (${missing.join(\", \")})`,\n    fix: \"run: almanac setup --yes\",\n  };\n}\n\nasync function describeImportLine(claudeDir: string): Promise<Check> {\n  const claudeMd = path.join(claudeDir, \"CLAUDE.md\");\n  if (!existsSync(claudeMd)) {\n    return {\n      status: \"problem\",\n      key: \"install.import\",\n      message: \"CLAUDE.md import not present (no ~/.claude/CLAUDE.md)\",\n      fix: \"run: almanac setup --yes\",\n    };\n  }\n  try {\n    const contents = await readFile(claudeMd, \"utf8\");\n    const lines = contents.split(/\\r?\\n/).map((l) => l.trim());\n    const present = lines.some((line) => {\n      if (line === IMPORT_LINE) return true;\n      if (!line.startsWith(IMPORT_LINE)) return false;\n      const next = line[IMPORT_LINE.length];\n      return next === \" \" || next === \"\\t\";\n    });\n    if (present) {\n      return {\n        status: \"ok\",\n        key: \"install.import\",\n        message: \"CLAUDE.md import present\",\n      };\n    }\n    return {\n      status: \"problem\",\n      key: \"install.import\",\n      message: \"CLAUDE.md import line missing\",\n      fix: \"run: almanac setup --yes\",\n    };\n  } catch (err: unknown) {\n    const msg = err instanceof Error ? err.message : String(err);\n    return {\n      status: \"problem\",\n      key: \"install.import\",\n      message: `could not read ${claudeMd}: ${msg}`,\n    };\n  }\n}\n","import { existsSync, readFileSync } from \"node:fs\";\nimport { createRequire } from \"node:module\";\nimport { homedir } from \"node:os\";\nimport path from \"node:path\";\nimport { fileURLToPath } from \"node:url\";\n\nimport { checkClaudeAuth, type ClaudeAuthStatus, type SpawnCliFn } from \"../../agent/auth.js\";\nimport type { SqliteProbeResult } from \"./types.js\";\n\n// Single `createRequire` instance — used by package/binding probes.\nconst req = createRequire(import.meta.url);\n\n/**\n * Detect where codealmanac is installed by walking up from the running\n * module until we find a `package.json` whose `name` is `codealmanac`.\n */\nexport function detectInstallPath(): string | null {\n  try {\n    const here = fileURLToPath(import.meta.url);\n    let dir = path.dirname(here);\n    for (let i = 0; i < 6; i++) {\n      const pkgPath = path.join(dir, \"package.json\");\n      if (existsSync(pkgPath)) {\n        try {\n          const raw = readFileSync(pkgPath, \"utf-8\");\n          const pkg = JSON.parse(raw) as { name?: unknown };\n          if (pkg.name === \"codealmanac\") return dir;\n        } catch {\n          // ignore — keep walking\n        }\n      }\n      const parent = path.dirname(dir);\n      if (parent === dir) break;\n      dir = parent;\n    }\n    return null;\n  } catch {\n    return null;\n  }\n}\n\n/**\n * Classify the detected install path as permanent or ephemeral.\n * Ephemeral locations (npm npx cache, pnpm dlx cache, /tmp/) are valid\n * installs but will disappear when the cache is evicted or the machine\n * reboots. Doctor reports them as `info` rather than `ok`.\n */\nexport function classifyInstallPath(\n  raw: string | null,\n): { installPath: string | null; isEphemeral: boolean } {\n  if (raw === null) return { installPath: null, isEphemeral: false };\n  const home = homedir();\n  const ephemeralPrefixes = [\n    path.join(home, \".npm\", \"_npx\"),\n    path.join(home, \".local\", \"share\", \"pnpm\", \"dlx\"),\n    \"/tmp/\",\n    \"/var/folders/\",\n  ];\n  const isEphemeral = ephemeralPrefixes.some((p) => raw.startsWith(p));\n  return { installPath: raw, isEphemeral };\n}\n\n/**\n * Probe the better-sqlite3 native binding by opening an in-memory DB.\n */\nexport function probeBetterSqlite3(): SqliteProbeResult {\n  try {\n    // eslint-disable-next-line @typescript-eslint/no-var-requires\n    const Database = req(\"better-sqlite3\") as typeof import(\"better-sqlite3\");\n    const db = new Database(\":memory:\");\n    db.close();\n    return { ok: true, summary: \"native binding loads cleanly\" };\n  } catch (err: unknown) {\n    const msg = err instanceof Error ? err.message : String(err);\n    const firstLine = msg.split(\"\\n\")[0] ?? msg;\n    return { ok: false, summary: firstLine };\n  }\n}\n\nexport async function safeCheckAuth(\n  spawnCli?: SpawnCliFn,\n): Promise<ClaudeAuthStatus> {\n  try {\n    return await checkClaudeAuth(spawnCli);\n  } catch {\n    return { loggedIn: false };\n  }\n}\n\nexport function readPackageVersion(): string | null {\n  const candidates = [\n    \"../../../package.json\",\n    \"../../package.json\",\n    \"../package.json\",\n  ];\n  for (const candidate of candidates) {\n    try {\n      const pkg = req(candidate) as { version?: unknown };\n      if (typeof pkg.version === \"string\" && pkg.version.length > 0) {\n        return pkg.version;\n      }\n    } catch {\n      // Fall through to the next runtime layout candidate.\n    }\n  }\n  return null;\n}\n","import { mkdir, readFile, rename, writeFile } from \"node:fs/promises\";\nimport { dirname, join } from \"node:path\";\n\nimport { getGlobalAlmanacDir } from \"../paths.js\";\n\n/**\n * `~/.almanac/config.json` — global, cross-wiki configuration. Today\n * the only field is `update_notifier` (on/off toggle for the pre-command\n * banner); designed as an object so we can add more knobs without\n * breaking users who already have the file on disk.\n *\n * Missing or malformed → defaults. Same tolerance as `UpdateState`:\n * the CLI must not be able to fail because this file drifted.\n */\nexport interface GlobalConfig {\n  /** When `false`, suppress the pre-command update-nag banner. Default: true. */\n  update_notifier: boolean;\n}\n\nexport function defaultConfig(): GlobalConfig {\n  return { update_notifier: true };\n}\n\nexport function getConfigPath(): string {\n  return join(getGlobalAlmanacDir(), \"config.json\");\n}\n\nexport async function readConfig(path?: string): Promise<GlobalConfig> {\n  const file = path ?? getConfigPath();\n  let raw: string;\n  try {\n    raw = await readFile(file, \"utf8\");\n  } catch {\n    return defaultConfig();\n  }\n  const trimmed = raw.trim();\n  if (trimmed.length === 0) return defaultConfig();\n  try {\n    const parsed = JSON.parse(trimmed) as Partial<GlobalConfig>;\n    return {\n      update_notifier:\n        typeof parsed.update_notifier === \"boolean\"\n          ? parsed.update_notifier\n          : true,\n    };\n  } catch {\n    return defaultConfig();\n  }\n}\n\nexport async function writeConfig(\n  config: GlobalConfig,\n  path?: string,\n): Promise<void> {\n  const file = path ?? getConfigPath();\n  await mkdir(dirname(file), { recursive: true });\n  const body = `${JSON.stringify(config, null, 2)}\\n`;\n  const tmp = `${file}.tmp`;\n  await writeFile(tmp, body, \"utf8\");\n  await rename(tmp, file);\n}\n","import { spawn } from \"node:child_process\";\nimport { readFileSync } from \"node:fs\";\n\nimport { checkForUpdate } from \"./check.js\";\nimport { getConfigPath } from \"./config.js\";\nimport { getStatePath, type UpdateState } from \"./state.js\";\n\n/**\n * Post-command scheduler for the background update check.\n *\n * After any normal `almanac <command>` exits, we want a fresh check to\n * have happened by the next invocation. We achieve that by spawning a\n * detached copy of ourselves with the hidden `--internal-check-updates`\n * flag; that child does nothing but hit the registry and write\n * `~/.almanac/update-state.json`, then exits.\n *\n * Why detach rather than check inline:\n *   - 3s network timeout in the foreground would feel sluggish on every\n *     command.\n *   - `npm test` and CI scripts shouldn't pay for a registry round-trip\n *     (gated below via env).\n *   - A detached child with `stdio: \"ignore\"` cannot leak output into\n *     the parent's stdout/stderr — critical for pipelines.\n *\n * Hazards we accept:\n *   - A Claude Code subprocess whose parent shell exits right after the\n *     `almanac` call may kill the child before it finishes. That's\n *     fine: a failed check just means we try again next invocation.\n *   - Detached child survival on Windows isn't as robust as on Unix.\n *     Same fallback: next invocation retries.\n */\n\nexport function scheduleBackgroundUpdateCheck(argv: string[]): void {\n  if (!shouldSchedule(argv)) return;\n\n  const scriptPath = argv[1];\n  const nodeBin = process.execPath;\n  if (scriptPath === undefined || scriptPath.length === 0) return;\n\n  // Spawn with the current Node and the same script path. `detached:\n  // true` + `stdio: \"ignore\"` + `unref()` detaches the child from our\n  // event loop so the parent can exit independently.\n  try {\n    const child = spawn(\n      nodeBin,\n      [scriptPath, \"--internal-check-updates\"],\n      {\n        detached: true,\n        stdio: \"ignore\",\n        // Windows: with `detached: true` and no `stdio`, Node opens a\n        // console window — `\"ignore\"` prevents that.\n      },\n    );\n    child.unref();\n    // Swallow any synchronous spawn errors (e.g. ENOENT in strange\n    // installs) — never propagate to the foreground command.\n    child.on(\"error\", () => {});\n  } catch {\n    // Last-resort swallow: background checks are best-effort.\n  }\n}\n\n/**\n * Should we spawn the worker at all?\n *\n *   - Respect the `update_notifier` config — no banner means no need\n *     for the data that feeds it.\n *   - Skip in test environments so `npm test` doesn't fork 300 copies\n *     of itself into the background and hammer the registry.\n *   - Skip on the worker invocation itself (prevents a fork bomb).\n *   - Skip when the user doesn't own the install path (permission\n *     weirdness) — detected by `~/.almanac` mkdir failing; simplest\n *     to just rely on the worker's own error handling, so we don't\n *     gate here.\n *   - Skip when the argv contains `--help`/`--version`/nothing — these\n *     commands are often run from scripts that care about clean exit;\n *     though the inline banner still shows, we don't kick off a check.\n */\nfunction shouldSchedule(argv: string[]): boolean {\n  if (process.env.CODEALMANAC_SKIP_UPDATE_CHECK === \"1\") return false;\n  if (process.env.NODE_ENV === \"test\") return false;\n  if (process.env.VITEST !== undefined) return false;\n\n  // Already the worker. argv[2..] contains the internal flag.\n  if (argv.slice(2).includes(\"--internal-check-updates\")) return false;\n\n  if (!notifierEnabled()) return false;\n\n  return true;\n}\n\nfunction notifierEnabled(): boolean {\n  try {\n    const raw = readFileSync(getConfigPath(), \"utf8\");\n    const parsed = JSON.parse(raw) as { update_notifier?: unknown };\n    if (parsed.update_notifier === false) return false;\n    return true;\n  } catch {\n    return true; // missing / malformed → default-on\n  }\n}\n\n/**\n * The worker body. Invoked when `--internal-check-updates` appears on\n * the argv. Must be fast and must never print: the parent spawned us\n * with `stdio: \"ignore\"` but a stray write could still surprise a\n * downstream debugger.\n *\n * We take a simple file lock at `~/.almanac/.update-check.lock` to\n * prevent two workers running at the same time (which could happen if\n * the user fires several commands in parallel). The lock is just the\n * existence of the file with our PID inside; if an existing lock is\n * stale (older than the 3s + cache-write budget), we steal it.\n */\nexport async function runInternalUpdateCheck(): Promise<void> {\n  // The worker is intentionally minimal. Any error (network, fs,\n  // JSON) is handled inside `checkForUpdate` and surfaces as a\n  // swallowed return; we just need to await it and exit.\n  try {\n    await checkForUpdate({});\n  } catch {\n    // Defense-in-depth: nothing must escape the worker.\n  }\n}\n\n/**\n * Read the current state snapshot for diagnostic surfaces (doctor, the\n * `update --check` command). Wraps the sync read so callers can grab\n * state without the `async readState` ceremony.\n */\nexport function readStateForDoctor(path?: string): UpdateState | null {\n  const file = path ?? getStatePath();\n  try {\n    const raw = readFileSync(file, \"utf8\");\n    const trimmed = raw.trim();\n    if (trimmed.length === 0) return null;\n    const parsed = JSON.parse(trimmed) as Partial<UpdateState>;\n    return {\n      last_check_at:\n        typeof parsed.last_check_at === \"number\" ? parsed.last_check_at : 0,\n      installed_version:\n        typeof parsed.installed_version === \"string\"\n          ? parsed.installed_version\n          : \"\",\n      latest_version:\n        typeof parsed.latest_version === \"string\" ? parsed.latest_version : \"\",\n      dismissed_versions: Array.isArray(parsed.dismissed_versions)\n        ? parsed.dismissed_versions.filter((v): v is string => typeof v === \"string\")\n        : [],\n      last_fetch_failed_at:\n        typeof parsed.last_fetch_failed_at === \"number\"\n          ? parsed.last_fetch_failed_at\n          : undefined,\n    };\n  } catch {\n    return null;\n  }\n}\n","import { createRequire } from \"node:module\";\n\nimport { readState, writeState, type UpdateState } from \"./state.js\";\n\n/**\n * Background update check. Called by the detached worker (`--internal-\n * check-updates`) after any normal command exits; also reachable via\n * `almanac update --check` for a synchronous \"am I current?\" readout.\n *\n * Contract:\n *   - Reads `~/.almanac/update-state.json` if present.\n *   - If the last check is older than `cacheSeconds` (default 24h), queries\n *     the npm registry for `codealmanac`'s `dist-tags.latest` and writes a\n *     new state file.\n *   - Network timeout is 3s: registry flakes must not prevent a check\n *     cycle on the next invocation.\n *   - All errors are swallowed; the returned state is always a usable\n *     snapshot (possibly the old one when the fetch failed).\n *\n * The fetch function is injectable. Tests pass a stub; production uses\n * the native `globalThis.fetch`. No dependency on `node-fetch`.\n */\n\nexport interface CheckOptions {\n  /** Override the installed version (prod: read from package.json). */\n  installedVersion?: string;\n  /** Cache window; no registry call if last check is newer than this. */\n  cacheSeconds?: number;\n  /** Network timeout in ms (default 3000). */\n  timeoutMs?: number;\n  /** Clock. Tests inject to make \"24h ago\" deterministic. */\n  now?: () => number;\n  /** Fetch function (default `globalThis.fetch`). */\n  fetchFn?: typeof fetch;\n  /** Override the state file path (tests point it at a tmpdir). */\n  statePath?: string;\n  /** Force a registry call regardless of the cache. Used by `update --check`. */\n  force?: boolean;\n}\n\nexport interface CheckResult {\n  /** The state after the check (either refreshed or unchanged). */\n  state: UpdateState;\n  /** True when a registry call actually happened this run. */\n  fetched: boolean;\n  /** True when the registry call failed (network / timeout / parse). */\n  fetchFailed: boolean;\n}\n\nconst DEFAULT_CACHE_SECONDS = 24 * 60 * 60;\nconst DEFAULT_TIMEOUT_MS = 3000;\nconst REGISTRY_URL = \"https://registry.npmjs.org/codealmanac\";\n\nexport async function checkForUpdate(\n  opts: CheckOptions = {},\n): Promise<CheckResult> {\n  const now = opts.now ?? (() => Math.floor(Date.now() / 1000));\n  const cacheSeconds = opts.cacheSeconds ?? DEFAULT_CACHE_SECONDS;\n  const timeoutMs = opts.timeoutMs ?? DEFAULT_TIMEOUT_MS;\n  const fetchFn = opts.fetchFn ?? globalThis.fetch;\n  const installed = opts.installedVersion ?? readInstalledVersion();\n\n  const state = await readState(opts.statePath);\n\n  // Cache gate. Skip the registry call when the previous check is\n  // fresh enough, unless `force: true` (used by `update --check` so\n  // the user can see real-time status without waiting out the window).\n  if (\n    !opts.force &&\n    state.last_check_at > 0 &&\n    now() - state.last_check_at < cacheSeconds\n  ) {\n    return { state, fetched: false, fetchFailed: false };\n  }\n\n  // Query the registry with a hard timeout. `AbortController` is the\n  // idiomatic Node 20+ way to bound a fetch; `setTimeout` fires abort,\n  // `clearTimeout` cancels if fetch resolves first.\n  let latest: string | null = null;\n  let failed = false;\n  try {\n    const ac = new AbortController();\n    const timer = setTimeout(() => ac.abort(), timeoutMs);\n    try {\n      const res = await fetchFn(REGISTRY_URL, {\n        signal: ac.signal,\n        headers: { accept: \"application/json\" },\n      });\n      if (!res.ok) {\n        failed = true;\n      } else {\n        const body = (await res.json()) as {\n          [\"dist-tags\"]?: { latest?: unknown };\n        };\n        const tag = body[\"dist-tags\"]?.latest;\n        if (typeof tag === \"string\" && tag.length > 0) {\n          latest = tag;\n        } else {\n          failed = true;\n        }\n      }\n    } finally {\n      clearTimeout(timer);\n    }\n  } catch {\n    failed = true;\n  }\n\n  if (failed || latest === null) {\n    // Record the failure but DON'T clobber the previous latest_version —\n    // an offline check shouldn't make us forget that 0.1.6 is out.\n    const next: UpdateState = {\n      ...state,\n      // We still bump last_check_at on a failed attempt; without this,\n      // every subsequent command would re-try the registry. A one-shot\n      // retry on the next invocation is enough; sustained failure gets\n      // retried on the 24h cadence like a success.\n      last_check_at: now(),\n      installed_version: installed,\n      last_fetch_failed_at: now(),\n    };\n    try {\n      await writeState(next, opts.statePath);\n    } catch {\n      // Even the state write failed (permissions, disk full). Return\n      // whatever we have — the CLI doesn't care.\n    }\n    return { state: next, fetched: true, fetchFailed: true };\n  }\n\n  const next: UpdateState = {\n    last_check_at: now(),\n    installed_version: installed,\n    latest_version: latest,\n    dismissed_versions: state.dismissed_versions,\n    // Clear the failure marker on success.\n    last_fetch_failed_at: undefined,\n  };\n  try {\n    await writeState(next, opts.statePath);\n  } catch {\n    // Silent — same rationale as above.\n  }\n  return { state: next, fetched: true, fetchFailed: false };\n}\n\n/**\n * Read the `version` field from `package.json`. Matches the same\n * lookup strategy as `readPackageVersion` in `cli.ts` and `doctor.ts`;\n * duplicated here to keep the update module self-contained and to\n * avoid a circular import at CLI startup.\n */\nfunction readInstalledVersion(): string {\n  try {\n    const require = createRequire(import.meta.url);\n    const pkg = require(\"../../package.json\") as { version?: unknown };\n    if (typeof pkg.version === \"string\" && pkg.version.length > 0) {\n      return pkg.version;\n    }\n  } catch {\n    // Fall through.\n  }\n  try {\n    const require = createRequire(import.meta.url);\n    const pkg = require(\"../package.json\") as { version?: unknown };\n    if (typeof pkg.version === \"string\" && pkg.version.length > 0) {\n      return pkg.version;\n    }\n  } catch {\n    // Fall through.\n  }\n  return \"unknown\";\n}\n","import { mkdir, readFile, rename, writeFile } from \"node:fs/promises\";\nimport { dirname, join } from \"node:path\";\n\nimport { getGlobalAlmanacDir } from \"../paths.js\";\n\n/**\n * `~/.almanac/update-state.json` — the only piece of persistent state\n * the update system owns. Written by the background check worker (once\n * per 24h) and by `almanac update` / `almanac update --dismiss`; read\n * by the pre-command banner, `almanac doctor`, and the check path to\n * decide whether 24h have elapsed since the last check.\n *\n * Format is a single flat object with no schema version: fields are\n * only ever added (and read with defaults), never removed or reshaped.\n * If we ever need a breaking migration, the file is trivially\n * regenerable — the worst case is a single extra registry round-trip.\n *\n * Corruption handling: every read path tolerates missing or malformed\n * JSON as \"no state\" (empty defaults). We never propagate a parse\n * error up to the CLI banner, because a corrupt state file must not\n * be able to break every invocation.\n */\nexport interface UpdateState {\n  /** Unix epoch seconds of the last registry query. */\n  last_check_at: number;\n  /** The codealmanac version running when we last wrote state. */\n  installed_version: string;\n  /** The newest version the registry has published at last check. */\n  latest_version: string;\n  /** Versions the user dismissed via `almanac update --dismiss`. */\n  dismissed_versions: string[];\n  /**\n   * Epoch seconds of the last registry fetch attempt that FAILED. Used\n   * by the check scheduler to back off (one failure shouldn't hammer\n   * the registry on every command) — reads tolerate a missing field.\n   */\n  last_fetch_failed_at?: number;\n}\n\nexport function emptyState(): UpdateState {\n  return {\n    last_check_at: 0,\n    installed_version: \"\",\n    latest_version: \"\",\n    dismissed_versions: [],\n  };\n}\n\nexport function getStatePath(): string {\n  return join(getGlobalAlmanacDir(), \"update-state.json\");\n}\n\n/**\n * Read the state file. Missing, empty, or malformed → empty state.\n * We deliberately swallow all errors here: the update system is\n * best-effort, and a read failure must not break any command.\n */\nexport async function readState(path?: string): Promise<UpdateState> {\n  const file = path ?? getStatePath();\n  let raw: string;\n  try {\n    raw = await readFile(file, \"utf8\");\n  } catch {\n    return emptyState();\n  }\n  const trimmed = raw.trim();\n  if (trimmed.length === 0) return emptyState();\n  try {\n    const parsed = JSON.parse(trimmed) as Partial<UpdateState>;\n    return {\n      last_check_at:\n        typeof parsed.last_check_at === \"number\" ? parsed.last_check_at : 0,\n      installed_version:\n        typeof parsed.installed_version === \"string\"\n          ? parsed.installed_version\n          : \"\",\n      latest_version:\n        typeof parsed.latest_version === \"string\" ? parsed.latest_version : \"\",\n      dismissed_versions: Array.isArray(parsed.dismissed_versions)\n        ? parsed.dismissed_versions.filter(\n            (v): v is string => typeof v === \"string\" && v.length > 0,\n          )\n        : [],\n      last_fetch_failed_at:\n        typeof parsed.last_fetch_failed_at === \"number\"\n          ? parsed.last_fetch_failed_at\n          : undefined,\n    };\n  } catch {\n    return emptyState();\n  }\n}\n\n/**\n * Write the state file atomically (tmp + rename). Makes the concurrent\n * \"two commands ran their update checks at once\" race safe — one rename\n * wins, the other is dropped. Creates `~/.almanac/` if missing.\n */\nexport async function writeState(\n  state: UpdateState,\n  path?: string,\n): Promise<void> {\n  const file = path ?? getStatePath();\n  await mkdir(dirname(file), { recursive: true });\n  const body = `${JSON.stringify(state, null, 2)}\\n`;\n  const tmp = `${file}.tmp`;\n  await writeFile(tmp, body, \"utf8\");\n  await rename(tmp, file);\n}\n","/**\n * Tiny semver comparator for update-version checks. We do NOT take a\n * dependency on `semver` — we only need a subset (compare two\n * well-formed `x.y.z` strings, optionally with a pre-release tag), and\n * adding a 400KB install for six lines of logic isn't a good trade.\n *\n * What we handle:\n *   - Numeric `major.minor.patch` with or without a `-pre` tag.\n *   - Missing parts default to 0 (`1.2` → `1.2.0`).\n *   - Leading `v` is stripped.\n *\n * What we don't handle:\n *   - Build metadata (`+sha.abcd`) — ignored.\n *   - Pre-release precedence rules beyond \"tagged < untagged at same\n *     numeric triple\". Good enough for codealmanac's linear release\n *     cadence; if we ever publish `-rc.1` vs `-rc.2` and care which\n *     comes first, revisit.\n */\n\ninterface Parsed {\n  major: number;\n  minor: number;\n  patch: number;\n  /** Empty string = no pre-release (counts as \"higher\" than a pre-release at the same triple). */\n  pre: string;\n}\n\nfunction parse(v: string): Parsed | null {\n  const trimmed = v.trim().replace(/^v/i, \"\");\n  // Strip build metadata (everything from the first `+`).\n  const noBuild = trimmed.split(\"+\")[0] ?? \"\";\n  // Split off pre-release tag.\n  const dashAt = noBuild.indexOf(\"-\");\n  const core = dashAt === -1 ? noBuild : noBuild.slice(0, dashAt);\n  const pre = dashAt === -1 ? \"\" : noBuild.slice(dashAt + 1);\n\n  const parts = core.split(\".\").map((p) => Number.parseInt(p, 10));\n  if (parts.length === 0 || parts.some((n) => !Number.isFinite(n) || n < 0)) {\n    return null;\n  }\n  return {\n    major: parts[0] ?? 0,\n    minor: parts[1] ?? 0,\n    patch: parts[2] ?? 0,\n    pre,\n  };\n}\n\n/**\n * Return `true` iff `latest` > `installed`. Returns `false` on unparseable\n * input rather than throwing — a bad version string must not be able to\n * crash the CLI's every-command banner path.\n */\nexport function isNewer(latest: string, installed: string): boolean {\n  const a = parse(latest);\n  const b = parse(installed);\n  if (a === null || b === null) return false;\n\n  if (a.major !== b.major) return a.major > b.major;\n  if (a.minor !== b.minor) return a.minor > b.minor;\n  if (a.patch !== b.patch) return a.patch > b.patch;\n\n  // Same numeric triple. Empty pre-release beats a tagged pre-release\n  // (1.2.3 > 1.2.3-rc.1). Two tagged pre-releases compare lexically.\n  if (a.pre === b.pre) return false;\n  if (a.pre === \"\" && b.pre !== \"\") return true;\n  if (a.pre !== \"\" && b.pre === \"\") return false;\n  return a.pre > b.pre;\n}\n","export function formatDuration(ms: number): string {\n  if (ms < 0) return \"just now\";\n  const seconds = Math.floor(ms / 1000);\n  if (seconds < 60) return `${seconds}s`;\n  const minutes = Math.floor(seconds / 60);\n  if (minutes < 60) return `${minutes}m`;\n  const hours = Math.floor(minutes / 60);\n  if (hours < 48) return `${hours}h`;\n  const days = Math.floor(hours / 24);\n  return `${days}d`;\n}\n","import { readConfig } from \"../../update/config.js\";\nimport { readStateForDoctor } from \"../../update/schedule.js\";\nimport { isNewer } from \"../../update/semver.js\";\nimport { formatDuration } from \"./duration.js\";\nimport type { Check, DoctorOptions } from \"./types.js\";\n\nexport async function gatherUpdateChecks(\n  options: DoctorOptions,\n  installedVersion: string,\n): Promise<Check[]> {\n  const checks: Check[] = [];\n  const state = readStateForDoctor(options.updateStatePath);\n  const config = await readConfig(options.updateConfigPath);\n\n  if (state === null || state.latest_version.length === 0) {\n    checks.push({\n      status: \"info\",\n      key: \"update.status\",\n      message: `on ${installedVersion}; no update check has run yet`,\n      fix: \"run: almanac update --check\",\n    });\n  } else if (isNewer(state.latest_version, installedVersion)) {\n    const dismissed = state.dismissed_versions.includes(state.latest_version)\n      ? \" (dismissed — run `almanac update` to install anyway)\"\n      : \"\";\n    checks.push({\n      status: \"problem\",\n      key: \"update.status\",\n      message:\n        `${state.latest_version} available (you're on ${installedVersion})${dismissed}`,\n      fix: \"run: almanac update\",\n    });\n  } else {\n    checks.push({\n      status: \"ok\",\n      key: \"update.status\",\n      message: `on latest (${installedVersion})`,\n    });\n  }\n\n  if (state !== null && state.last_check_at > 0) {\n    const now = (options.now?.() ?? new Date()).getTime();\n    const ageMs = now - state.last_check_at * 1000;\n    const failedSuffix =\n      state.last_fetch_failed_at !== undefined &&\n      state.last_fetch_failed_at === state.last_check_at\n        ? \" (last attempt failed — will retry next invocation)\"\n        : \"\";\n    checks.push({\n      status: \"info\",\n      key: \"update.last_check\",\n      message: `last checked: ${formatDuration(ageMs)} ago${failedSuffix}`,\n    });\n  } else {\n    checks.push({\n      status: \"info\",\n      key: \"update.last_check\",\n      message: \"last checked: never\",\n    });\n  }\n\n  checks.push({\n    status: \"info\",\n    key: \"update.notifier\",\n    message: `update notifier: ${config.update_notifier ? \"enabled\" : \"disabled\"}`,\n    fix: config.update_notifier\n      ? undefined\n      : \"run: almanac update --enable-notifier\",\n  });\n\n  if (state !== null && state.dismissed_versions.length > 0) {\n    checks.push({\n      status: \"info\",\n      key: \"update.dismissed\",\n      message: `dismissed versions: ${state.dismissed_versions.join(\", \")}`,\n    });\n  }\n\n  return checks;\n}\n","import { existsSync, readdirSync, statSync } from \"node:fs\";\nimport path from \"node:path\";\n\nimport type Database from \"better-sqlite3\";\n\nimport { ensureFreshIndex } from \"../../indexer/index.js\";\nimport { openIndex } from \"../../indexer/schema.js\";\nimport { findNearestAlmanacDir } from \"../../paths.js\";\nimport { findEntry } from \"../../registry/index.js\";\nimport { runHealth, type HealthReport } from \"../health.js\";\nimport { formatDuration } from \"./duration.js\";\nimport type { Check, DoctorOptions } from \"./types.js\";\n\nexport async function gatherWikiChecks(options: DoctorOptions): Promise<Check[]> {\n  const checks: Check[] = [];\n  const repoRoot = findNearestAlmanacDir(options.cwd);\n\n  if (repoRoot === null) {\n    checks.push({\n      status: \"info\",\n      key: \"wiki.none\",\n      message: \"No wiki in current directory\",\n      fix: \"run: almanac bootstrap  (to create one in this repo)\",\n    });\n    return checks;\n  }\n\n  checks.push({\n    status: \"info\",\n    key: \"wiki.repo\",\n    message: `repo: ${repoRoot}`,\n  });\n\n  try {\n    await ensureFreshIndex({ repoRoot });\n  } catch {\n    // non-fatal: counts below and the health probe report any real issue.\n  }\n\n  checks.push(await describeRegistry(repoRoot));\n\n  const almanacDir = path.join(repoRoot, \".almanac\");\n  const dbPath = path.join(almanacDir, \"index.db\");\n  checks.push(...describeCounts(dbPath));\n  checks.push(describeIndexFreshness(dbPath));\n  checks.push(describeLastCapture(almanacDir, options.now));\n  checks.push(await describeHealth(repoRoot, options));\n\n  return checks;\n}\n\nasync function describeRegistry(repoRoot: string): Promise<Check> {\n  try {\n    const entry = await findEntry({ path: repoRoot });\n    if (entry !== null) {\n      return {\n        status: \"ok\",\n        key: \"wiki.registered\",\n        message: `registered as '${entry.name}'`,\n      };\n    }\n    return {\n      status: \"info\",\n      key: \"wiki.registered\",\n      message: \"not yet registered (will register on first command)\",\n    };\n  } catch (err: unknown) {\n    const msg = err instanceof Error ? err.message : String(err);\n    return {\n      status: \"problem\",\n      key: \"wiki.registered\",\n      message: `could not read registry: ${msg}`,\n      fix: \"inspect ~/.almanac/registry.json; remove or fix the malformed entry\",\n    };\n  }\n}\n\nfunction describeCounts(dbPath: string): Check[] {\n  const checks: Check[] = [];\n  let pageCount: number | null = null;\n  let topicCount: number | null = null;\n\n  if (existsSync(dbPath)) {\n    try {\n      const db = openIndex(dbPath);\n      try {\n        pageCount = countRows(db, \"pages\");\n        topicCount = countRows(db, \"topics\");\n      } finally {\n        db.close();\n      }\n    } catch {\n      pageCount = null;\n    }\n  }\n\n  if (pageCount !== null) {\n    checks.push({\n      status: \"info\",\n      key: \"wiki.pages\",\n      message: `pages: ${pageCount}`,\n    });\n  }\n  if (topicCount !== null) {\n    checks.push({\n      status: \"info\",\n      key: \"wiki.topics\",\n      message: `topics: ${topicCount}`,\n    });\n  }\n\n  return checks;\n}\n\nfunction countRows(db: Database.Database, table: string): number {\n  const row = db\n    .prepare<[], { n: number }>(`SELECT COUNT(*) AS n FROM ${table}`)\n    .get();\n  return row?.n ?? 0;\n}\n\nfunction describeIndexFreshness(dbPath: string): Check {\n  if (!existsSync(dbPath)) {\n    return {\n      status: \"info\",\n      key: \"wiki.index\",\n      message: \"index: not built yet (run any query command)\",\n    };\n  }\n  try {\n    const dbMtime = statSync(dbPath).mtimeMs;\n    const age = Date.now() - dbMtime;\n    return {\n      status: \"info\",\n      key: \"wiki.index\",\n      message: `index: rebuilt ${formatDuration(age)} ago`,\n    };\n  } catch {\n    return {\n      status: \"info\",\n      key: \"wiki.index\",\n      message: \"index: present\",\n    };\n  }\n}\n\nfunction describeLastCapture(\n  almanacDir: string,\n  nowFn?: () => Date,\n): Check {\n  if (!existsSync(almanacDir)) {\n    return {\n      status: \"info\",\n      key: \"wiki.capture\",\n      message: \"last capture: never\",\n    };\n  }\n  let entries: string[];\n  try {\n    entries = readdirSync(almanacDir);\n  } catch {\n    return {\n      status: \"info\",\n      key: \"wiki.capture\",\n      message: \"last capture: unknown\",\n    };\n  }\n  const captures = entries\n    .filter(\n      (e) =>\n        e.startsWith(\".capture-\") &&\n        (e.endsWith(\".log\") || e.endsWith(\".jsonl\")),\n    )\n    .map((e) => {\n      try {\n        return {\n          name: e,\n          mtime: statSync(path.join(almanacDir, e)).mtimeMs,\n        };\n      } catch {\n        return null;\n      }\n    })\n    .filter((e): e is { name: string; mtime: number } => e !== null);\n  if (captures.length === 0) {\n    return {\n      status: \"info\",\n      key: \"wiki.capture\",\n      message: \"last capture: never\",\n    };\n  }\n  captures.sort((a, b) => b.mtime - a.mtime);\n  const latest = captures[0]!;\n  const now = (nowFn?.() ?? new Date()).getTime();\n  const age = now - latest.mtime;\n  return {\n    status: \"info\",\n    key: \"wiki.capture\",\n    message: `last capture: ${formatDuration(age)} ago (${latest.name})`,\n  };\n}\n\nasync function describeHealth(\n  repoRoot: string,\n  options: DoctorOptions,\n): Promise<Check> {\n  const healthFn = options.runHealthFn ?? runHealth;\n  try {\n    const healthRes = await healthFn({\n      cwd: repoRoot,\n      json: true,\n    });\n    const problems = countHealthProblems(healthRes.stdout);\n    if (problems === 0) {\n      return {\n        status: \"ok\",\n        key: \"wiki.health\",\n        message: \"almanac health reports 0 problems\",\n      };\n    }\n    return {\n      status: \"problem\",\n      key: \"wiki.health\",\n      message: `almanac health reports ${problems} problem${problems === 1 ? \"\" : \"s\"}`,\n      fix: \"run: almanac health\",\n    };\n  } catch (err: unknown) {\n    const msg = err instanceof Error ? err.message : String(err);\n    return {\n      status: \"info\",\n      key: \"wiki.health\",\n      message: `could not run almanac health: ${msg}`,\n    };\n  }\n}\n\nconst HEALTH_PROBLEM_KEYS: (keyof HealthReport)[] = [\n  \"orphans\",\n  \"stale\",\n  \"dead_refs\",\n  \"broken_links\",\n  \"broken_xwiki\",\n  \"empty_topics\",\n  \"empty_pages\",\n  \"slug_collisions\",\n];\n\nfunction countHealthProblems(jsonStdout: string): number {\n  try {\n    const report = JSON.parse(jsonStdout) as Partial<HealthReport>;\n    let total = 0;\n    for (const key of HEALTH_PROBLEM_KEYS) {\n      const arr = report[key];\n      if (Array.isArray(arr)) total += arr.length;\n    }\n    return total;\n  } catch {\n    return 0;\n  }\n}\n","import { formatReport } from \"./doctor-checks/format.js\";\nimport { gatherInstallChecks } from \"./doctor-checks/install.js\";\nimport { readPackageVersion } from \"./doctor-checks/probes.js\";\nimport type {\n  Check,\n  CheckStatus,\n  DoctorOptions,\n  DoctorReport,\n  DoctorResult,\n  SqliteProbeResult,\n} from \"./doctor-checks/types.js\";\nimport { gatherUpdateChecks } from \"./doctor-checks/updates.js\";\nimport { gatherWikiChecks } from \"./doctor-checks/wiki.js\";\n\nexport type {\n  Check,\n  CheckStatus,\n  DoctorOptions,\n  DoctorReport,\n  DoctorResult,\n  SqliteProbeResult,\n};\n\n/**\n * `almanac doctor` — install + wiki health report.\n *\n * Separate from `almanac health` (which checks graph integrity of a\n * specific wiki). `doctor` answers the \"is this install even set up\n * correctly?\" question that users hit when first trying the tool or when\n * sessions silently stop getting captured.\n *\n * This file is the command composition root. The section-specific probes\n * and formatting live in `doctor-checks/` so each durable fact has one\n * obvious owner.\n */\nexport async function runDoctor(\n  options: DoctorOptions,\n): Promise<DoctorResult> {\n  const version =\n    options.versionOverride ?? readPackageVersion() ?? \"unknown\";\n\n  const install: Check[] = options.wikiOnly === true\n    ? []\n    : await gatherInstallChecks(options);\n\n  const updates: Check[] = options.wikiOnly === true\n    ? []\n    : await gatherUpdateChecks(options, version);\n\n  const wiki: Check[] = options.installOnly === true\n    ? []\n    : await gatherWikiChecks(options);\n\n  const report: DoctorReport = { version, install, updates, wiki };\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, options),\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n","import { existsSync } from \"node:fs\";\nimport { readFile, rm, writeFile } from \"node:fs/promises\";\nimport { homedir } from \"node:os\";\nimport path from \"node:path\";\n\nimport { runHookUninstall } from \"./hook.js\";\nimport { IMPORT_LINE } from \"./setup.js\";\n\n/**\n * `almanac uninstall` — the reverse of `setup`.\n *\n * Idempotent and order-insensitive: each step is a no-op if that\n * artifact was never installed. We remove exactly the things setup added,\n * nothing else:\n *\n *   1. The `@~/.claude/codealmanac.md` line from `~/.claude/CLAUDE.md`.\n *      Other content stays untouched. If removing our line leaves the\n *      file empty, we delete the file so our fingerprint doesn't persist\n *      as zero bytes.\n *   2. The guide files `~/.claude/codealmanac.md` and\n *      `~/.claude/codealmanac-reference.md`.\n *   3. The SessionEnd hook entry (delegated to `runHookUninstall`, which\n *      already knows how to leave foreign entries alone).\n *\n * Flags:\n *   --yes           skip confirmations; remove everything\n *   --keep-hook     leave the hook alone\n *   --keep-guides   leave the guides + CLAUDE.md import alone\n *\n * Non-interactive (no TTY) → behaves as if `--yes` was passed. Same\n * contract as `setup`.\n */\n\nexport interface UninstallOptions {\n  yes?: boolean;\n  keepHook?: boolean;\n  keepGuides?: boolean;\n\n  // ─── Injection points ────────────────────────────────────────────\n  settingsPath?: string;\n  hookScriptPath?: string;\n  claudeDir?: string;\n  isTTY?: boolean;\n  stdout?: NodeJS.WritableStream;\n}\n\nexport interface UninstallResult {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\nconst BLUE = \"\\x1b[38;5;75m\";\nconst DIM = \"\\x1b[2m\";\nconst RST = \"\\x1b[0m\";\n\nexport async function runUninstall(\n  options: UninstallOptions = {},\n): Promise<UninstallResult> {\n  const out = options.stdout ?? process.stdout;\n  const isTTY =\n    options.isTTY ?? (process.stdin.isTTY === true);\n  const interactive = isTTY && options.yes !== true;\n  const claudeDir = options.claudeDir ?? path.join(homedir(), \".claude\");\n\n  out.write(\"\\n\");\n\n  // Hook removal.\n  let removeHook = true;\n  if (options.keepHook === true) {\n    removeHook = false;\n  } else if (interactive) {\n    removeHook = await confirm(\n      out,\n      \"Remove the SessionEnd hook from ~/.claude/settings.json?\",\n      true,\n    );\n  }\n  if (removeHook) {\n    const res = await runHookUninstall({\n      settingsPath: options.settingsPath,\n      hookScriptPath: options.hookScriptPath,\n    });\n    if (res.exitCode !== 0) {\n      return { stdout: \"\", stderr: res.stderr, exitCode: res.exitCode };\n    }\n    out.write(`  ${BLUE}\\u25c7${RST}  ${res.stdout.trim()}\\n`);\n  } else {\n    out.write(`  ${DIM}\\u25cb  Hook kept${RST}\\n`);\n  }\n\n  // Guide + import removal.\n  let removeGuides = true;\n  if (options.keepGuides === true) {\n    removeGuides = false;\n  } else if (interactive) {\n    removeGuides = await confirm(\n      out,\n      \"Remove the guides + CLAUDE.md import line?\",\n      true,\n    );\n  }\n  if (removeGuides) {\n    const summary = await removeGuideFiles(claudeDir);\n    if (summary.anyChanges) {\n      out.write(\n        `  ${BLUE}\\u25c7${RST}  Guides removed (${summary.filesTouched.join(\", \")})\\n`,\n      );\n    } else {\n      out.write(`  ${DIM}\\u25cb  Guides not installed${RST}\\n`);\n    }\n  } else {\n    out.write(`  ${DIM}\\u25cb  Guides kept${RST}\\n`);\n  }\n\n  out.write(`\\n  ${BLUE}\\u25c7${RST}  ${BLUE}Uninstall complete${RST}\\n\\n`);\n\n  return { stdout: \"\", stderr: \"\", exitCode: 0 };\n}\n\ninterface RemoveGuidesResult {\n  anyChanges: boolean;\n  filesTouched: string[];\n}\n\nasync function removeGuideFiles(\n  claudeDir: string,\n): Promise<RemoveGuidesResult> {\n  const touched: string[] = [];\n\n  const mini = path.join(claudeDir, \"codealmanac.md\");\n  const ref = path.join(claudeDir, \"codealmanac-reference.md\");\n  const claudeMd = path.join(claudeDir, \"CLAUDE.md\");\n\n  if (existsSync(mini)) {\n    await rm(mini, { force: true });\n    touched.push(\"codealmanac.md\");\n  }\n  if (existsSync(ref)) {\n    await rm(ref, { force: true });\n    touched.push(\"codealmanac-reference.md\");\n  }\n\n  if (existsSync(claudeMd)) {\n    const existing = await readFile(claudeMd, \"utf8\");\n    const { changed, body } = removeImportLine(existing);\n    if (changed) {\n      // If the file is now content-free, delete it outright so our\n      // installation leaves no trace. A user who was using CLAUDE.md\n      // before we touched it still has their content; only the case\n      // where CLAUDE.md contained nothing but our line gets cleaned up.\n      if (body.trim().length === 0) {\n        await rm(claudeMd, { force: true });\n        touched.push(\"CLAUDE.md (deleted)\");\n      } else {\n        await writeFile(claudeMd, body, \"utf8\");\n        touched.push(\"CLAUDE.md\");\n      }\n    }\n  }\n\n  return { anyChanges: touched.length > 0, filesTouched: touched };\n}\n\n/**\n * Remove the import line from a CLAUDE.md body. Match is line-anchored\n * (trimmed equality) so we don't munge a line that happens to include\n * the token as part of a longer string. Returns the unchanged body (and\n * `changed: false`) if the line isn't present — this is what makes the\n * command safe to run repeatedly.\n */\nexport function removeImportLine(contents: string): {\n  changed: boolean;\n  body: string;\n} {\n  const eol = contents.includes(\"\\r\\n\") ? \"\\r\\n\" : \"\\n\";\n  const lines = contents.split(/\\r?\\n/);\n\n  const indices: number[] = [];\n  for (let i = 0; i < lines.length; i++) {\n    if (lines[i]!.trim() === IMPORT_LINE) indices.push(i);\n  }\n  if (indices.length === 0) return { changed: false, body: contents };\n\n  // Remove the line(s). Iterate from the end so earlier indices stay\n  // valid as we splice.\n  for (let i = indices.length - 1; i >= 0; i--) {\n    lines.splice(indices[i]!, 1);\n  }\n\n  let body = lines.join(eol);\n\n  // Cleanup: collapse any double-blank that our removal created at the\n  // spot the line used to live. A best-effort tidy — we don't try to\n  // normalize the whole file.\n  body = body.replace(/\\n\\n\\n+/g, \"\\n\\n\");\n\n  return { changed: true, body };\n}\n\nfunction confirm(\n  out: NodeJS.WritableStream,\n  question: string,\n  defaultYes: boolean,\n): Promise<boolean> {\n  return new Promise((resolve) => {\n    const hint = defaultYes ? \"[Y/n]\" : \"[y/N]\";\n    out.write(`  ${BLUE}\\u25c6${RST}  ${question} ${DIM}${hint}${RST} `);\n\n    let buf = \"\";\n    const onData = (chunk: Buffer): void => {\n      buf += chunk.toString(\"utf8\");\n      const nl = buf.indexOf(\"\\n\");\n      if (nl === -1) return;\n      process.stdin.removeListener(\"data\", onData);\n      process.stdin.pause();\n\n      const answer = buf.slice(0, nl).trim().toLowerCase();\n      const accepted =\n        answer.length === 0\n          ? defaultYes\n          : answer === \"y\" || answer === \"yes\";\n      resolve(accepted);\n    };\n\n    process.stdin.resume();\n    process.stdin.on(\"data\", onData);\n  });\n}\n","import { spawn, type SpawnOptions } from \"node:child_process\";\nimport { createRequire } from \"node:module\";\n\nimport { checkForUpdate } from \"../update/check.js\";\nimport {\n  readConfig,\n  writeConfig,\n  type GlobalConfig,\n} from \"../update/config.js\";\nimport { isNewer } from \"../update/semver.js\";\nimport { readState, writeState } from \"../update/state.js\";\n\n/**\n * `almanac update` — manual upgrade command, the counterpart to the\n * persistent nag banner.\n *\n * Default action: shell out to `npm i -g codealmanac@latest` with\n * inherited stdio so the user sees real-time download/install/permission\n * output. Synchronous in the user's terminal — no background install,\n * no mid-invocation swap (see the pair review's Tier-B design for\n * rationale).\n *\n * Flags:\n *   --dismiss — mark the current `latest_version` as \"don't nag about\n *     this one again\". No install. Writes state and exits.\n *   --check — force a registry query regardless of the 24h cache.\n *     Shows the result and exits. No install.\n *   --enable-notifier / --disable-notifier — flip the global\n *     `update_notifier` config. Default is enabled; after\n *     `--disable-notifier` the banner won't show even when a new\n *     version is available.\n */\n\nexport interface UpdateOptions {\n  dismiss?: boolean;\n  check?: boolean;\n  enableNotifier?: boolean;\n  disableNotifier?: boolean;\n\n  // ─── Test injection points ──────────────────────────────────────\n  /** Override state file path (tests point at a tmpdir). */\n  statePath?: string;\n  /** Override config file path (tests point at a tmpdir). */\n  configPath?: string;\n  /** Override the installed version report. */\n  installedVersion?: string;\n  /**\n   * Replace `checkForUpdate` — tests inject a stub that returns a\n   * canned state without hitting the registry.\n   */\n  checkFn?: typeof checkForUpdate;\n  /** Replace `spawn` for tests (install path shouldn't run npm). */\n  spawnFn?: typeof spawn;\n  /** Clock for deterministic `last_check_at` assertions. */\n  now?: () => number;\n}\n\nexport interface UpdateResult {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\nexport async function runUpdate(\n  opts: UpdateOptions = {},\n): Promise<UpdateResult> {\n  // Precedence: config toggles > --dismiss > --check > install.\n  // Config toggles are disjoint from the other flags (you'd never\n  // `update --dismiss --disable-notifier`), but if someone does we\n  // apply them in order and take the last action as the \"command\"\n  // that sets the exit code.\n  if (opts.enableNotifier === true) {\n    return await toggleNotifier(true, opts);\n  }\n  if (opts.disableNotifier === true) {\n    return await toggleNotifier(false, opts);\n  }\n  if (opts.dismiss === true) {\n    return await dismissLatest(opts);\n  }\n  if (opts.check === true) {\n    return await forceCheck(opts);\n  }\n  return await installLatest(opts);\n}\n\n// ─── --dismiss ────────────────────────────────────────────────────\n\nasync function dismissLatest(opts: UpdateOptions): Promise<UpdateResult> {\n  const state = await readState(opts.statePath);\n  // Nothing to dismiss when we don't know of a newer version. Silently\n  // no-op with a message — more helpful than pretending to write state\n  // that no future banner would consult.\n  if (state.latest_version.length === 0) {\n    return {\n      stdout:\n        \"codealmanac: no pending update to dismiss. \" +\n        \"Run `almanac update --check` to query the registry.\\n\",\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n  const installed = opts.installedVersion ?? readInstalledVersion();\n  if (!isNewer(state.latest_version, installed)) {\n    return {\n      stdout: `codealmanac: already on latest (${installed}); nothing to dismiss.\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n  if (state.dismissed_versions.includes(state.latest_version)) {\n    return {\n      stdout: `codealmanac: ${state.latest_version} already dismissed.\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n  const next = {\n    ...state,\n    dismissed_versions: [...state.dismissed_versions, state.latest_version],\n  };\n  await writeState(next, opts.statePath);\n  return {\n    stdout:\n      `codealmanac: dismissed ${state.latest_version}. The nag banner ` +\n      `will not show for this version.\\n` +\n      `Run \\`almanac update\\` to upgrade, or \\`almanac update --enable-notifier\\` to re-enable nags.\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\n// ─── --check ───────────────────────────────────────────────────────\n\nasync function forceCheck(opts: UpdateOptions): Promise<UpdateResult> {\n  const installed = opts.installedVersion ?? readInstalledVersion();\n  const checkFn = opts.checkFn ?? checkForUpdate;\n  const result = await checkFn({\n    installedVersion: installed,\n    force: true,\n    statePath: opts.statePath,\n    now: opts.now,\n  });\n  if (result.fetchFailed) {\n    return {\n      stdout: \"\",\n      stderr:\n        `codealmanac: could not reach registry.npmjs.org (timeout or network error).\\n` +\n        `Installed: ${installed}. No cached latest available.\\n`,\n      exitCode: 1,\n    };\n  }\n  const latest = result.state.latest_version;\n  if (latest.length === 0) {\n    return {\n      stdout: `codealmanac: installed ${installed}; registry did not report a latest tag.\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n  if (isNewer(latest, installed)) {\n    const dismissed = result.state.dismissed_versions.includes(latest)\n      ? \" (dismissed — banner suppressed; `almanac update` still installs)\"\n      : \"\";\n    return {\n      stdout:\n        `codealmanac ${latest} available (you're on ${installed})${dismissed}.\\n` +\n        `Run: almanac update\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n  return {\n    stdout: `codealmanac: up to date (${installed}).\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\n// ─── --enable/--disable-notifier ──────────────────────────────────\n\nasync function toggleNotifier(\n  enable: boolean,\n  opts: UpdateOptions,\n): Promise<UpdateResult> {\n  const config = await readConfig(opts.configPath);\n  const next: GlobalConfig = { ...config, update_notifier: enable };\n  await writeConfig(next, opts.configPath);\n  return {\n    stdout:\n      enable\n        ? \"codealmanac: update notifier enabled. \" +\n          \"The pre-command banner will show when a new version is available.\\n\"\n        : \"codealmanac: update notifier disabled. \" +\n          \"No more pre-command banners. Run `almanac update --check` to see status.\\n\",\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\n// ─── default: install ─────────────────────────────────────────────\n\nasync function installLatest(opts: UpdateOptions): Promise<UpdateResult> {\n  const spawnFn = opts.spawnFn ?? spawn;\n  const installed = opts.installedVersion ?? readInstalledVersion();\n\n  // Inherit stdio so npm's progress bar, permission prompts, and\n  // peer-dep warnings land in the user's terminal verbatim. No\n  // wrapping, no capture — npm output is its own contract.\n  const spawnOpts: SpawnOptions = { stdio: \"inherit\" };\n\n  return await new Promise<UpdateResult>((resolve) => {\n    const child = spawnFn(\n      \"npm\",\n      [\"i\", \"-g\", \"codealmanac@latest\"],\n      spawnOpts,\n    );\n\n    // Two failure modes need distinct messaging:\n    //   - ENOENT: npm isn't on PATH. Rare on dev laptops, common in\n    //     stripped-down CI containers. Tell the user what we tried to\n    //     run so they can diagnose.\n    //   - EACCES / exit code 243 / etc.: npm ran but couldn't write\n    //     to the global prefix. Suggest sudo; don't try it ourselves\n    //     (silently escalating privileges would be a trust violation,\n    //     and the pair review explicitly rejected it).\n    child.on(\"error\", (err: NodeJS.ErrnoException) => {\n      if (err.code === \"ENOENT\") {\n        resolve({\n          stdout: \"\",\n          stderr:\n            \"codealmanac: `npm` not found on PATH. \" +\n            \"Install Node.js + npm, or install codealmanac via your package manager.\\n\",\n          exitCode: 1,\n        });\n        return;\n      }\n      resolve({\n        stdout: \"\",\n        stderr: `codealmanac: failed to run npm: ${err.message}\\n`,\n        exitCode: 1,\n      });\n    });\n\n    child.on(\"exit\", async (code, _signal) => {\n      const exitCode = code ?? 1;\n      if (exitCode !== 0) {\n        // Check for the common EACCES cause. npm prints \"EACCES\" to\n        // stderr, which we don't have (inherited stdio), so we rely\n        // on exit code heuristics + a generic hint.\n        const hint =\n          `codealmanac: npm install failed (exit ${exitCode}).\\n` +\n          `If you see \"EACCES\" above, try: sudo npm i -g codealmanac@latest\\n` +\n          `Or install with a version manager (nvm, volta, fnm) to avoid sudo.\\n`;\n        resolve({ stdout: \"\", stderr: hint, exitCode });\n        return;\n      }\n      // On success, refresh the state file so the next command's\n      // banner reflects that we're current. We can't read the new\n      // version out of our own process (we're still running the old\n      // build); we record what the state file's latest_version was,\n      // on the assumption that npm installed that version.\n      try {\n        const state = await readState(opts.statePath);\n        const now =\n          opts.now ?? (() => Math.floor(Date.now() / 1000));\n        await writeState(\n          {\n            last_check_at: now(),\n            installed_version: state.latest_version || installed,\n            latest_version: state.latest_version || installed,\n            dismissed_versions: state.dismissed_versions,\n          },\n          opts.statePath,\n        );\n      } catch {\n        // Non-fatal: the next `almanac` invocation will re-run the\n        // background check and refresh state properly.\n      }\n      resolve({\n        stdout: \"codealmanac: updated.\\n\",\n        stderr: \"\",\n        exitCode: 0,\n      });\n    });\n  });\n}\n\nfunction readInstalledVersion(): string {\n  // Dev layout: `src/commands/update.ts` → `../../package.json`.\n  // Bundled layout: `dist/codealmanac.js` → `../package.json`. We try\n  // both so the version lookup works from both. (Same approach as\n  // `cli.ts` and `doctor.ts`, which hit the same ambiguity.)\n  try {\n    const require = createRequire(import.meta.url);\n    const pkg = require(\"../../package.json\") as { version?: unknown };\n    if (typeof pkg.version === \"string\" && pkg.version.length > 0) {\n      return pkg.version;\n    }\n  } catch {\n    // Fall through.\n  }\n  try {\n    const require = createRequire(import.meta.url);\n    const pkg = require(\"../package.json\") as { version?: unknown };\n    if (typeof pkg.version === \"string\" && pkg.version.length > 0) {\n      return pkg.version;\n    }\n  } catch {\n    // Fall through.\n  }\n  return \"unknown\";\n}\n","import { Command } from \"commander\";\n\nimport { runDoctor } from \"../commands/doctor.js\";\nimport { runSetup } from \"../commands/setup.js\";\nimport { runUninstall } from \"../commands/uninstall.js\";\nimport { runUpdate } from \"../commands/update.js\";\nimport { emit } from \"./helpers.js\";\n\nexport function registerSetupCommands(program: Command): void {\n  program\n    .command(\"setup\")\n    .description(\"install the hook + CLAUDE.md guides (bare codealmanac alias)\")\n    .option(\"-y, --yes\", \"skip prompts; install everything\")\n    .option(\"--skip-hook\", \"opt out of the SessionEnd hook\")\n    .option(\"--skip-guides\", \"opt out of the CLAUDE.md guides\")\n    .action(\n      async (opts: {\n        yes?: boolean;\n        skipHook?: boolean;\n        skipGuides?: boolean;\n      }) => {\n        const result = await runSetup({\n          yes: opts.yes,\n          skipHook: opts.skipHook,\n          skipGuides: opts.skipGuides,\n        });\n        emit(result);\n      },\n    );\n\n  program\n    .command(\"doctor\")\n    .description(\"report on the codealmanac install + current wiki health\")\n    .option(\"--json\", \"emit structured JSON\")\n    .option(\"--install-only\", \"report only on the install (skip wiki checks)\")\n    .option(\"--wiki-only\", \"report only on the current wiki (skip install checks)\")\n    .action(\n      async (opts: {\n        json?: boolean;\n        installOnly?: boolean;\n        wikiOnly?: boolean;\n      }) => {\n        const result = await runDoctor({\n          cwd: process.cwd(),\n          json: opts.json,\n          installOnly: opts.installOnly,\n          wikiOnly: opts.wikiOnly,\n        });\n        emit(result);\n      },\n    );\n\n  program\n    .command(\"update\")\n    .description(\"install the latest codealmanac (synchronous foreground `npm i -g`)\")\n    .option(\n      \"--dismiss\",\n      \"silence the update banner for the current `latest_version` without installing\",\n    )\n    .option(\"--check\", \"force a registry check now (bypasses the 24h cache); no install\")\n    .option(\n      \"--enable-notifier\",\n      \"re-enable the pre-command update banner (writes ~/.almanac/config.json)\",\n    )\n    .option(\n      \"--disable-notifier\",\n      \"silence the pre-command update banner (writes ~/.almanac/config.json)\",\n    )\n    .action(\n      async (opts: {\n        dismiss?: boolean;\n        check?: boolean;\n        enableNotifier?: boolean;\n        disableNotifier?: boolean;\n      }) => {\n        const result = await runUpdate({\n          dismiss: opts.dismiss,\n          check: opts.check,\n          enableNotifier: opts.enableNotifier,\n          disableNotifier: opts.disableNotifier,\n        });\n        emit(result);\n      },\n    );\n\n  program\n    .command(\"uninstall\")\n    .description(\"remove the hook + guides + import line\")\n    .option(\"-y, --yes\", \"skip confirmations; remove everything\")\n    .option(\"--keep-hook\", \"don't remove the SessionEnd hook (guides still prompted unless --yes)\")\n    .option(\n      \"--keep-guides\",\n      \"don't remove the guides or CLAUDE.md import (hook still prompted unless --yes)\",\n    )\n    .action(\n      async (opts: {\n        yes?: boolean;\n        keepHook?: boolean;\n        keepGuides?: boolean;\n      }) => {\n        const result = await runUninstall({\n          yes: opts.yes,\n          keepHook: opts.keepHook,\n          keepGuides: opts.keepGuides,\n        });\n        emit(result);\n      },\n    );\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 { 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 { 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    // Capture/bootstrap/ingest log files written by the AI pipeline.\n    // These can be multi-megabyte JSONL files and should never be\n    // committed. Bug #4 from codealmanac-known-bugs.md: a 1.8MB bootstrap\n    // log was accidentally committed before this line was added.\n    \".almanac/.capture-*\",\n    \".almanac/.bootstrap-*\",\n    \".almanac/.ingest-*\",\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","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 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. Prefer the Claude Code session-id when we\n  // have one (`--session` was passed — which is what the SessionEnd\n  // hook does) so the SDK transcript and the hook's human-readable\n  // sidecar share a stem: `.capture-<sid>.jsonl` (this file) alongside\n  // `.capture-<sid>.log` (the hook's stdout redirect). `ls -lah\n  // .capture-<sid>.*` tells one coherent story per session. Fall back\n  // to a timestamp for manual `almanac capture` invocations where no\n  // session-id is available — we don't have the SDK session_id either\n  // at this point; it arrives on the first SDK message, too late to\n  // use as a filename.\n  //\n  // The file extension is `.jsonl` because that's what's actually\n  // written (one JSON SDK message per line). Using `.log` here would\n  // collide with the hook's stdout-redirect sidecar, which happens to\n  // share the session-id stem; distinct extensions keep them from\n  // clobbering each other.\n  const now = options.now?.() ?? new Date();\n  const logStem =\n    options.sessionId !== undefined && options.sessionId.length > 0\n      ? options.sessionId\n      : formatTimestamp(now);\n  const logName = `.capture-${logStem}.jsonl`;\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 { runIndexer, type IndexResult } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolve-wiki.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 { 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 { runReindex } from \"../commands/reindex.js\";\nimport { autoRegisterIfNeeded } from \"../registry/autoregister.js\";\nimport { emit } from \"./helpers.js\";\n\nexport function registerWikiLifecycleCommands(program: Command): void {\n  program\n    .command(\"bootstrap\")\n    .description(\n      \"scaffold a wiki in this repo via an AI agent (requires ANTHROPIC_API_KEY or Claude subscription)\",\n    )\n    .option(\"--quiet\", \"suppress per-tool streaming; print only the final line\")\n    .option(\"--model <model>\", \"override the agent model\")\n    .option(\"--force\", \"overwrite an existing populated wiki (default: refuse)\")\n    .action(\n      async (opts: { quiet?: boolean; model?: string; force?: boolean }) => {\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  program\n    .command(\"capture [transcript]\")\n    .description(\"run the writer/reviewer pipeline on a session (usually automatic)\")\n    .option(\"--session <id>\", \"target a specific session by ID\")\n    .option(\"--quiet\", \"suppress per-tool streaming; print only the final summary\")\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        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  const hook = program\n    .command(\"hook\")\n    .description(\"manage the SessionEnd auto-capture hook\");\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  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","import { Command } from \"commander\";\n\nimport { registerEditCommands } from \"./register-edit-commands.js\";\nimport { registerQueryCommands } from \"./register-query-commands.js\";\nimport { registerSetupCommands } from \"./register-setup-commands.js\";\nimport { registerWikiLifecycleCommands } from \"./register-wiki-lifecycle-commands.js\";\n\nexport function registerCommands(program: Command): void {\n  registerQueryCommands(program);\n  registerEditCommands(program);\n  registerWikiLifecycleCommands(program);\n  registerSetupCommands(program);\n}\n","import { readFileSync } from \"node:fs\";\nimport { createRequire } from \"node:module\";\n\nimport { getConfigPath } from \"./config.js\";\nimport { isNewer } from \"./semver.js\";\nimport { getStatePath, type UpdateState } from \"./state.js\";\n\n/**\n * Pre-command update-nag banner. Runs synchronously at the very top of\n * every `run()` invocation, before commander even touches argv. Prints\n * one line to stderr if:\n *\n *   1. `~/.almanac/update-state.json` exists and parses.\n *   2. `latest_version` is strictly newer than `installed_version`.\n *   3. `latest_version` is NOT in `dismissed_versions`.\n *   4. `~/.almanac/config.json`.`update_notifier` is not `false`.\n *\n * Otherwise silent. Deliberately synchronous and filesystem-blocking:\n * this runs in the CLI critical path and waiting on a Promise would\n * force every command to become async upfront. The files are tiny\n * (<1KB each); a sync read is cheap.\n *\n * Why stderr: agents and scripts parse stdout; stderr is the\n * conventional channel for diagnostics and nags. A tool piping\n * `almanac search` into `xargs` shouldn't see the banner mixed into\n * its slug list. Users running interactively see stderr anyway, so\n * the nag is visible in practice.\n */\n\nexport interface AnnounceOptions {\n  statePath?: string;\n  configPath?: string;\n  /** Override for tests — normally reads from package.json at import time. */\n  installedVersion?: string;\n  /** Enable ANSI coloring regardless of isTTY. Tests pass `false`. */\n  color?: boolean;\n}\n\nconst RST = \"\\x1b[0m\";\nconst BOLD = \"\\x1b[1m\";\nconst YELLOW = \"\\x1b[33m\";\n\nexport function announceUpdateIfAvailable(\n  stderr: NodeJS.WritableStream,\n  opts: AnnounceOptions = {},\n): void {\n  const statePath = opts.statePath ?? getStatePath();\n  const configPath = opts.configPath ?? getConfigPath();\n  const installed = opts.installedVersion ?? readInstalledVersion();\n\n  // Config gate. Must be checked before state: a user who disabled the\n  // notifier shouldn't pay even a state-file read.\n  if (!shouldNotify(configPath)) return;\n\n  const state = readStateSync(statePath);\n  if (state === null) return;\n  if (state.latest_version.length === 0) return;\n  if (!isNewer(state.latest_version, installed)) return;\n  if (state.dismissed_versions.includes(state.latest_version)) return;\n\n  const useColor =\n    opts.color ?? (process.stderr.isTTY === true && !(\"NO_COLOR\" in process.env));\n  const warn = useColor ? `${YELLOW}${BOLD}\\u26a0${RST}` : \"!\";\n  const cmd = useColor ? `${BOLD}almanac update${RST}` : \"almanac update\";\n  stderr.write(\n    `${warn} codealmanac ${state.latest_version} available ` +\n      `(you're on ${installed}) — run: ${cmd}\\n`,\n  );\n}\n\n/**\n * Sync-read the state file. Returns `null` when missing, empty, or\n * malformed — the announce path MUST NOT throw into the CLI critical\n * path. Avoids the `async readState` used by the worker because\n * `run()` would otherwise need `await announceUpdateIfAvailable(...)`\n * on every invocation, which turns into a multi-millisecond penalty\n * on commands that don't care.\n */\nfunction readStateSync(path: string): UpdateState | null {\n  let raw: string;\n  try {\n    raw = readFileSync(path, \"utf8\");\n  } catch {\n    return null;\n  }\n  const trimmed = raw.trim();\n  if (trimmed.length === 0) return null;\n  try {\n    const parsed = JSON.parse(trimmed) as Partial<UpdateState>;\n    return {\n      last_check_at:\n        typeof parsed.last_check_at === \"number\" ? parsed.last_check_at : 0,\n      installed_version:\n        typeof parsed.installed_version === \"string\"\n          ? parsed.installed_version\n          : \"\",\n      latest_version:\n        typeof parsed.latest_version === \"string\" ? parsed.latest_version : \"\",\n      dismissed_versions: Array.isArray(parsed.dismissed_versions)\n        ? parsed.dismissed_versions.filter(\n            (v): v is string => typeof v === \"string\",\n          )\n        : [],\n    };\n  } catch {\n    return null;\n  }\n}\n\nfunction shouldNotify(configPath: string): boolean {\n  let raw: string;\n  try {\n    raw = readFileSync(configPath, \"utf8\");\n  } catch {\n    return true; // no config file → default notify on\n  }\n  const trimmed = raw.trim();\n  if (trimmed.length === 0) return true;\n  try {\n    const parsed = JSON.parse(trimmed) as { update_notifier?: unknown };\n    if (parsed.update_notifier === false) return false;\n    return true;\n  } catch {\n    return true;\n  }\n}\n\nfunction readInstalledVersion(): string {\n  // Dev: `src/update/announce.ts` → `../../package.json`. Bundled:\n  // `dist/codealmanac.js` → `../package.json`. Try both.\n  try {\n    const require = createRequire(import.meta.url);\n    const pkg = require(\"../../package.json\") as { version?: unknown };\n    if (typeof pkg.version === \"string\" && pkg.version.length > 0) {\n      return pkg.version;\n    }\n  } catch {\n    // Fall through.\n  }\n  try {\n    const require = createRequire(import.meta.url);\n    const pkg = require(\"../package.json\") as { version?: unknown };\n    if (typeof pkg.version === \"string\" && pkg.version.length > 0) {\n      return pkg.version;\n    }\n  } catch {\n    // Fall through.\n  }\n  return 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