codealmanac 0.2.5 → 0.2.7

package/dist/chunk-GFUB57IT.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/commands/setup.ts","../src/commands/setup/install-path.ts","../src/commands/setup/next-steps.ts"],"sourcesContent":["import { existsSync } from \"node:fs\";\nimport { spawn } from \"node:child_process\";\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 type { SpawnCliFn } from \"../agent/providers/claude/index.js\";\nimport {\n  buildProviderModelChoices,\n  buildProviderSetupView,\n  getProviderLabel,\n  parseAgentSelection,\n} from \"../agent/provider-view.js\";\nimport type {\n  ProviderModelChoice,\n  ProviderSetupView,\n} from \"../agent/provider-view.js\";\nimport {\n  isAgentProviderId,\n  readConfig,\n  writeConfig,\n  type AgentProviderId,\n} from \"../update/config.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. Provider-specific agent guidance for the chosen default provider.\n *      Claude uses `~/.claude/CLAUDE.md`; Codex uses `~/.codex/AGENTS.md`;\n *      Cursor uses a project rule in `.cursor/rules/`.\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 auto-capture hooks. */\n  skipHook?: boolean;\n  /** Don't install provider-specific guides. */\n  skipGuides?: boolean;\n  /** Set the default provider during setup. */\n  agent?: string;\n  /** Set the default model for the selected provider during setup. */\n  model?: string;\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 provider integrations${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  const agentChoice = await chooseDefaultAgent({\n    out,\n    interactive,\n    requested: options.agent,\n    requestedModel: options.model,\n    spawnCli: options.spawnCli,\n  });\n  if (!agentChoice.ok) {\n    return {\n      stdout: \"\",\n      stderr: `almanac: ${agentChoice.error}\\n`,\n      exitCode: 1,\n    };\n  }\n  stepDone(\n    out,\n    `Default provider: ${WHITE_BOLD}${agentChoice.provider}${RST}` +\n      ` (${agentChoice.model ?? \"provider default\"})`,\n  );\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 auto-capture hooks for supported agents?\",\n      true,\n    );\n  }\n\n  let hookResultLine = \"\";\n  if (hookAction === \"install\") {\n    const res = await runHookInstall({\n      source: \"all\",\n      settingsPath: options.settingsPath,\n      hookScriptPath: options.hookScriptPath,\n      stableHooksDir: options.stableHooksDir,\n    });\n    if (res.exitCode !== 0) {\n      stepActive(out, `Auto-capture 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      ? `Auto-capture hooks ${DIM}already installed${RST}`\n      : `Auto-capture hooks installed`;\n    stepDone(out, hookResultLine);\n  } else {\n    stepSkipped(out, `Auto-capture hooks ${DIM}skipped${RST}`);\n  }\n  out.write(BAR + \"\\n\");\n\n  // Step 3: install the provider-specific guide.\n  let guidesAction: InstallDecision = \"install\";\n  const providerLabel = getProviderLabel(agentChoice.provider);\n  if (options.skipGuides === true) {\n    guidesAction = \"skip\";\n  } else if (interactive) {\n    guidesAction = await confirm(\n      out,\n      `Install the codealmanac guide for ${providerLabel}?`,\n      true,\n    );\n  }\n\n  let guidesSummary: string;\n  if (guidesAction === \"install\") {\n    try {\n      const summary = await installGuides({\n        provider: agentChoice.provider,\n        claudeDir: options.claudeDir ?? path.join(homedir(), \".claude\"),\n        guidesDir: options.guidesDir ?? resolveGuidesDir(),\n        cwd: process.cwd(),\n      });\n      guidesSummary = summary.anyChanges\n        ? `Guide installed for ${summary.providerLabel} (${summary.filesWritten.join(\", \")})`\n        : `Guide for ${summary.providerLabel} ${DIM}already installed${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  printProviderNextSteps(out);\n\n  return { stdout: \"\", stderr: \"\", exitCode: 0 };\n}\n\ntype AgentChoice =\n  | { ok: true; provider: AgentProviderId; model: string | null }\n  | { ok: false; error: string };\n\nasync function chooseDefaultAgent(args: {\n  out: NodeJS.WritableStream;\n  interactive: boolean;\n  requested?: string;\n  requestedModel?: string;\n  spawnCli?: SpawnCliFn;\n}): Promise<AgentChoice> {\n  const config = await readConfig();\n  let view: ProviderSetupView | null = null;\n  let selected = args.requested ?? config.agent.default;\n  if (args.interactive || args.requested !== undefined) {\n    view = await buildProviderSetupView({ config, spawnCli: args.spawnCli });\n  }\n  if (args.interactive && args.requested === undefined && view !== null) {\n    args.out.write(\"  Choose default provider for bootstrap/capture:\\n\");\n    view.choices.forEach((choice, index) => {\n      const tag = choice.recommended ? \" recommended\" : \"\";\n      const status = choice.ready ? \"ready\" : \"not ready\";\n      const detail = choice.account ?? choice.fixCommand ?? choice.detail;\n      args.out.write(\n        `    ${index + 1}. ${choice.label.padEnd(6)} ${status.padEnd(9)}${tag}  ${detail}\\n`,\n      );\n    });\n    selected = (await promptText(\n      args.out,\n      \"Default provider\",\n      view.recommendedProvider,\n    )).toLowerCase();\n    const number = Number.parseInt(selected, 10);\n    if (\n      Number.isInteger(number) &&\n      number >= 1 &&\n      number <= view.choices.length\n    ) {\n      selected = view.choices[number - 1]?.id ?? selected;\n    }\n  }\n  const parsed = parseAgentSelection(selected);\n  if (parsed.provider === null || !isAgentProviderId(parsed.provider)) {\n    return {\n      ok: false,\n      error:\n        `unknown agent '${selected}'. Expected one of: claude, codex, cursor.`,\n    };\n  }\n  const provider = parsed.provider;\n  let selectedChoice = view?.choices.find((choice) => choice.id === provider);\n  if (\n    args.interactive &&\n    selectedChoice !== undefined &&\n    !selectedChoice.ready &&\n    selectedChoice.fixCommand?.startsWith(\"run: \") === true\n  ) {\n    const command = selectedChoice.fixCommand.slice(\"run: \".length);\n    const runLogin = await confirm(\n      args.out,\n      `${selectedChoice.label} is not ready. Run '${command}' now?`,\n      true,\n    );\n    if (runLogin === \"install\") {\n      const login = await runLoginCommand(command);\n      if (login.ok) {\n        view = await buildProviderSetupView({ config, spawnCli: args.spawnCli });\n        selectedChoice = view.choices.find((choice) => choice.id === provider);\n      } else {\n        stepActive(args.out, `${selectedChoice.label} login failed: ${login.error}`);\n      }\n    }\n  }\n  const requestedModel = args.requestedModel ?? parsed.model;\n  const model = requestedModel ?? await chooseProviderModel({\n    out: args.out,\n    interactive: args.interactive,\n    provider,\n    choice: selectedChoice,\n    configuredModel: config.agent.models[provider] ?? null,\n  });\n  await writeConfig({\n    ...config,\n    agent: {\n      ...config.agent,\n      default: provider,\n      models: {\n        ...config.agent.models,\n        [provider]: model,\n      },\n    },\n  });\n  if (!args.interactive || args.requested !== undefined) {\n    const detail = selectedChoice?.ready === true\n      ? \"ready\"\n      : selectedChoice?.fixCommand ?? selectedChoice?.detail ?? \"status unknown\";\n    stepDone(args.out, `Agent readiness: ${detail}`);\n  }\n  return { ok: true, provider, model };\n}\n\nasync function chooseProviderModel(args: {\n  out: NodeJS.WritableStream;\n  interactive: boolean;\n  provider: AgentProviderId;\n  choice?: ProviderSetupView[\"choices\"][number];\n  configuredModel: string | null;\n}): Promise<string | null> {\n  const choices =\n    args.choice?.modelChoices ??\n    buildProviderModelChoices(args.provider, args.configuredModel);\n  const recommended =\n    choices.find((choice) => choice.recommended) ??\n    choices.find((choice) => choice.source === \"provider-default\");\n  if (!args.interactive) {\n    return args.configuredModel ?? recommended?.value ?? null;\n  }\n\n  args.out.write(`  Choose model for ${getProviderLabel(args.provider)}:\\n`);\n  choices.forEach((choice, index) => {\n    const marker = choice.recommended ? \" recommended\" : \"\";\n    const current = choice.value === args.configuredModel ? \" current\" : \"\";\n    args.out.write(\n      `    ${index + 1}. ${choice.label}${marker}${current}\\n`,\n    );\n  });\n  const currentIndex = choices.findIndex((choice) =>\n    choice.value === args.configuredModel\n  );\n  const recommendedIndex = choices.findIndex((choice) => choice.recommended);\n  const defaultIndex =\n    currentIndex >= 0\n      ? currentIndex + 1\n      : recommendedIndex >= 0\n        ? recommendedIndex + 1\n        : 1;\n  const selected = await promptText(args.out, \"Model\", String(defaultIndex));\n  const number = Number.parseInt(selected, 10);\n  let modelChoice: ProviderModelChoice | undefined;\n  if (\n    Number.isInteger(number) &&\n    number >= 1 &&\n    number <= choices.length\n  ) {\n    modelChoice = choices[number - 1];\n  } else {\n    modelChoice = choices.find((choice) => choice.value === selected);\n  }\n  if (modelChoice?.source === \"custom\") {\n    const custom = await promptText(args.out, \"Custom model id\", \"\");\n    return custom.length > 0 ? custom : recommended?.value ?? null;\n  }\n  return modelChoice?.value ?? recommended?.value ?? null;\n}\n\nasync function runLoginCommand(command: string): Promise<\n  | { ok: true }\n  | { ok: false; error: string }\n> {\n  return new Promise((resolve) => {\n    const child = spawn(command, {\n      shell: true,\n      stdio: \"inherit\",\n    });\n    child.on(\"error\", (err) => {\n      resolve({ ok: false, error: err.message });\n    });\n    child.on(\"close\", (code) => {\n      if (code === 0) {\n        resolve({ ok: true });\n        return;\n      }\n      resolve({ ok: false, error: `exited ${code ?? 1}` });\n    });\n  });\n}\n\n// ─── Guide installation ──────────────────────────────────────────────\n\ninterface InstallGuidesOptions {\n  provider: AgentProviderId;\n  claudeDir: string;\n  guidesDir: string;\n  cwd: string;\n}\n\ninterface InstallGuidesResult {\n  providerLabel: string;\n  anyChanges: boolean;\n  filesWritten: string[];\n}\n\nconst CODEX_BLOCK_START = \"<!-- codealmanac:start -->\";\nconst CODEX_BLOCK_END = \"<!-- codealmanac:end -->\";\n\n/**\n * Install provider-specific usage guidance. Each provider gets the same\n * core instructions, but in the place that provider actually reads.\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  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  switch (options.provider) {\n    case \"claude\":\n      return await installClaudeGuides(options, srcMini, srcRef);\n    case \"codex\":\n      return await installCodexGuides(srcMini, srcRef);\n    case \"cursor\":\n      return await installCursorGuides(options.cwd, srcMini);\n  }\n}\n\nasync function installClaudeGuides(\n  options: InstallGuidesOptions,\n  srcMini: string,\n  srcRef: string,\n): Promise<InstallGuidesResult> {\n  await mkdir(options.claudeDir, { recursive: true });\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 {\n    providerLabel: \"Claude\",\n    anyChanges: filesWritten.length > 0,\n    filesWritten,\n  };\n}\n\nasync function installCodexGuides(\n  srcMini: string,\n  srcRef: string,\n): Promise<InstallGuidesResult> {\n  const codexDir = path.join(homedir(), \".codex\");\n  await mkdir(codexDir, { recursive: true });\n  const destMini = path.join(codexDir, \"codealmanac.md\");\n  const destRef = path.join(codexDir, \"codealmanac-reference.md\");\n  const miniChanged = await copyIfChanged(srcMini, destMini);\n  const refChanged = await copyIfChanged(srcRef, destRef);\n  const agentsChanged = await ensureManagedBlock(\n    path.join(codexDir, \"AGENTS.md\"),\n    codexGuideBlock(),\n  );\n\n  const filesWritten: string[] = [];\n  if (miniChanged) filesWritten.push(\"codealmanac.md\");\n  if (refChanged) filesWritten.push(\"codealmanac-reference.md\");\n  if (agentsChanged) filesWritten.push(\"AGENTS.md\");\n\n  return {\n    providerLabel: \"Codex\",\n    anyChanges: filesWritten.length > 0,\n    filesWritten,\n  };\n}\n\nasync function installCursorGuides(\n  cwd: string,\n  srcMini: string,\n): Promise<InstallGuidesResult> {\n  const rulesDir = path.join(cwd, \".cursor\", \"rules\");\n  await mkdir(rulesDir, { recursive: true });\n  const mini = await readFile(srcMini, \"utf8\");\n  const dest = path.join(rulesDir, \"codealmanac.mdc\");\n  const body =\n    \"---\\n\" +\n    \"description: Use codealmanac wiki context during coding work\\n\" +\n    \"alwaysApply: true\\n\" +\n    \"---\\n\\n\" +\n    mini;\n  const changed = await writeIfChanged(dest, body);\n\n  return {\n    providerLabel: \"Cursor\",\n    anyChanges: changed,\n    filesWritten: changed ? [\".cursor/rules/codealmanac.mdc\"] : [],\n  };\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\nasync function writeIfChanged(dest: string, body: string): Promise<boolean> {\n  if (existsSync(dest)) {\n    try {\n      if (await readFile(dest, \"utf8\") === body) return false;\n    } catch {\n      // Fall through to write.\n    }\n  }\n  await writeFile(dest, body, \"utf8\");\n  return true;\n}\n\nasync function ensureManagedBlock(\n  file: string,\n  block: string,\n): Promise<boolean> {\n  let existing = \"\";\n  if (existsSync(file)) existing = await readFile(file, \"utf8\");\n  const pattern = new RegExp(\n    `${escapeRegex(CODEX_BLOCK_START)}[\\\\s\\\\S]*?${escapeRegex(CODEX_BLOCK_END)}`,\n  );\n  const next = pattern.test(existing)\n    ? existing.replace(pattern, block.trimEnd())\n    : `${existing.trimEnd()}${existing.trim().length > 0 ? \"\\n\\n\" : \"\"}${block.trimEnd()}\\n`;\n  const normalized = next.endsWith(\"\\n\") ? next : `${next}\\n`;\n  if (normalized === existing) return false;\n  await writeFile(file, normalized, \"utf8\");\n  return true;\n}\n\nfunction codexGuideBlock(): string {\n  return [\n    CODEX_BLOCK_START,\n    \"# codealmanac\",\n    \"\",\n    \"This machine has codealmanac installed: a local wiki for codebases.\",\n    \"Before codealmanac/wiki-related work, read `~/.codex/codealmanac.md`.\",\n    \"For the full command reference, read `~/.codex/codealmanac-reference.md` on demand.\",\n    CODEX_BLOCK_END,\n    \"\",\n  ].join(\"\\n\");\n}\n\nfunction escapeRegex(value: string): string {\n  return value.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\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\nfunction promptText(\n  out: NodeJS.WritableStream,\n  question: string,\n  defaultValue: string,\n): Promise<string> {\n  return new Promise((resolve) => {\n    out.write(\n      `  ${BLUE}\\u25c6${RST}  ${question} ${DIM}[${defaultValue}]${RST} `,\n    );\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();\n      resolve(answer.length === 0 ? defaultValue : answer);\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\nfunction printProviderNextSteps(out: NodeJS.WritableStream): void {\n  out.write(`  ${DIM}Change provider/model later:${RST}\\n`);\n  out.write(`  ${DIM}  almanac agents list${RST}\\n`);\n  out.write(`  ${DIM}  almanac agents use <claude|codex|cursor>${RST}\\n`);\n  out.write(\n    `  ${DIM}  almanac agents model <provider> <model|--default>${RST}\\n\\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 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package/dist/chunk-KQUVMF27.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/indexer/schema.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/topics-yaml.ts","../src/indexer/wikilinks.ts","../src/registry/index.ts","../src/commands/health.ts","../src/indexer/duration.ts","../src/indexer/resolve-wiki.ts","../src/topics/dag.ts"],"sourcesContent":["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 { 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    // Keep read-side freshness even when CLI/agent write paths eagerly\n    // reindex: users can still change `.almanac/pages/` directly via\n    // manual edits, git pulls, merges, or branch switches.\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 { 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 { 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 { 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) ?? 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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 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, 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package/dist/chunk-P5WGG4FJ.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/update/config.ts"],"sourcesContent":["import { existsSync } from \"node:fs\";\nimport { mkdir, readFile, rename, writeFile } from \"node:fs/promises\";\nimport { dirname, join } from \"node:path\";\n\nimport {\n  findNearestAlmanacDir,\n  getGlobalAlmanacDir,\n  getRepoAlmanacDir,\n} from \"../paths.js\";\n\nexport const AGENT_PROVIDER_IDS = [\"claude\", \"codex\", \"cursor\"] as const;\nexport type AgentProviderId = (typeof AGENT_PROVIDER_IDS)[number];\n\nexport function isAgentProviderId(value: string): value is AgentProviderId {\n  return (AGENT_PROVIDER_IDS as readonly string[]).includes(value);\n}\n\nexport interface AgentConfig {\n  /** Default provider for bootstrap/capture. Default: \"claude\". */\n  default: AgentProviderId;\n  /** Optional per-provider model override. `null` means provider default. */\n  models: Partial<Record<AgentProviderId, string | null>>;\n}\n\n/**\n * `~/.almanac/config.toml` — global, cross-wiki configuration. Legacy\n * `config.json` is read and migrated forward on first normal access.\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  /** Agent-provider settings for bootstrap/capture. */\n  agent: AgentConfig;\n}\n\nexport function defaultConfig(): GlobalConfig {\n  return {\n    update_notifier: true,\n    agent: {\n      default: \"claude\",\n      models: {\n        claude: null,\n        codex: null,\n        cursor: null,\n      },\n    },\n  };\n}\n\nexport function getConfigPath(): string {\n  return join(getGlobalAlmanacDir(), \"config.toml\");\n}\n\nexport function getLegacyConfigPath(): string {\n  return join(getGlobalAlmanacDir(), \"config.json\");\n}\n\nexport function getProjectConfigPath(cwd: string): string | null {\n  const repoRoot = findNearestAlmanacDir(cwd);\n  return repoRoot === null ? null : join(getRepoAlmanacDir(repoRoot), \"config.toml\");\n}\n\nexport type ConfigOrigin = \"default\" | \"user\" | \"project\";\n\nexport interface ConfigReadOptions {\n  path?: string;\n  cwd?: string;\n}\n\nexport interface ConfigReadResult {\n  config: GlobalConfig;\n  origins: Record<string, ConfigOrigin>;\n  raw: Record<string, unknown>;\n}\n\nexport async function readConfig(\n  input?: string | ConfigReadOptions,\n): Promise<GlobalConfig> {\n  return (await readConfigWithOrigins(input)).config;\n}\n\nexport async function readConfigWithOrigins(\n  input?: string | ConfigReadOptions,\n): Promise<ConfigReadResult> {\n  const opts = normalizeReadOptions(input);\n  if (opts.path !== undefined) {\n    const raw = await readRawConfigObject(opts.path);\n    return {\n      config: normalizeRawConfig(raw),\n      origins: originsFromRaw(raw, \"user\"),\n      raw,\n    };\n  }\n\n  const file = getConfigPath();\n  await migrateLegacyConfigIfNeeded(file);\n  const userRaw = await readRawConfigObject(file);\n  const mergedRaw = cloneJsonObject(userRaw);\n  const origins = originsFromRaw(userRaw, \"user\");\n  const projectPath = opts.cwd !== undefined ? getProjectConfigPath(opts.cwd) : null;\n  if (projectPath !== null) {\n    const projectRaw = await readRawConfigObject(projectPath);\n    applyProjectConfig(mergedRaw, projectRaw);\n    Object.assign(origins, originsFromRaw(projectRaw, \"project\", true));\n  }\n  return {\n    config: normalizeRawConfig(mergedRaw),\n    origins,\n    raw: mergedRaw,\n  };\n}\n\nfunction normalizeReadOptions(\n  input?: string | ConfigReadOptions,\n): ConfigReadOptions {\n  return typeof input === \"string\" ? { path: input } : input ?? {};\n}\n\nasync function migrateLegacyConfigIfNeeded(file: string): Promise<void> {\n  if (existsSync(file)) return;\n  const legacy = getLegacyConfigPath();\n  if (!existsSync(legacy)) return;\n  const raw = await readRawConfigObject(legacy);\n  if (Object.keys(raw).length === 0) return;\n  await writeConfig(normalizeRawConfig(raw), file);\n}\n\nfunction normalizeRawConfig(raw: Record<string, unknown>): GlobalConfig {\n  const defaults = defaultConfig();\n  const rawAgent =\n    raw.agent !== undefined &&\n    raw.agent !== null &&\n    typeof raw.agent === \"object\" &&\n    !Array.isArray(raw.agent)\n      ? (raw.agent as Partial<AgentConfig>)\n      : {};\n  const rawDefault =\n    typeof rawAgent.default === \"string\" &&\n    isAgentProviderId(rawAgent.default)\n      ? rawAgent.default\n      : defaults.agent.default;\n  const rawModels =\n    rawAgent.models !== undefined &&\n    rawAgent.models !== null &&\n    typeof rawAgent.models === \"object\" &&\n    !Array.isArray(rawAgent.models)\n      ? (rawAgent.models as Record<string, unknown>)\n      : {};\n  const models: Partial<Record<AgentProviderId, string | null>> = {\n    ...defaults.agent.models,\n  };\n  for (const id of AGENT_PROVIDER_IDS) {\n    const value = rawModels[id];\n    if (typeof value === \"string\" && value.length > 0) {\n      models[id] = value === \"default\" || value === \"null\" ? null : value;\n    } else if (value === null) {\n      models[id] = null;\n    }\n  }\n  return {\n    update_notifier:\n      typeof raw.update_notifier === \"boolean\"\n        ? raw.update_notifier\n        : defaults.update_notifier,\n    agent: {\n      default: rawDefault,\n      models,\n    },\n  };\n}\n\nfunction applyProjectConfig(\n  target: Record<string, unknown>,\n  projectRaw: Record<string, unknown>,\n): void {\n  const projectAgent =\n    projectRaw.agent !== null &&\n    typeof projectRaw.agent === \"object\" &&\n    !Array.isArray(projectRaw.agent)\n      ? projectRaw.agent as Record<string, unknown>\n      : {};\n  if (Object.keys(projectAgent).length === 0) return;\n  const targetAgent =\n    target.agent !== null &&\n    typeof target.agent === \"object\" &&\n    !Array.isArray(target.agent)\n      ? target.agent as Record<string, unknown>\n      : {};\n  target.agent = targetAgent;\n  if (typeof projectAgent.default === \"string\") {\n    targetAgent.default = projectAgent.default;\n  }\n  const projectModels =\n    projectAgent.models !== null &&\n    typeof projectAgent.models === \"object\" &&\n    !Array.isArray(projectAgent.models)\n      ? projectAgent.models as Record<string, unknown>\n      : {};\n  if (Object.keys(projectModels).length === 0) return;\n  const targetModels =\n    targetAgent.models !== null &&\n    typeof targetAgent.models === \"object\" &&\n    !Array.isArray(targetAgent.models)\n      ? targetAgent.models as Record<string, unknown>\n      : {};\n  targetAgent.models = targetModels;\n  for (const id of AGENT_PROVIDER_IDS) {\n    if (Object.prototype.hasOwnProperty.call(projectModels, id)) {\n      targetModels[id] = projectModels[id];\n    }\n  }\n}\n\nfunction originsFromRaw(\n  raw: Record<string, unknown>,\n  origin: ConfigOrigin,\n  agentOnly = false,\n): Record<string, ConfigOrigin> {\n  const origins: Record<string, ConfigOrigin> = {};\n  if (!agentOnly && Object.prototype.hasOwnProperty.call(raw, \"update_notifier\")) {\n    origins.update_notifier = origin;\n  }\n  const agent =\n    raw.agent !== null &&\n    typeof raw.agent === \"object\" &&\n    !Array.isArray(raw.agent)\n      ? raw.agent as Record<string, unknown>\n      : {};\n  if (Object.prototype.hasOwnProperty.call(agent, \"default\")) {\n    origins[\"agent.default\"] = origin;\n  }\n  const models =\n    agent.models !== null &&\n    typeof agent.models === \"object\" &&\n    !Array.isArray(agent.models)\n      ? agent.models as Record<string, unknown>\n      : {};\n  for (const id of AGENT_PROVIDER_IDS) {\n    if (Object.prototype.hasOwnProperty.call(models, id)) {\n      origins[`agent.models.${id}`] = origin;\n    }\n  }\n  return origins;\n}\n\nasync function readSingleConfig(file: string): Promise<GlobalConfig> {\n  let raw: string;\n  try {\n    raw = await readFile(file, \"utf8\");\n  } catch {\n    return defaultConfig();\n  }\n  const trimmed = raw.trim();\n  if (trimmed.length === 0) return defaultConfig();\n  try {\n    return normalizeRawConfig(parseConfigText(trimmed, file));\n  } catch {\n    return defaultConfig();\n  }\n}\n\nexport async function writeConfig(\n  config: GlobalConfig | Partial<GlobalConfig>,\n  path?: string,\n): Promise<void> {\n  const file = path ?? getConfigPath();\n  await mkdir(dirname(file), { recursive: true });\n  const current = await readSingleConfig(file);\n  const existingRaw = await readRawConfigObject(file);\n  const stored = toStoredConfigPatch(config, current, existingRaw);\n  const body = serializeConfig(stored, file);\n  const tmp = `${file}.tmp`;\n  await writeFile(tmp, body, \"utf8\");\n  await rename(tmp, file);\n}\n\nfunction normalizeConfig(config: GlobalConfig | Partial<GlobalConfig>): GlobalConfig {\n  const defaults = defaultConfig();\n  return {\n    update_notifier:\n      typeof config.update_notifier === \"boolean\"\n        ? config.update_notifier\n        : defaults.update_notifier,\n    agent: {\n      default:\n        config.agent !== undefined && isAgentProviderId(config.agent.default)\n          ? config.agent.default\n          : defaults.agent.default,\n      models: {\n        ...defaults.agent.models,\n        ...(config.agent?.models ?? {}),\n      },\n    },\n  };\n}\n\nasync function readRawConfigObject(\n  path: string,\n): Promise<Record<string, unknown>> {\n  try {\n    return parseConfigText(await readFile(path, \"utf8\"), path);\n  } catch {\n    // Fall through to empty.\n  }\n  return {};\n}\n\nexport function parseConfigText(\n  raw: string,\n  path = \"config.toml\",\n): Record<string, unknown> {\n  const trimmed = raw.trim();\n  if (trimmed.length === 0) return {};\n  if (path.endsWith(\".json\") || trimmed.startsWith(\"{\")) {\n    const parsed = JSON.parse(trimmed) as unknown;\n    return parsed !== null && typeof parsed === \"object\" && !Array.isArray(parsed)\n      ? parsed as Record<string, unknown>\n      : {};\n  }\n  return parseTomlConfig(trimmed);\n}\n\nexport function serializeConfig(\n  raw: Record<string, unknown>,\n  path = \"config.toml\",\n): string {\n  return path.endsWith(\".json\")\n    ? `${JSON.stringify(raw, null, 2)}\\n`\n    : serializeTomlConfig(raw);\n}\n\nfunction parseTomlConfig(raw: string): Record<string, unknown> {\n  const result: Record<string, unknown> = {};\n  let section: string[] = [];\n  for (const original of raw.split(/\\r?\\n/)) {\n    const line = stripTomlComment(original).trim();\n    if (line.length === 0) continue;\n    const sectionMatch = line.match(/^\\[([A-Za-z0-9_.-]+)\\]$/);\n    if (sectionMatch !== null) {\n      section = sectionMatch[1]!.split(\".\");\n      continue;\n    }\n    const eq = line.indexOf(\"=\");\n    if (eq === -1) continue;\n    const key = line.slice(0, eq).trim();\n    const value = parseTomlValue(line.slice(eq + 1).trim());\n    setObjectPath(result, [...section, key], value);\n  }\n  return result;\n}\n\nfunction serializeTomlConfig(raw: Record<string, unknown>): string {\n  const lines: string[] = [];\n  if (typeof raw.update_notifier === \"boolean\") {\n    lines.push(`update_notifier = ${raw.update_notifier ? \"true\" : \"false\"}`);\n  }\n  const agent =\n    raw.agent !== null &&\n    typeof raw.agent === \"object\" &&\n    !Array.isArray(raw.agent)\n      ? raw.agent as Record<string, unknown>\n      : {};\n  if (typeof agent.default === \"string\") {\n    if (lines.length > 0) lines.push(\"\");\n    lines.push(\"[agent]\");\n    lines.push(`default = ${tomlString(agent.default)}`);\n  }\n  const models =\n    agent.models !== null &&\n    typeof agent.models === \"object\" &&\n    !Array.isArray(agent.models)\n      ? agent.models as Record<string, unknown>\n      : {};\n  const modelLines: string[] = [];\n  for (const id of AGENT_PROVIDER_IDS) {\n    if (!Object.prototype.hasOwnProperty.call(models, id)) continue;\n    const value = models[id] === null ? \"default\" : models[id];\n    if (typeof value === \"string\" && value.length > 0) {\n      modelLines.push(`${id} = ${tomlString(value)}`);\n    }\n  }\n  if (modelLines.length > 0) {\n    if (lines.length > 0) lines.push(\"\");\n    lines.push(\"[agent.models]\", ...modelLines);\n  }\n  return `${lines.join(\"\\n\")}\\n`;\n}\n\nfunction stripTomlComment(line: string): string {\n  let inString = false;\n  let escaped = false;\n  for (let i = 0; i < line.length; i++) {\n    const ch = line[i];\n    if (escaped) {\n      escaped = false;\n      continue;\n    }\n    if (ch === \"\\\\\") {\n      escaped = true;\n      continue;\n    }\n    if (ch === \"\\\"\") inString = !inString;\n    if (ch === \"#\" && !inString) return line.slice(0, i);\n  }\n  return line;\n}\n\nfunction parseTomlValue(raw: string): string | boolean {\n  if (raw === \"true\") return true;\n  if (raw === \"false\") return false;\n  if (raw.startsWith(\"\\\"\") && raw.endsWith(\"\\\"\")) {\n    return JSON.parse(raw) as string;\n  }\n  return raw;\n}\n\nfunction tomlString(value: string): string {\n  return JSON.stringify(value);\n}\n\nfunction setObjectPath(\n  raw: Record<string, unknown>,\n  path: string[],\n  value: string | boolean,\n): void {\n  let cursor = raw;\n  for (const part of path.slice(0, -1)) {\n    const next = cursor[part];\n    if (next === null || typeof next !== \"object\" || Array.isArray(next)) {\n      cursor[part] = {};\n    }\n    cursor = cursor[part] as Record<string, unknown>;\n  }\n  const leaf = path[path.length - 1];\n  if (leaf !== undefined) cursor[leaf] = value;\n}\n\nfunction toStoredConfigPatch(\n  config: GlobalConfig | Partial<GlobalConfig>,\n  current: GlobalConfig,\n  raw: Record<string, unknown>,\n): Record<string, unknown> {\n  const normalized = normalizeConfig(config);\n  const defaults = defaultConfig();\n  const stored = cloneJsonObject(raw);\n\n  if (\n    config.update_notifier !== undefined &&\n    normalized.update_notifier !== current.update_notifier\n  ) {\n    setStoredValue(\n      stored,\n      [\"update_notifier\"],\n      normalized.update_notifier,\n      defaults.update_notifier,\n    );\n  }\n\n  if (config.agent !== undefined) {\n    if (\n      config.agent.default !== undefined &&\n      normalized.agent.default !== current.agent.default\n    ) {\n      setStoredValue(\n        stored,\n        [\"agent\", \"default\"],\n        normalized.agent.default,\n        defaults.agent.default,\n      );\n    }\n\n    const inputModels = config.agent.models ?? {};\n    for (const id of AGENT_PROVIDER_IDS) {\n      if (!Object.prototype.hasOwnProperty.call(inputModels, id)) continue;\n      const value = normalized.agent.models[id] ?? null;\n      const currentValue = current.agent.models[id] ?? null;\n      const defaultValue = defaults.agent.models[id] ?? null;\n      if (value !== currentValue) {\n        setStoredValue(stored, [\"agent\", \"models\", id], value, defaultValue);\n      }\n    }\n  }\n  pruneEmptyObjects(stored);\n  return stored;\n}\n\nfunction setStoredValue(\n  raw: Record<string, unknown>,\n  path: string[],\n  value: string | boolean | null,\n  defaultValue: string | boolean | null,\n): void {\n  let cursor = raw;\n  for (const part of path.slice(0, -1)) {\n    const next = cursor[part];\n    if (next === null || typeof next !== \"object\" || Array.isArray(next)) {\n      cursor[part] = {};\n    }\n    cursor = cursor[part] as Record<string, unknown>;\n  }\n  const leaf = path[path.length - 1];\n  if (leaf === undefined) return;\n  cursor[leaf] = value;\n  if (value !== defaultValue) return;\n  // Keep explicit defaults only when the caller changed the value to the\n  // default. Unchanged explicit defaults are preserved by cloning `raw`.\n}\n\nfunction cloneJsonObject(raw: Record<string, unknown>): Record<string, unknown> {\n  return JSON.parse(JSON.stringify(raw)) as Record<string, unknown>;\n}\n\nfunction pruneEmptyObjects(raw: Record<string, unknown>): void {\n  for (const [key, value] of Object.entries(raw)) {\n    if (value === null || typeof value !== \"object\" || Array.isArray(value)) {\n      continue;\n    }\n    pruneEmptyObjects(value as Record<string, unknown>);\n    if (Object.keys(value).length === 0) delete raw[key];\n  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package/dist/chunk-SMIK2YLU.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/commands/doctor-checks/format.ts","../src/commands/doctor-checks/install.ts","../src/commands/doctor-checks/probes.ts","../src/commands/doctor-checks/agents.ts","../src/commands/doctor-checks/updates.ts","../src/commands/doctor.ts"],"sourcesContent":["import { BLUE, BOLD, DIM, GREEN, RED, RST } from \"../../ansi.js\";\nimport type {\n  AgentDoctorCheck,\n  Check,\n  CheckStatus,\n  DoctorOptions,\n  DoctorReport,\n} 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${RST}` : \"## Install\");\n    for (const c of report.install) {\n      lines.push(formatCheck(c, color));\n    }\n    lines.push(\"\");\n  }\n  if (report.agents.length > 0) {\n    lines.push(color ? `${BOLD}## Agents${RST}` : \"## Agents\");\n    for (const c of report.agents.map(agentToCheck)) {\n      lines.push(formatCheck(c, color));\n    }\n    lines.push(\"\");\n  }\n  if (report.updates.length > 0) {\n    lines.push(color ? `${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 agentToCheck(agent: AgentDoctorCheck): Check {\n  const message = [\n    agent.label,\n    agent.selected ? \"(default)\" : null,\n    agent.recommended ? \"(recommended)\" : null,\n    agent.status === \"ok\" ? \"ready\" : readinessMessage(agent),\n    `model: ${agent.model ?? \"provider default\"}`,\n    agent.account,\n  ].filter((part): part is string => part !== null).join(\" \");\n  return {\n    status: agent.status,\n    key: `agents.${agent.id}`,\n    message,\n    fix: agent.fix,\n  };\n}\n\nfunction readinessMessage(agent: AgentDoctorCheck): string {\n  if (!agent.installed) return \"missing\";\n  if (!agent.authenticated) return `not ready: ${agent.detail}`;\n  return agent.detail;\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 { IMPORT_LINE } from \"../setup.js\";\nimport {\n  classifyInstallPath,\n  detectInstallPath,\n  probeBetterSqlite3,\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  checks.push(describeProviderAuthSurface());\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, options.cwd));\n  checks.push(await describeGuideActivation(claudeDir, options.cwd));\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 describeProviderAuthSurface(): Check {\n  return {\n    status: \"info\",\n    key: \"install.auth\",\n    message: \"provider auth is reported under Agents\",\n    fix: \"run: almanac agents list\",\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}: ${msg}`,\n      fix: \"check the file for malformed JSON\",\n    };\n  }\n}\n\nfunction describeGuides(claudeDir: string, cwd: string): Check {\n  const mini = path.join(claudeDir, \"codealmanac.md\");\n  const ref = path.join(claudeDir, \"codealmanac-reference.md\");\n  const haveMini = existsSync(mini);\n  const haveRef = existsSync(ref);\n  if (haveMini && haveRef) {\n    return {\n      status: \"ok\",\n      key: \"install.guides\",\n      message: `Agent guides installed for Claude (${path.basename(mini)}, ${path.basename(ref)})`,\n    };\n  }\n  const codexMini = path.join(homedir(), \".codex\", \"codealmanac.md\");\n  const codexRef = path.join(homedir(), \".codex\", \"codealmanac-reference.md\");\n  if (existsSync(codexMini) && existsSync(codexRef)) {\n    return {\n      status: \"ok\",\n      key: \"install.guides\",\n      message: \"Agent guides installed for Codex (codealmanac.md, codealmanac-reference.md)\",\n    };\n  }\n  const cursorRule = path.join(cwd, \".cursor\", \"rules\", \"codealmanac.mdc\");\n  if (existsSync(cursorRule)) {\n    return {\n      status: \"ok\",\n      key: \"install.guides\",\n      message: \"Agent guide installed for Cursor (.cursor/rules/codealmanac.mdc)\",\n    };\n  }\n  const missing = [\n    haveMini ? null : \"codealmanac.md\",\n    haveRef ? null : \"codealmanac-reference.md\",\n  ].filter((s): s is string => s !== null);\n  return {\n    status: \"problem\",\n    key: \"install.guides\",\n    message: `Agent guides missing (${missing.join(\", \")})`,\n    fix: \"run: almanac setup --yes\",\n  };\n}\n\nasync function describeGuideActivation(\n  claudeDir: string,\n  cwd: string,\n): Promise<Check> {\n  const claudeMd = path.join(claudeDir, \"CLAUDE.md\");\n  if (existsSync(claudeMd)) {\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 guide import present\",\n        };\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\n  const codexAgents = path.join(homedir(), \".codex\", \"AGENTS.md\");\n  if (existsSync(codexAgents)) {\n    try {\n      const contents = await readFile(codexAgents, \"utf8\");\n      if (\n        contents.includes(\"<!-- codealmanac:start -->\") &&\n        contents.includes(\"<!-- codealmanac:end -->\")\n      ) {\n        return {\n          status: \"ok\",\n          key: \"install.import\",\n          message: \"Codex guide block present\",\n        };\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 ${codexAgents}: ${msg}`,\n      };\n    }\n  }\n\n  const cursorRule = path.join(cwd, \".cursor\", \"rules\", \"codealmanac.mdc\");\n  if (existsSync(cursorRule)) {\n    return {\n      status: \"ok\",\n      key: \"install.import\",\n      message: \"Cursor guide rule present\",\n    };\n  }\n\n  return {\n    status: \"problem\",\n    key: \"install.import\",\n    message: \"provider guide activation missing\",\n    fix: \"run: almanac setup --yes\",\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 {\n  checkClaudeAuth,\n  type ClaudeAuthStatus,\n  type SpawnCliFn,\n} from \"../../agent/providers/claude/index.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 { buildProviderSetupView } from \"../../agent/provider-view.js\";\nimport { checkClaudeAuth } from \"../../agent/providers/claude/index.js\";\nimport type { ProviderStatus } from \"../../agent/types.js\";\nimport type { AgentDoctorCheck, DoctorOptions } from \"./types.js\";\n\nexport async function gatherAgentChecks(\n  options: DoctorOptions,\n): Promise<AgentDoctorCheck[]> {\n  const view = await buildProviderSetupView({\n    spawnCli: options.spawnCli,\n    statuses:\n      options.providerStatuses ??\n      (options.spawnCli === undefined\n        ? undefined\n        : await injectedProviderStatuses(options)),\n  });\n  return view.choices.map((choice) => {\n    return {\n      status: choice.ready ? \"ok\" : \"problem\",\n      id: choice.id,\n      label: choice.label,\n      readiness: choice.readiness,\n      selected: choice.selected,\n      recommended: choice.recommended,\n      installed: choice.installed,\n      authenticated: choice.authenticated,\n      model: choice.effectiveModel,\n      providerDefaultModel: choice.providerDefaultModel,\n      configuredModel: choice.configuredModel,\n      account: choice.account,\n      detail: choice.detail,\n      fix: choice.fixCommand ?? undefined,\n    };\n  });\n}\n\nasync function injectedProviderStatuses(\n  options: DoctorOptions,\n): Promise<ProviderStatus[]> {\n  const auth = await checkClaudeAuth(options.spawnCli);\n  const hasApiKey =\n    process.env.ANTHROPIC_API_KEY !== undefined &&\n    process.env.ANTHROPIC_API_KEY.length > 0;\n  const claudeReady = auth.loggedIn || hasApiKey;\n  return [\n    {\n      id: \"claude\",\n      installed: true,\n      authenticated: claudeReady,\n      detail: claudeReady\n        ? auth.email ?? (hasApiKey ? \"ANTHROPIC_API_KEY set\" : \"logged in\")\n        : \"not logged in\",\n    },\n    {\n      id: \"codex\",\n      installed: false,\n      authenticated: false,\n      detail: \"codex status not injected\",\n    },\n    {\n      id: \"cursor\",\n      installed: false,\n      authenticated: false,\n      detail: \"cursor-agent status not injected\",\n    },\n  ];\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 config set update_notifier true\",\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: ${state.dismissed_versions.join(\", \")}`,\n    });\n  }\n\n  return checks;\n}\n","import { formatReport } from \"./doctor-checks/format.js\";\nimport { gatherInstallChecks } from \"./doctor-checks/install.js\";\nimport { readPackageVersion } from \"./doctor-checks/probes.js\";\nimport type {\n  Check,\n  CheckStatus,\n  AgentDoctorCheck,\n  DoctorOptions,\n  DoctorReport,\n  DoctorResult,\n  SqliteProbeResult,\n} from \"./doctor-checks/types.js\";\nimport { gatherAgentChecks } from \"./doctor-checks/agents.js\";\nimport { gatherUpdateChecks } from \"./doctor-checks/updates.js\";\n\nexport type {\n  Check,\n  CheckStatus,\n  DoctorOptions,\n  DoctorReport,\n  DoctorResult,\n  SqliteProbeResult,\n};\n\n/**\n * `almanac doctor` — install + wiki health report.\n *\n * Separate from `almanac health` (which checks graph integrity of a\n * specific wiki). `doctor` answers the \"is this install even set up\n * correctly?\" question that users hit when first trying the tool or when\n * sessions silently stop getting captured.\n *\n * This file is the command composition root. The section-specific probes\n * and formatting live in `doctor-checks/` so each durable fact has one\n * obvious owner.\n */\nexport async function runDoctor(\n  options: DoctorOptions,\n): Promise<DoctorResult> {\n  const version =\n    options.versionOverride ?? readPackageVersion() ?? \"unknown\";\n\n  const install: Check[] = options.wikiOnly === true\n    ? []\n    : await gatherInstallChecks(options);\n\n  const agents: AgentDoctorCheck[] = options.wikiOnly === true\n    ? []\n    : await gatherAgentChecks(options);\n\n  const updates: Check[] = options.wikiOnly === true\n    ? []\n    : await gatherUpdateChecks(options, version);\n\n  const wiki: Check[] = options.installOnly === true\n    ? []\n    : await safeGatherWikiChecks(options);\n\n  const report: DoctorReport = { version, install, agents, updates, wiki };\n\n  if (options.json === true) {\n    return {\n      stdout: `${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\nasync function safeGatherWikiChecks(\n  options: DoctorOptions,\n): Promise<Check[]> {\n  try {\n    const { gatherWikiChecks } = await import(\"./doctor-checks/wiki.js\");\n    return await gatherWikiChecks(options);\n  } catch (err: unknown) {\n    const msg = err instanceof Error ? err.message : String(err);\n    return [\n      {\n        status: \"problem\",\n        key: \"wiki.checks\",\n        message: `could not run wiki checks: ${msg.split(\"\\n\")[0] ?? msg}`,\n        fix: \"run: npm rebuild better-sqlite3 (in the install directory)\",\n      },\n    ];\n  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