codealmanac 0.2.6 → 0.2.7

package/dist/chunk-J7DNV2DH.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/agent/providers/claude/index.ts","../src/agent/providers/claude/auth.ts","../src/agent/providers/cli-status.ts","../src/agent/providers/jsonl-cli.ts","../src/agent/providers/prompt.ts","../src/agent/providers/codex-cli.ts","../src/agent/providers/cursor-cli.ts","../src/agent/providers/status.ts","../src/agent/providers/index.ts","../src/agent/provider-view.ts"],"sourcesContent":["import { query } from \"@anthropic-ai/claude-agent-sdk\";\n\nimport type {\n  AgentProvider,\n  AgentProviderMetadata,\n  AgentResult,\n  ProviderModelChoice,\n  ProviderStatus,\n  RunAgentOptions,\n  SpawnCliFn,\n} from \"../../types.js\";\nimport {\n  assertClaudeAuth,\n  checkClaudeAuth,\n  resolveClaudeExecutable,\n  UNAUTHENTICATED_MESSAGE,\n  type ClaudeAuthStatus,\n} from \"./auth.js\";\n\nexport const DEFAULT_AGENT_MODEL = \"claude-sonnet-4-6\";\n\nconst metadata: AgentProviderMetadata = {\n  id: \"claude\",\n  displayName: \"Claude\",\n  defaultModel: DEFAULT_AGENT_MODEL,\n  executable: \"claude\",\n  capabilities: {\n    transport: \"sdk\",\n    writesFiles: true,\n    supportsModelOverride: true,\n    supportsStreaming: true,\n    supportsSessionId: true,\n    supportsUsage: false,\n    supportsCost: true,\n    supportsProviderReportedTurns: true,\n    supportsProgrammaticSubagents: true,\n    supportsStrictToolAllowlist: false,\n  },\n};\n\nexport const claudeProvider: AgentProvider = {\n  metadata,\n  checkStatus,\n  assertReady,\n  run,\n  modelChoices,\n};\n\nconst CLAUDE_MODELS = [\n  {\n    value: \"claude-opus-4-7\",\n    label: \"Opus 4.7\",\n    recommended: false,\n  },\n  {\n    value: \"claude-sonnet-4-6\",\n    label: \"Sonnet 4.6\",\n    recommended: true,\n  },\n  {\n    value: \"claude-haiku-4-5-20251001\",\n    label: \"Haiku 4.5\",\n    recommended: false,\n  },\n] as const;\n\nfunction modelChoices(args: {\n  configuredModel: string | null;\n}): ProviderModelChoice[] {\n  const choices: ProviderModelChoice[] = [];\n  if (\n    args.configuredModel !== null &&\n    !CLAUDE_MODELS.some((model) => model.value === args.configuredModel)\n  ) {\n    choices.push({\n      value: args.configuredModel,\n      label: args.configuredModel,\n      recommended: false,\n      source: \"configured\",\n    });\n  }\n  for (const model of CLAUDE_MODELS) {\n    choices.push({\n      value: model.value,\n      label: model.label,\n      recommended: model.recommended,\n      source: \"catalog\",\n    });\n  }\n  choices.push({\n    value: \"__custom__\",\n    label: \"Enter a model name\",\n    recommended: false,\n    source: \"custom\",\n  });\n  return choices;\n}\n\nasync function run(opts: RunAgentOptions): Promise<AgentResult> {\n  const claudeExecutable = resolveClaudeExecutable();\n\n  const q = query({\n    prompt: opts.prompt,\n    options: {\n      systemPrompt: opts.systemPrompt,\n      allowedTools: opts.allowedTools,\n      agents: opts.agents ?? {},\n      cwd: opts.cwd,\n      model: opts.model ?? metadata.defaultModel ?? undefined,\n      maxTurns: opts.maxTurns ?? 100,\n      ...(claudeExecutable !== undefined\n        ? { pathToClaudeCodeExecutable: claudeExecutable }\n        : {}),\n      env: {\n        ...process.env,\n        CODEALMANAC_INTERNAL_SESSION: \"1\",\n      },\n      includePartialMessages: true,\n    },\n  });\n\n  let cost = 0;\n  let turns = 0;\n  let result = \"\";\n  let sessionId: string | undefined;\n  let success = false;\n  let errorMsg: string | undefined;\n\n  try {\n    for await (const msg of q) {\n      opts.onMessage?.(msg);\n\n      if (\n        sessionId === undefined &&\n        typeof (msg as { session_id?: unknown }).session_id === \"string\"\n      ) {\n        sessionId = (msg as { session_id: string }).session_id;\n      }\n\n      if (msg.type === \"result\") {\n        cost = msg.total_cost_usd;\n        turns = msg.num_turns;\n        if (msg.subtype === \"success\") {\n          success = true;\n          result = msg.result;\n        } else {\n          success = false;\n          errorMsg =\n            (msg.errors?.join(\"; \") ?? \"\") || `agent error: ${msg.subtype}`;\n        }\n      }\n    }\n  } catch (err: unknown) {\n    errorMsg = err instanceof Error ? err.message : String(err);\n    success = false;\n  }\n\n  return { success, cost, turns, result, sessionId, error: errorMsg };\n}\n\nasync function checkStatus(spawnCli?: SpawnCliFn): Promise<ProviderStatus> {\n  let auth: ClaudeAuthStatus = { loggedIn: false };\n  try {\n    auth = await checkClaudeAuth(spawnCli);\n  } catch {\n    auth = { loggedIn: false };\n  }\n  const hasApiKey =\n    process.env.ANTHROPIC_API_KEY !== undefined &&\n    process.env.ANTHROPIC_API_KEY.length > 0;\n  const installed = resolveClaudeExecutable() !== undefined;\n  const authenticated = auth.loggedIn || hasApiKey;\n  const detail = authenticated\n    ? auth.email ?? (hasApiKey ? \"ANTHROPIC_API_KEY set\" : \"logged in\")\n    : installed\n      ? \"not logged in\"\n      : `${metadata.executable} not found on PATH`;\n  return { id: metadata.id, installed, authenticated, detail };\n}\n\nasync function assertReady(spawnCli?: SpawnCliFn): Promise<void> {\n  await assertClaudeAuth(spawnCli);\n}\n\nexport { assertClaudeAuth, checkClaudeAuth, UNAUTHENTICATED_MESSAGE };\nexport type { ClaudeAuthStatus } from \"./auth.js\";\nexport type { SpawnCliFn, SpawnedProcess } from \"../../types.js\";\n","import { spawn, spawnSync, type ChildProcess } from \"node:child_process\";\nimport { createRequire } from \"node:module\";\nimport { dirname, join } from \"node:path\";\n\nimport type { SpawnCliFn, SpawnedProcess } from \"../../types.js\";\n\n/**\n * Claude auth gate — accepts either an active Claude subscription login\n * OR an `ANTHROPIC_API_KEY` environment variable.\n *\n * Claude Code owns subscription OAuth credentials. Users who are logged in\n * via `claude auth login --claudeai` should be able to run bootstrap/capture\n * without exporting an API key. Conversely, users on pay-per-token API keys\n * shouldn't be required to go through the OAuth flow.\n *\n * Current Claude Agent SDK packages no longer ship the old private\n * `cli.js` entrypoint, so the primary probe is the public Claude Code CLI:\n * `claude auth status --json`. We keep the SDK `cli.js` probe as a legacy\n * fallback for older SDK layouts.\n */\n\nexport interface ClaudeAuthStatus {\n  loggedIn: boolean;\n  email?: string;\n  subscriptionType?: string;\n  authMethod?: string;\n}\n\nconst AUTH_TIMEOUT_MS = 10_000;\n\n/**\n * Resolve the installed Claude Code executable from PATH. The Agent SDK can\n * accept this path via `pathToClaudeCodeExecutable`, and the auth probe uses\n * the same binary so CodeAlmanac agrees with `claude auth status`.\n */\nexport function resolveClaudeExecutable(): string | undefined {\n  const result = spawnSync(\"sh\", [\"-lc\", \"command -v claude\"], {\n    encoding: \"utf8\",\n  });\n  if (result.status !== 0) return undefined;\n  const found = result.stdout.trim().split(\"\\n\")[0]?.trim();\n  return found !== undefined && found.length > 0 ? found : undefined;\n}\n\n/**\n * Resolve legacy `cli.js` from older `@anthropic-ai/claude-agent-sdk`\n * installs. SDK 0.2.129+ no longer ships this file; callers must treat\n * failure as expected and fall back to the public `claude` binary.\n */\nfunction resolveCliJsPath(): string {\n  const require = createRequire(import.meta.url);\n  const entry = require.resolve(\"@anthropic-ai/claude-agent-sdk\");\n  return join(dirname(entry), \"cli.js\");\n}\n\n/**\n * Default subprocess spawner for production use — invokes the installed\n * Claude Code CLI.\n */\nexport const defaultSpawnCli: SpawnCliFn = (args: string[]) => {\n  const command = resolveClaudeExecutable() ?? \"claude\";\n  const child = spawn(command, args, {\n    stdio: [\"ignore\", \"pipe\", \"pipe\"],\n  });\n  return child as unknown as SpawnedProcess;\n};\n\nexport const legacySdkSpawnCli: SpawnCliFn = (args: string[]) => {\n  const cliPath = resolveCliJsPath();\n  const child = spawn(process.execPath, [cliPath, ...args], {\n    stdio: [\"ignore\", \"pipe\", \"pipe\"],\n  });\n  return child as unknown as SpawnedProcess;\n};\n\n/**\n * Check whether the user is authenticated via Claude subscription OAuth.\n *\n * Spawns `claude auth status --json`, falling back to the legacy SDK CLI\n * layout when available. On any failure (spawn error, non-JSON stdout,\n * non-zero exit, timeout) we return `{ loggedIn: false }` rather than\n * propagating the error — the caller will fall back to the\n * `ANTHROPIC_API_KEY` path and, if that's also missing, produce a clean\n * two-option error message.\n *\n * The 10s timeout guards against the CLI hanging on a broken network or\n * keychain prompt. In practice `auth status` is a cheap local read.\n */\nexport async function checkClaudeAuth(\n  spawnCli: SpawnCliFn = defaultSpawnCli,\n): Promise<ClaudeAuthStatus> {\n  if (spawnCli === defaultSpawnCli) {\n    const status = await checkClaudeAuthWith(defaultSpawnCli);\n    if (status.loggedIn) return status;\n    return await checkClaudeAuthWith(legacySdkSpawnCli);\n  }\n  return await checkClaudeAuthWith(spawnCli);\n}\n\nasync function checkClaudeAuthWith(\n  spawnCli: SpawnCliFn,\n): Promise<ClaudeAuthStatus> {\n  let child: SpawnedProcess;\n  try {\n    child = spawnCli([\"auth\", \"status\", \"--json\"]);\n  } catch {\n    return { loggedIn: false };\n  }\n\n  return new Promise<ClaudeAuthStatus>((resolve) => {\n    let stdout = \"\";\n    let stderr = \"\";\n    let settled = false;\n\n    const settle = (value: ClaudeAuthStatus): void => {\n      if (settled) return;\n      settled = true;\n      clearTimeout(timer);\n      resolve(value);\n    };\n\n    const timer = setTimeout(() => {\n      try {\n        child.kill(\"SIGTERM\");\n      } catch {\n        // Kill can fail if the process already exited; nothing we can do.\n      }\n      settle({ loggedIn: false });\n    }, AUTH_TIMEOUT_MS);\n\n    child.stdout.on(\"data\", (data) => {\n      stdout += data.toString();\n    });\n    child.stderr.on(\"data\", (data) => {\n      stderr += data.toString();\n    });\n\n    child.on(\"error\", () => {\n      settle({ loggedIn: false });\n    });\n\n    child.on(\"close\", (code) => {\n      // The SDK writes `{\"loggedIn\": false, ...}` to stdout with a zero\n      // exit code when the user isn't signed in, so we only reject on\n      // non-zero + empty stdout. An empty stdout with zero exit (shouldn't\n      // happen in practice) also fails safely to `loggedIn: false`.\n      if (code !== 0 && stdout.trim().length === 0) {\n        // `stderr` isn't surfaced to the user here — the caller's error\n        // message covers both auth paths — but it would be captured by\n        // `stderr` if we ever wanted to log it for debugging.\n        void stderr;\n        settle({ loggedIn: false });\n        return;\n      }\n      try {\n        settle(parseClaudeAuthStatus(stdout.trim()));\n      } catch {\n        settle({ loggedIn: false });\n      }\n    });\n  });\n}\n\nfunction parseClaudeAuthStatus(raw: string): ClaudeAuthStatus {\n  const parsed = JSON.parse(raw) as Record<string, unknown>;\n  const loggedIn = parsed.loggedIn === true;\n  const out: ClaudeAuthStatus = { loggedIn };\n  if (typeof parsed.email === \"string\") out.email = parsed.email;\n  if (typeof parsed.subscriptionType === \"string\") {\n    out.subscriptionType = parsed.subscriptionType;\n  }\n  if (typeof parsed.authMethod === \"string\") {\n    out.authMethod = parsed.authMethod;\n  }\n  return out;\n}\n\n/**\n * Human-readable error when neither auth path is available. The text is\n * deliberately verbose — users hitting this wall for the first time\n * deserve both options in front of them, not a terse hint.\n */\nexport const UNAUTHENTICATED_MESSAGE =\n  \"not authenticated to Claude.\\n\\n\" +\n  \"Option 1 — use your Claude subscription (Pro/Max):\\n\" +\n  \"  claude auth login --claudeai\\n\\n\" +\n  \"Option 2 — use a pay-per-token API key:\\n\" +\n  \"  Get one at https://console.anthropic.com\\n\" +\n  \"  export ANTHROPIC_API_KEY=sk-ant-...\\n\\n\" +\n  \"Verify with: claude auth status\";\n\n/**\n * Assert that at least one auth path is satisfied. Prefers subscription\n * auth (fewer surprises for Claude Pro/Max users) but accepts\n * `ANTHROPIC_API_KEY` as a fallback. On failure throws with\n * `code = \"CLAUDE_AUTH_MISSING\"` so callers can distinguish this from\n * other errors if they ever want to.\n *\n * Returns the resolved auth status so callers that want to display the\n * logged-in email in a preamble can do so without a second subprocess.\n */\nexport async function assertClaudeAuth(\n  spawnCli: SpawnCliFn = defaultSpawnCli,\n): Promise<ClaudeAuthStatus> {\n  const status = await checkClaudeAuth(spawnCli);\n  if (status.loggedIn) {\n    return status;\n  }\n  const apiKey = process.env.ANTHROPIC_API_KEY;\n  if (apiKey !== undefined && apiKey.length > 0) {\n    // Signal to callers that we're on the API-key path. Not \"loggedIn\"\n    // in the OAuth sense, but the SDK will pick up the env var and\n    // succeed — so we return a status that tells bootstrap/capture the\n    // gate is open.\n    return { loggedIn: true, authMethod: \"apiKey\" };\n  }\n  const err = new Error(UNAUTHENTICATED_MESSAGE);\n  (err as { code?: string }).code = \"CLAUDE_AUTH_MISSING\";\n  throw err;\n}\n\n// Internal re-export — helps keep the public type surface minimal while\n// still letting tests import the `ChildProcess` shape when needed.\nexport type { ChildProcess };\nexport type { SpawnCliFn, SpawnedProcess };\n","import { spawn, spawnSync, type ChildProcess } from \"node:child_process\";\n\nimport type { SpawnCliFn } from \"../types.js\";\n\nconst STATUS_TIMEOUT_MS = 3_000;\n\nexport function commandExists(command: string): boolean {\n  const result = spawnSync(\"sh\", [\"-lc\", `command -v ${command}`], {\n    encoding: \"utf8\",\n  });\n  return result.status === 0 && result.stdout.trim().length > 0;\n}\n\nexport function runStatusCommand(\n  command: string,\n  args: string[],\n): Promise<{ ok: boolean; detail: string }> {\n  return new Promise((resolve) => {\n    let stdout = \"\";\n    let stderr = \"\";\n    let child: ChildProcess;\n    let settled = false;\n    const settle = (value: { ok: boolean; detail: string }): void => {\n      if (settled) return;\n      settled = true;\n      clearTimeout(timer);\n      resolve(value);\n    };\n    try {\n      child = spawn(command, args, { stdio: [\"ignore\", \"pipe\", \"pipe\"] });\n    } catch (err: unknown) {\n      const msg = err instanceof Error ? err.message : String(err);\n      resolve({ ok: false, detail: msg });\n      return;\n    }\n    const timer = setTimeout(() => {\n      try {\n        child.kill(\"SIGTERM\");\n        setTimeout(() => {\n          if (child.exitCode === null && child.signalCode === null) {\n            try {\n              child.kill(\"SIGKILL\");\n            } catch {\n              // already exited\n            }\n          }\n        }, 500).unref();\n      } catch {\n        // already exited\n      }\n      settle({ ok: false, detail: `${command} status timed out` });\n    }, STATUS_TIMEOUT_MS);\n    child.stdout?.on(\"data\", (chunk) => {\n      stdout += chunk.toString(\"utf8\");\n    });\n    child.stderr?.on(\"data\", (chunk) => {\n      stderr += chunk.toString(\"utf8\");\n    });\n    child.on(\"error\", (err) => {\n      settle({ ok: false, detail: err.message });\n    });\n    child.on(\"close\", (code) => {\n      const text = `${stdout}\\n${stderr}`.trim();\n      settle({\n        ok: code === 0,\n        detail:\n          text\n            .split(\"\\n\")\n            .find((line) => line.trim().length > 0)\n            ?.trim() ?? (code === 0 ? \"ready\" : `${command} exited ${code ?? 1}`),\n      });\n    });\n  });\n}\n\nexport function runInjectedStatusCommand(\n  spawnCli: SpawnCliFn,\n  args: string[],\n): Promise<{ ok: boolean; detail: string }> {\n  return new Promise((resolve) => {\n    let stdout = \"\";\n    let stderr = \"\";\n    let settled = false;\n    const settle = (value: { ok: boolean; detail: string }): void => {\n      if (settled) return;\n      settled = true;\n      resolve(value);\n    };\n    try {\n      const child = spawnCli(args);\n      child.stdout.on(\"data\", (chunk) => {\n        stdout += chunk.toString();\n      });\n      child.stderr.on(\"data\", (chunk) => {\n        stderr += chunk.toString();\n      });\n      child.on(\"error\", (err) => {\n        settle({\n          ok: false,\n          detail: err instanceof Error ? err.message : String(err),\n        });\n      });\n      child.on(\"close\", (codeOrError) => {\n        const code = typeof codeOrError === \"number\" ? codeOrError : 1;\n        const text = `${stdout}\\n${stderr}`.trim();\n        settle({\n          ok: code === 0,\n          detail:\n            text\n              .split(\"\\n\")\n              .find((line) => line.trim().length > 0)\n              ?.trim() ?? (code === 0 ? \"ready\" : `${args[0] ?? \"command\"} exited ${code}`),\n        });\n      });\n    } catch (err: unknown) {\n      settle({\n        ok: false,\n        detail: err instanceof Error ? err.message : String(err),\n      });\n    }\n  });\n}\n","import { spawn } from \"node:child_process\";\n\nimport type {\n  AgentResult,\n  AgentStreamMessage,\n  AgentUsage,\n} from \"../types.js\";\n\nexport interface JsonlCliOptions {\n  command: string;\n  args: string[];\n  cwd: string;\n  env: NodeJS.ProcessEnv;\n  onMessage?: (msg: AgentStreamMessage) => void;\n  parseFinal: (msg: Record<string, unknown>) => Partial<AgentResult> | null;\n}\n\nexport function runJsonlCli(opts: JsonlCliOptions): Promise<AgentResult> {\n  return new Promise((resolve) => {\n    const child = spawn(opts.command, opts.args, {\n      cwd: opts.cwd,\n      env: opts.env,\n      stdio: [\"ignore\", \"pipe\", \"pipe\"],\n    });\n\n    let stdoutBuf = \"\";\n    let stderr = \"\";\n    let cost = 0;\n    let turns = 0;\n    let result = \"\";\n    let sessionId: string | undefined;\n    let usage: AgentUsage | undefined;\n    let success = false;\n    let finalSeen = false;\n    let error: string | undefined;\n\n    const observe = (msg: Record<string, unknown>): void => {\n      opts.onMessage?.(msg);\n      if (\n        sessionId === undefined &&\n        typeof msg.session_id === \"string\" &&\n        msg.session_id.length > 0\n      ) {\n        sessionId = msg.session_id;\n      }\n      if (\n        sessionId === undefined &&\n        typeof msg.thread_id === \"string\" &&\n        msg.thread_id.length > 0\n      ) {\n        sessionId = msg.thread_id;\n      }\n      const final = opts.parseFinal(msg);\n      if (final === null) return;\n      finalSeen = true;\n      if (final.cost !== undefined) cost = final.cost;\n      if (final.turns !== undefined) turns = final.turns;\n      if (final.result !== undefined) result = final.result;\n      if (final.sessionId !== undefined) sessionId = final.sessionId;\n      if (final.usage !== undefined) usage = final.usage;\n      if (final.success !== undefined) success = final.success;\n      if (final.error !== undefined) error = final.error;\n    };\n\n    const flushLines = (): void => {\n      let idx = stdoutBuf.indexOf(\"\\n\");\n      while (idx !== -1) {\n        const rawLine = stdoutBuf.slice(0, idx);\n        stdoutBuf = stdoutBuf.slice(idx + 1);\n        const line = rawLine.trim();\n        if (line.length > 0) {\n          try {\n            observe(JSON.parse(line) as Record<string, unknown>);\n          } catch {\n            // Ignore non-JSON chatter; stderr is captured for failures.\n          }\n        }\n        idx = stdoutBuf.indexOf(\"\\n\");\n      }\n    };\n\n    child.stdout.on(\"data\", (chunk) => {\n      stdoutBuf += chunk.toString(\"utf8\");\n      flushLines();\n    });\n    child.stderr.on(\"data\", (chunk) => {\n      stderr += chunk.toString(\"utf8\");\n    });\n    child.on(\"error\", (err: NodeJS.ErrnoException) => {\n      resolve({\n        success: false,\n        cost,\n        turns,\n        result,\n        sessionId,\n        usage,\n        error:\n          err.code === \"ENOENT\"\n            ? `${opts.command} not found on PATH`\n            : err.message,\n      });\n    });\n    child.on(\"close\", (code) => {\n      flushLines();\n      if (stdoutBuf.trim().length > 0) {\n        try {\n          observe(JSON.parse(stdoutBuf.trim()) as Record<string, unknown>);\n        } catch {\n          // Ignore trailing non-JSON.\n        }\n      }\n\n      if (code === 0 && finalSeen && success) {\n        resolve({ success, cost, turns, result, sessionId, usage });\n        return;\n      }\n\n      const firstStderr = stderr.trim().split(\"\\n\")[0];\n      resolve({\n        success: false,\n        cost,\n        turns,\n        result,\n        sessionId,\n        usage,\n        error:\n          error ??\n          (firstStderr !== undefined && firstStderr.length > 0\n            ? firstStderr\n            : `${opts.command} exited ${code ?? 1}`),\n      });\n    });\n  });\n}\n\nexport function parseUsage(value: unknown): AgentUsage | undefined {\n  if (value === null || typeof value !== \"object\") return undefined;\n  const obj = value as Record<string, unknown>;\n  return {\n    inputTokens: numberField(obj, \"input_tokens\") ?? numberField(obj, \"inputTokens\"),\n    cachedInputTokens:\n      numberField(obj, \"cached_input_tokens\") ??\n      numberField(obj, \"cachedInputTokens\") ??\n      numberField(obj, \"cacheReadTokens\"),\n    outputTokens:\n      numberField(obj, \"output_tokens\") ?? numberField(obj, \"outputTokens\"),\n    reasoningOutputTokens:\n      numberField(obj, \"reasoning_output_tokens\") ??\n      numberField(obj, \"reasoningOutputTokens\"),\n  };\n}\n\nfunction numberField(\n  input: Record<string, unknown>,\n  key: string,\n): number | undefined {\n  const value = input[key];\n  return typeof value === \"number\" ? value : undefined;\n}\n","import type { AgentProviderMetadata, RunAgentOptions } from \"../types.js\";\n\nexport function combinedPrompt(\n  opts: RunAgentOptions,\n  metadata: AgentProviderMetadata,\n): string {\n  const reviewerFallback = buildReviewerFallback(opts, metadata);\n  return `${opts.systemPrompt}${reviewerFallback}\\n\\n---\\n\\n${opts.prompt}`;\n}\n\nfunction buildReviewerFallback(\n  opts: RunAgentOptions,\n  metadata: AgentProviderMetadata,\n): string {\n  if (metadata.capabilities.supportsProgrammaticSubagents) return \"\";\n\n  const reviewer = opts.agents?.reviewer;\n  if (reviewer === undefined) return \"\";\n  return (\n    \"\\n\\nNon-Claude provider note: this runtime does not receive Claude's \" +\n    \"nested Agent tool contract. When the writer prompt asks you to invoke \" +\n    \"the reviewer subagent, perform that review pass yourself before final \" +\n    \"wiki edits. Treat this reviewer prompt as read-only review guidance:\\n\\n\" +\n    reviewer.prompt\n  );\n}\n","import type {\n  AgentProvider,\n  AgentProviderMetadata,\n  AgentResult,\n  ProviderModelChoice,\n  ProviderStatus,\n  RunAgentOptions,\n  SpawnCliFn,\n} from \"../types.js\";\nimport {\n  commandExists,\n  runInjectedStatusCommand,\n  runStatusCommand,\n} from \"./cli-status.js\";\nimport { parseUsage, runJsonlCli } from \"./jsonl-cli.js\";\nimport { combinedPrompt } from \"./prompt.js\";\n\nconst metadata: AgentProviderMetadata = {\n  id: \"codex\",\n  displayName: \"Codex\",\n  defaultModel: null,\n  executable: \"codex\",\n  capabilities: {\n    transport: \"cli-jsonl\",\n    writesFiles: true,\n    supportsModelOverride: true,\n    supportsStreaming: true,\n    supportsSessionId: false,\n    supportsUsage: true,\n    supportsCost: false,\n    supportsProviderReportedTurns: false,\n    supportsProgrammaticSubagents: false,\n    supportsStrictToolAllowlist: false,\n  },\n};\n\nexport const codexProvider: AgentProvider = {\n  metadata,\n  checkStatus,\n  assertReady,\n  run,\n  modelChoices,\n};\n\ninterface CodexCatalogModel {\n  slug: string;\n  displayName: string;\n}\n\nconst CODEX_MODEL_ORDER = [\n  \"gpt-5.5\",\n  \"gpt-5.4\",\n  \"gpt-5.4-mini\",\n  \"gpt-5.3-codex\",\n] as const;\n\nconst CODEX_MODEL_LABELS: Record<string, string> = {\n  \"gpt-5.5\": \"GPT-5.5\",\n  \"gpt-5.4\": \"GPT-5.4\",\n  \"gpt-5.4-mini\": \"GPT-5.4 Mini\",\n  \"gpt-5.3-codex\": \"GPT-5.3 Codex\",\n};\n\nasync function modelChoices(args: {\n  configuredModel: string | null;\n  spawnCli?: SpawnCliFn;\n}): Promise<ProviderModelChoice[]> {\n  const catalog = await readCodexModelCatalog(args.spawnCli);\n  const choices: ProviderModelChoice[] = [];\n  if (args.configuredModel !== null) {\n    choices.push({\n      value: args.configuredModel,\n      label: modelLabel(args.configuredModel, catalog),\n      recommended: false,\n      source: \"configured\",\n    });\n  }\n  for (const slug of CODEX_MODEL_ORDER) {\n    if (choices.some((choice) => choice.value === slug)) continue;\n    if (catalog !== undefined && !catalog.some((model) => model.slug === slug)) {\n      continue;\n    }\n    choices.push({\n      value: slug,\n      label: modelLabel(slug, catalog),\n      recommended: slug === \"gpt-5.4\",\n      source: \"catalog\",\n    });\n  }\n  choices.push({\n    value: \"__custom__\",\n    label: \"Enter a model name\",\n    recommended: false,\n    source: \"custom\",\n  });\n  return choices;\n}\n\nasync function readCodexModelCatalog(\n  spawnCli?: SpawnCliFn,\n): Promise<CodexCatalogModel[] | undefined> {\n  if (spawnCli === undefined) return undefined;\n  try {\n    const result = await collectSpawn(spawnCli([\"codex\", \"debug\", \"models\"]));\n    if (result.code !== 0) return undefined;\n    const parsed = JSON.parse(result.stdout) as unknown;\n    if (parsed === null || typeof parsed !== \"object\") return undefined;\n    const models = (parsed as { models?: unknown }).models;\n    if (!Array.isArray(models)) return undefined;\n    const out: CodexCatalogModel[] = [];\n    for (const model of models) {\n      if (model === null || typeof model !== \"object\") continue;\n      const record = model as Record<string, unknown>;\n      if (record.visibility !== \"list\") continue;\n      if (typeof record.slug !== \"string\") continue;\n      out.push({\n        slug: record.slug,\n        displayName: typeof record.display_name === \"string\"\n          ? record.display_name\n          : record.slug,\n      });\n    }\n    return out;\n  } catch {\n    return undefined;\n  }\n}\n\nfunction collectSpawn(\n  child: ReturnType<SpawnCliFn>,\n): Promise<{ stdout: string; code: number }> {\n  return new Promise((resolve) => {\n    let stdout = \"\";\n    let settled = false;\n    const settle = (code: number): void => {\n      if (settled) return;\n      settled = true;\n      resolve({ stdout, code });\n    };\n    child.stdout.on(\"data\", (chunk) => {\n      stdout += chunk.toString();\n    });\n    child.on(\"error\", () => {\n      settle(1);\n    });\n    child.on(\"close\", (codeOrError) => {\n      settle(typeof codeOrError === \"number\" ? codeOrError ?? 1 : 1);\n    });\n  });\n}\n\nfunction modelLabel(\n  slug: string,\n  catalog: CodexCatalogModel[] | undefined,\n): string {\n  return CODEX_MODEL_LABELS[slug] ??\n    catalog?.find((model) => model.slug === slug)?.displayName ??\n    slug;\n}\n\nasync function run(opts: RunAgentOptions): Promise<AgentResult> {\n  const args = [\n    \"exec\",\n    \"--json\",\n    \"--sandbox\",\n    \"workspace-write\",\n    \"--skip-git-repo-check\",\n    \"-C\",\n    opts.cwd,\n  ];\n  if (opts.model !== undefined && opts.model.length > 0) {\n    args.push(\"--model\", opts.model);\n  }\n  args.push(combinedPrompt({ ...opts, provider: \"codex\" }, metadata));\n\n  return await runJsonlCli({\n    command: metadata.executable,\n    args,\n    cwd: opts.cwd,\n    env: { ...process.env, CODEALMANAC_INTERNAL_SESSION: \"1\" },\n    onMessage: opts.onMessage,\n    parseFinal: parseCodexFinal,\n  });\n}\n\nasync function checkStatus(spawnCli?: SpawnCliFn): Promise<ProviderStatus> {\n  if (spawnCli === undefined && !commandExists(metadata.executable)) {\n    return {\n      id: metadata.id,\n      installed: false,\n      authenticated: false,\n      detail: `${metadata.executable} not found on PATH`,\n    };\n  }\n\n  const auth = spawnCli !== undefined\n    ? await runInjectedStatusCommand(spawnCli, [\n      metadata.executable,\n      \"login\",\n      \"status\",\n    ])\n    : await runStatusCommand(metadata.executable, [\"login\", \"status\"]);\n  return {\n    id: metadata.id,\n    installed: true,\n    authenticated: auth.ok,\n    detail: auth.detail,\n  };\n}\n\nasync function assertReady(spawnCli?: SpawnCliFn): Promise<void> {\n  const status = await checkStatus(spawnCli);\n  if (!status.installed || !status.authenticated) {\n    const err = new Error(`${status.id} not ready: ${status.detail}`);\n    (err as { code?: string }).code = \"AGENT_AUTH_MISSING\";\n    throw err;\n  }\n}\n\nfunction parseCodexFinal(\n  msg: Record<string, unknown>,\n): Partial<AgentResult> | null {\n  if (msg.type === \"item.completed\") {\n    const item = msg.item;\n    if (item !== null && typeof item === \"object\") {\n      const obj = item as Record<string, unknown>;\n      if (obj.type === \"agent_message\" && typeof obj.text === \"string\") {\n        return { result: obj.text };\n      }\n    }\n    return null;\n  }\n  if (msg.type === \"turn.completed\") {\n    return { success: true, turns: 1, usage: parseUsage(msg.usage) };\n  }\n  if (msg.type === \"turn.failed\" || msg.type === \"error\") {\n    return {\n      success: false,\n      error:\n        typeof msg.message === \"string\"\n          ? msg.message\n          : typeof msg.error === \"string\"\n            ? msg.error\n            : \"codex turn failed\",\n    };\n  }\n  return null;\n}\n","import type {\n  AgentProvider,\n  AgentProviderMetadata,\n  AgentResult,\n  ProviderStatus,\n  RunAgentOptions,\n  SpawnCliFn,\n} from \"../types.js\";\nimport {\n  commandExists,\n  runInjectedStatusCommand,\n  runStatusCommand,\n} from \"./cli-status.js\";\nimport { parseUsage, runJsonlCli } from \"./jsonl-cli.js\";\nimport { combinedPrompt } from \"./prompt.js\";\n\nconst metadata: AgentProviderMetadata = {\n  id: \"cursor\",\n  displayName: \"Cursor\",\n  defaultModel: null,\n  executable: \"cursor-agent\",\n  capabilities: {\n    transport: \"cli-jsonl\",\n    writesFiles: true,\n    supportsModelOverride: true,\n    supportsStreaming: true,\n    supportsSessionId: true,\n    supportsUsage: true,\n    supportsCost: false,\n    supportsProviderReportedTurns: false,\n    supportsProgrammaticSubagents: false,\n    supportsStrictToolAllowlist: false,\n  },\n};\n\nexport const cursorProvider: AgentProvider = {\n  metadata,\n  checkStatus,\n  assertReady,\n  run,\n};\n\nasync function run(opts: RunAgentOptions): Promise<AgentResult> {\n  const args = [\n    \"--print\",\n    \"--output-format\",\n    \"stream-json\",\n    \"--stream-partial-output\",\n    \"--trust\",\n    \"--workspace\",\n    opts.cwd,\n  ];\n  if (opts.model !== undefined && opts.model.length > 0) {\n    args.push(\"--model\", opts.model);\n  }\n  args.push(combinedPrompt({ ...opts, provider: \"cursor\" }, metadata));\n\n  return await runJsonlCli({\n    command: metadata.executable,\n    args,\n    cwd: opts.cwd,\n    env: { ...process.env, CODEALMANAC_INTERNAL_SESSION: \"1\" },\n    onMessage: opts.onMessage,\n    parseFinal: parseCursorFinal,\n  });\n}\n\nasync function checkStatus(spawnCli?: SpawnCliFn): Promise<ProviderStatus> {\n  if (spawnCli === undefined && !commandExists(metadata.executable)) {\n    return {\n      id: metadata.id,\n      installed: false,\n      authenticated: false,\n      detail: `${metadata.executable} not found on PATH`,\n    };\n  }\n\n  const auth = spawnCli !== undefined\n    ? await runInjectedStatusCommand(spawnCli, [\n      metadata.executable,\n      \"status\",\n    ])\n    : await runStatusCommand(metadata.executable, [\"status\"]);\n  return {\n    id: metadata.id,\n    installed: true,\n    authenticated: auth.ok,\n    detail: auth.detail,\n  };\n}\n\nasync function assertReady(spawnCli?: SpawnCliFn): Promise<void> {\n  const status = await checkStatus(spawnCli);\n  if (!status.installed || !status.authenticated) {\n    const err = new Error(`${status.id} not ready: ${status.detail}`);\n    (err as { code?: string }).code = \"AGENT_AUTH_MISSING\";\n    throw err;\n  }\n}\n\nfunction parseCursorFinal(\n  msg: Record<string, unknown>,\n): Partial<AgentResult> | null {\n  if (msg.type !== \"result\") return null;\n  const isError = msg.is_error === true || msg.subtype !== \"success\";\n  return {\n    success: !isError,\n    turns: 1,\n    result: typeof msg.result === \"string\" ? msg.result : \"\",\n    sessionId:\n      typeof msg.session_id === \"string\" ? msg.session_id : undefined,\n    usage: parseUsage(msg.usage),\n    error: isError\n      ? typeof msg.result === \"string\"\n        ? msg.result\n        : `cursor result: ${String(msg.subtype ?? \"error\")}`\n      : undefined,\n  };\n}\n","import {\n  getEnabledAgentProviderIds,\n  type AgentProviderId,\n} from \"../../update/config.js\";\nimport type { ProviderStatus, SpawnCliFn } from \"../types.js\";\nimport { getAgentProvider } from \"./index.js\";\n\nexport async function assertAgentAuth(args: {\n  provider: AgentProviderId;\n  spawnCli?: SpawnCliFn;\n}): Promise<void> {\n  await getAgentProvider(args.provider).assertReady(args.spawnCli);\n}\n\nexport async function listProviderStatuses(\n  spawnCli?: SpawnCliFn,\n): Promise<ProviderStatus[]> {\n  const out: ProviderStatus[] = [];\n  for (const id of getEnabledAgentProviderIds()) {\n    out.push(await getAgentProvider(id).checkStatus(spawnCli));\n  }\n  return out;\n}\n","import type { AgentProvider } from \"../types.js\";\nimport { claudeProvider, DEFAULT_AGENT_MODEL } from \"./claude/index.js\";\nimport { codexProvider } from \"./codex-cli.js\";\nimport { cursorProvider } from \"./cursor-cli.js\";\n\nconst AGENT_PROVIDERS = {\n  claude: claudeProvider,\n  codex: codexProvider,\n  cursor: cursorProvider,\n} satisfies Record<string, AgentProvider>;\n\nexport function getAgentProvider(id: keyof typeof AGENT_PROVIDERS): AgentProvider {\n  return AGENT_PROVIDERS[id];\n}\n\nexport const AGENT_PROVIDER_METADATA = {\n  claude: claudeProvider.metadata,\n  codex: codexProvider.metadata,\n  cursor: cursorProvider.metadata,\n};\nexport { DEFAULT_AGENT_MODEL };\nexport { assertAgentAuth, listProviderStatuses } from \"./status.js\";\n","import {\n  AGENT_PROVIDER_METADATA,\n  getAgentProvider,\n  listProviderStatuses,\n} from \"./providers.js\";\nimport type {\n  ProviderModelChoice,\n  ProviderStatus,\n  SpawnCliFn,\n} from \"./types.js\";\nimport {\n  formatEnabledAgentProviderList,\n  getEnabledAgentProviderIds,\n  isAgentProviderId,\n  readConfig,\n  type AgentProviderId,\n  type GlobalConfig,\n} from \"../update/config.js\";\n\nexport type ProviderReadiness = \"ready\" | \"not-authenticated\" | \"missing\";\n\nexport interface ProviderSetupChoice {\n  id: AgentProviderId;\n  label: string;\n  selected: boolean;\n  recommended: boolean;\n  readiness: ProviderReadiness;\n  ready: boolean;\n  installed: boolean;\n  authenticated: boolean;\n  effectiveModel: string | null;\n  providerDefaultModel: string | null;\n  configuredModel: string | null;\n  account: string | null;\n  detail: string;\n  fixCommand: string | null;\n  modelChoices: ProviderModelChoice[];\n}\n\nexport interface ProviderSetupView {\n  defaultProvider: AgentProviderId;\n  recommendedProvider: AgentProviderId;\n  choices: ProviderSetupChoice[];\n}\n\nexport interface ProviderViewOptions {\n  config?: GlobalConfig;\n  statuses?: ProviderStatus[];\n  spawnCli?: SpawnCliFn;\n}\n\nconst LOGIN_FIXES: Record<AgentProviderId, string> = {\n  claude: \"run: claude auth login --claudeai\",\n  codex: \"run: codex login\",\n  cursor: \"run: cursor-agent login\",\n};\n\nconst INSTALL_FIXES: Record<AgentProviderId, string> = {\n  claude: \"install Claude Code, then run: claude auth login --claudeai\",\n  codex: \"install Codex CLI, then run: codex login\",\n  cursor: \"install cursor-agent, then run: cursor-agent login\",\n};\n\nexport function getProviderLabel(id: AgentProviderId): string {\n  return AGENT_PROVIDER_METADATA[id].displayName;\n}\n\nexport function getProviderDefaultModel(id: AgentProviderId): string | null {\n  return AGENT_PROVIDER_METADATA[id].defaultModel;\n}\n\nexport async function buildProviderSetupView(\n  opts: ProviderViewOptions = {},\n): Promise<ProviderSetupView> {\n  const config = opts.config ?? await readConfig();\n  const statuses = opts.statuses ?? await listProviderStatuses(opts.spawnCli);\n  const statusById = new Map(statuses.map((status) => [status.id, status]));\n  const recommendedProvider = chooseRecommendedProvider(statuses);\n  const choices: ProviderSetupChoice[] = [];\n  for (const id of getEnabledAgentProviderIds()) {\n    const status = statusById.get(id) ?? missingStatus(id);\n    const readiness = getReadiness(status);\n    const configuredModel = normalizeModel(config.agent.models[id]);\n    const providerDefaultModel = getProviderDefaultModel(id);\n    const effectiveModel = configuredModel ?? providerDefaultModel;\n    choices.push({\n      id,\n      label: getProviderLabel(id),\n      selected: id === config.agent.default,\n      recommended: id === recommendedProvider,\n      readiness,\n      ready: readiness === \"ready\",\n      installed: status.installed,\n      authenticated: status.authenticated,\n      effectiveModel,\n      providerDefaultModel,\n      configuredModel,\n      account: status.authenticated ? accountFromDetail(status.detail) : null,\n      detail: status.detail,\n      fixCommand: fixFor(id, readiness),\n      modelChoices: await buildProviderModelChoices(id, configuredModel, {\n        spawnCli: opts.spawnCli,\n      }),\n    });\n  }\n  return {\n    defaultProvider: config.agent.default,\n    recommendedProvider,\n    choices,\n  };\n}\n\nexport function buildProviderModelChoices(\n  id: AgentProviderId,\n  configuredModel: string | null = null,\n  opts: { spawnCli?: SpawnCliFn } = {},\n): Promise<ProviderModelChoice[]> | ProviderModelChoice[] {\n  const provider = getAgentProvider(id);\n  if (provider.modelChoices !== undefined) {\n    return provider.modelChoices({ configuredModel, spawnCli: opts.spawnCli });\n  }\n  const choices: ProviderModelChoice[] = [];\n  if (configuredModel !== null) {\n    choices.push({\n      value: configuredModel,\n      label: configuredModel,\n      recommended: false,\n      source: \"configured\",\n    });\n  }\n\n  const providerDefault = getProviderDefaultModel(id);\n  if (providerDefault !== null) {\n    if (!choices.some((choice) => choice.value === providerDefault)) {\n      choices.push({\n        value: providerDefault,\n        label: providerDefault,\n        recommended: true,\n        source: \"provider-default\",\n      });\n    } else {\n      choices[0] = { ...choices[0]!, recommended: true };\n    }\n  } else {\n    choices.push({\n      value: null,\n      label: \"provider default\",\n      recommended: true,\n      source: \"provider-default\",\n    });\n  }\n\n  choices.push({\n    value: \"__custom__\",\n    label: \"Enter a model name\",\n    recommended: false,\n    source: \"custom\",\n  });\n  return choices;\n}\n\nexport function chooseRecommendedProvider(\n  statuses: ProviderStatus[],\n): AgentProviderId {\n  const ready = statuses\n    .filter((status) => getReadiness(status) === \"ready\")\n    .map((status) => status.id);\n  if (ready.includes(\"claude\")) return \"claude\";\n  for (const id of getEnabledAgentProviderIds()) {\n    if (ready.includes(id)) return id;\n  }\n  return \"claude\";\n}\n\nexport function parseAgentSelection(value: string): {\n  provider: AgentProviderId | null;\n  model?: string;\n} {\n  const [rawProvider, ...modelParts] = value.split(\"/\");\n  if (rawProvider === undefined || !isAgentProviderId(rawProvider)) {\n    return { provider: null };\n  }\n  const model = modelParts.join(\"/\");\n  return {\n    provider: rawProvider,\n    model: model.length > 0 ? model : undefined,\n  };\n}\n\nfunction getReadiness(status: ProviderStatus): ProviderReadiness {\n  if (!status.installed) return \"missing\";\n  if (/not (logged|signed) in|not authenticated/i.test(status.detail)) {\n    return \"not-authenticated\";\n  }\n  if (!status.authenticated) return \"not-authenticated\";\n  return \"ready\";\n}\n\nfunction fixFor(\n  id: AgentProviderId,\n  readiness: ProviderReadiness,\n): string | null {\n  if (readiness === \"ready\") return null;\n  if (readiness === \"missing\") return INSTALL_FIXES[id];\n  return LOGIN_FIXES[id];\n}\n\nfunction accountFromDetail(detail: string): string | null {\n  const clean = detail.trim();\n  if (\n    clean.length === 0 ||\n    clean === \"ready\" ||\n    clean === \"logged in\" ||\n    clean === \"ANTHROPIC_API_KEY set\"\n  ) {\n    return null;\n  }\n  return clean;\n}\n\nfunction normalizeModel(value: string | null | undefined): string | null {\n  return typeof value === \"string\" && value.length > 0 ? value : null;\n}\n\nfunction missingStatus(id: AgentProviderId): ProviderStatus {\n  return {\n    id,\n    installed: false,\n    authenticated: false,\n    detail: \"provider status unavailable\",\n  };\n}\n\nexport function enabledProviderListForMessage(): string {\n  return 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package/dist/chunk-K2JBCB7R.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/commands/uninstall.ts"],"sourcesContent":["import { existsSync } from \"node:fs\";\nimport { readFile, rm, writeFile } from \"node:fs/promises\";\nimport { homedir } from \"node:os\";\nimport path from \"node:path\";\n\nimport { runHookUninstall } from \"./hook.js\";\nimport {\n  CODEX_INSTRUCTIONS_END,\n  CODEX_INSTRUCTIONS_START,\n  IMPORT_LINE,\n} from \"./setup.js\";\n\n/**\n * `almanac uninstall` — the reverse of `setup`.\n *\n * Idempotent and order-insensitive: each step is a no-op if that\n * artifact was never installed. We remove exactly the things setup added,\n * nothing else:\n *\n *   1. The `@~/.claude/codealmanac.md` line from `~/.claude/CLAUDE.md`.\n *      Other content stays untouched. If removing our line leaves the\n *      file empty, we delete the file so our fingerprint doesn't persist\n *      as zero bytes.\n *   2. The guide files `~/.claude/codealmanac.md` and\n *      `~/.claude/codealmanac-reference.md`.\n *   3. The managed codealmanac block from Codex's global AGENTS file.\n *   4. The SessionEnd hook entry (delegated to `runHookUninstall`, which\n *      already knows how to leave foreign entries alone).\n *\n * Flags:\n *   --yes           skip confirmations; remove everything\n *   --keep-hook     leave the hook alone\n *   --keep-guides   leave the guides + CLAUDE.md import alone\n *\n * Non-interactive (no TTY) → behaves as if `--yes` was passed. Same\n * contract as `setup`.\n */\n\nexport interface UninstallOptions {\n  yes?: boolean;\n  keepHook?: boolean;\n  keepGuides?: boolean;\n\n  // ─── Injection points ────────────────────────────────────────────\n  settingsPath?: string;\n  hookScriptPath?: string;\n  claudeDir?: string;\n  codexDir?: string;\n  isTTY?: boolean;\n  stdout?: NodeJS.WritableStream;\n}\n\nexport interface UninstallResult {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\nconst BLUE = \"\\x1b[38;5;75m\";\nconst DIM = \"\\x1b[2m\";\nconst RST = \"\\x1b[0m\";\n\nexport async function runUninstall(\n  options: UninstallOptions = {},\n): Promise<UninstallResult> {\n  const out = options.stdout ?? process.stdout;\n  const isTTY =\n    options.isTTY ?? (process.stdin.isTTY === true);\n  const interactive = isTTY && options.yes !== true;\n  const claudeDir = options.claudeDir ?? path.join(homedir(), \".claude\");\n  const codexDir = options.codexDir ?? path.join(homedir(), \".codex\");\n\n  out.write(\"\\n\");\n\n  // Hook removal.\n  let removeHook = true;\n  if (options.keepHook === true) {\n    removeHook = false;\n  } else if (interactive) {\n    removeHook = await confirm(\n      out,\n      \"Remove the SessionEnd hook from ~/.claude/settings.json?\",\n      true,\n    );\n  }\n  if (removeHook) {\n    const res = await runHookUninstall({\n      settingsPath: options.settingsPath,\n      hookScriptPath: options.hookScriptPath,\n    });\n    if (res.exitCode !== 0) {\n      return { stdout: \"\", stderr: res.stderr, exitCode: res.exitCode };\n    }\n    out.write(`  ${BLUE}\\u25c7${RST}  ${res.stdout.trim()}\\n`);\n  } else {\n    out.write(`  ${DIM}\\u25cb  Hook kept${RST}\\n`);\n  }\n\n  // Guide + import removal.\n  let removeGuides = true;\n  if (options.keepGuides === true) {\n    removeGuides = false;\n  } else if (interactive) {\n    removeGuides = await confirm(\n      out,\n      \"Remove agent instructions?\",\n      true,\n    );\n  }\n  if (removeGuides) {\n    const summary = await removeGuideFiles(claudeDir, codexDir);\n    if (summary.anyChanges) {\n      out.write(\n        `  ${BLUE}\\u25c7${RST}  Guides removed (${summary.filesTouched.join(\", \")})\\n`,\n      );\n    } else {\n      out.write(`  ${DIM}\\u25cb  Guides not installed${RST}\\n`);\n    }\n  } else {\n    out.write(`  ${DIM}\\u25cb  Guides kept${RST}\\n`);\n  }\n\n  out.write(`\\n  ${BLUE}\\u25c7${RST}  ${BLUE}Uninstall complete${RST}\\n\\n`);\n\n  return { stdout: \"\", stderr: \"\", exitCode: 0 };\n}\n\ninterface RemoveGuidesResult {\n  anyChanges: boolean;\n  filesTouched: string[];\n}\n\nasync function removeGuideFiles(\n  claudeDir: string,\n  codexDir: string,\n): Promise<RemoveGuidesResult> {\n  const touched: string[] = [];\n\n  const mini = path.join(claudeDir, \"codealmanac.md\");\n  const ref = path.join(claudeDir, \"codealmanac-reference.md\");\n  const claudeMd = path.join(claudeDir, \"CLAUDE.md\");\n\n  if (existsSync(mini)) {\n    await rm(mini, { force: true });\n    touched.push(\"codealmanac.md\");\n  }\n  if (existsSync(ref)) {\n    await rm(ref, { force: true });\n    touched.push(\"codealmanac-reference.md\");\n  }\n\n  if (existsSync(claudeMd)) {\n    const existing = await readFile(claudeMd, \"utf8\");\n    const { changed, body } = removeImportLine(existing);\n    if (changed) {\n      // If the file is now content-free, delete it outright so our\n      // installation leaves no trace. A user who was using CLAUDE.md\n      // before we touched it still has their content; only the case\n      // where CLAUDE.md contained nothing but our line gets cleaned up.\n      if (body.trim().length === 0) {\n        await rm(claudeMd, { force: true });\n        touched.push(\"CLAUDE.md (deleted)\");\n      } else {\n        await writeFile(claudeMd, body, \"utf8\");\n        touched.push(\"CLAUDE.md\");\n      }\n    }\n  }\n\n  for (const agentsFile of [\n    path.join(codexDir, \"AGENTS.md\"),\n    path.join(codexDir, \"AGENTS.override.md\"),\n  ]) {\n    if (!existsSync(agentsFile)) continue;\n    const existing = await readFile(agentsFile, \"utf8\");\n    const { changed, body } = removeManagedBlock(\n      existing,\n      CODEX_INSTRUCTIONS_START,\n      CODEX_INSTRUCTIONS_END,\n    );\n    if (!changed) continue;\n    if (body.trim().length === 0) {\n      await rm(agentsFile, { force: true });\n      touched.push(`${path.basename(agentsFile)} (deleted)`);\n    } else {\n      await writeFile(agentsFile, body, \"utf8\");\n      touched.push(path.basename(agentsFile));\n    }\n  }\n\n  return { anyChanges: touched.length > 0, filesTouched: touched };\n}\n\n/**\n * Remove the import line from a CLAUDE.md body. Match is line-anchored\n * (trimmed equality) so we don't munge a line that happens to include\n * the token as part of a longer string. Returns the unchanged body (and\n * `changed: false`) if the line isn't present — this is what makes the\n * command safe to run repeatedly.\n */\nexport function removeImportLine(contents: string): {\n  changed: boolean;\n  body: string;\n} {\n  const eol = contents.includes(\"\\r\\n\") ? \"\\r\\n\" : \"\\n\";\n  const lines = contents.split(/\\r?\\n/);\n\n  const indices: number[] = [];\n  for (let i = 0; i < lines.length; i++) {\n    if (lines[i]!.trim() === IMPORT_LINE) indices.push(i);\n  }\n  if (indices.length === 0) return { changed: false, body: contents };\n\n  // Remove the line(s). 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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) ?? [];\n    list.push(rel);\n    bySlug.set(slug, list);\n  }\n  const out: { slug: string; paths: string[] }[] = [];\n  for (const [slug, paths] of bySlug.entries()) {\n    if (paths.length > 1) {\n      out.push({ slug, paths: paths.sort() });\n    }\n  }\n  out.sort((a, b) => a.slug.localeCompare(b.slug));\n  return out;\n}\n\n// ─────────────────────────────────────────────────────────────────────\n// pretty-print\n// ─────────────────────────────────────────────────────────────────────\n\nfunction formatReport(r: HealthReport): string {\n  const sections: string[] = [];\n  sections.push(\n    section(\n      \"orphans\",\n      r.orphans.length,\n      r.orphans.map((o) => `  ${BLUE}${o.slug}${RST}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"stale\",\n      r.stale.length,\n      r.stale.map((s) => `  ${BLUE}${s.slug}${RST}     ${DIM}(${s.days_since_update} days)${RST}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"dead-refs\",\n      r.dead_refs.length,\n      r.dead_refs.map((d) => `  ${BLUE}${d.slug}${RST}  references ${d.path} ${DIM}(missing)${RST}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"broken-links\",\n      r.broken_links.length,\n      r.broken_links.map(\n        (b) => `  ${BLUE}${b.source_slug}${RST} → ${b.target_slug} ${DIM}(target does not exist)${RST}`,\n      ),\n    ),\n  );\n  sections.push(\n    section(\n      \"broken-xwiki\",\n      r.broken_xwiki.length,\n      r.broken_xwiki.map(\n        (b) =>\n          `  ${BLUE}${b.source_slug}${RST} → ${b.target_wiki}:${b.target_slug} ${DIM}(wiki unregistered or unreachable)${RST}`,\n      ),\n    ),\n  );\n  sections.push(\n    section(\n      \"empty-topics\",\n      r.empty_topics.length,\n      r.empty_topics.map((e) => `  ${BLUE}${e.slug}${RST}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"empty-pages\",\n      r.empty_pages.length,\n      r.empty_pages.map((e) => `  ${BLUE}${e.slug}${RST}`),\n    ),\n  );\n  sections.push(\n    section(\n      \"slug-collisions\",\n      r.slug_collisions.length,\n      r.slug_collisions.map((c) => `  ${BLUE}${c.slug}${RST}: ${c.paths.join(\", \")}`),\n    ),\n  );\n  return `${sections.join(\"\\n\\n\")}\\n`;\n}\n\nfunction section(label: string, count: number, lines: string[]): string {\n  if (count === 0) return `${BOLD}${label}${RST} ${GREEN}(0): (ok)${RST}`;\n  return `${BOLD}${label}${RST} ${RED}(${count})${RST}:\\n${lines.join(\"\\n\")}`;\n}\n","/**\n * Parse a compact duration string of the form `<N><unit>` into seconds.\n *\n * Accepted units (from the spec, `--since` / `--stale`):\n *   - `m` — minutes\n *   - `h` — hours\n *   - `d` — days\n *   - `w` — weeks\n *\n * Examples: `2w` → 1209600, `30d` → 2592000, `12h` → 43200.\n *\n * Anything else throws — the CLI surfaces the error with the usual\n * `almanac: <message>` prefix, which is clearer than silently treating\n * `2weeks` or `30 days` as zero.\n */\nexport function parseDuration(input: string): number {\n  const trimmed = input.trim();\n  const m = trimmed.match(/^(\\d+)([mhdw])$/);\n  if (m === null) {\n    throw new Error(\n      `invalid duration \"${input}\" (expected Nw, Nd, Nh, or Nm — e.g. 2w, 30d)`,\n    );\n  }\n  const n = Number.parseInt(m[1] ?? \"0\", 10);\n  const unit = m[2];\n  switch (unit) {\n    case \"m\":\n      return n * 60;\n    case \"h\":\n      return n * 60 * 60;\n    case \"d\":\n      return n * 60 * 60 * 24;\n    case \"w\":\n      return n * 60 * 60 * 24 * 7;\n    default:\n      // Unreachable — regex pins the unit — but satisfies exhaustiveness.\n      throw new Error(`invalid duration unit \"${unit ?? \"\"}\"`);\n  }\n}\n","import { existsSync } from \"node:fs\";\nimport { join } from \"node:path\";\n\nimport { findNearestAlmanacDir } from \"../paths.js\";\nimport { findEntry } from \"../registry/index.js\";\n\n/**\n * Figure out which repo root a query command should run against.\n *\n * Two modes, in order of precedence:\n *   1. `--wiki <name>`  — look it up in the global registry. Fails\n *      explicitly if the name isn't registered or its path has gone\n *      missing (unmounted drive, deleted repo). No silent fallback, which\n *      would hide the real problem from the user.\n *   2. default — walk up from `cwd` like git does. Fails if we're not\n *      inside a `.almanac/` repo.\n *\n * Returns the absolute path to the repo root (the directory containing\n * `.almanac/`).\n *\n * NOTE (spec contract, not yet implemented): when `--all` lands in a\n * future slice, it must silently skip wikis whose paths have gone\n * unreachable — the asymmetry with `--wiki <name>` is deliberate.\n * Explicit lookup is loud about failures (user named a specific wiki);\n * bulk `--all` is quiet (user asked \"whatever's available\"). Don't\n * unify the error behavior when adding `--all`.\n */\nexport async function resolveWikiRoot(params: {\n  cwd: string;\n  wiki?: string;\n}): Promise<string> {\n  if (params.wiki !== undefined) {\n    const entry = await findEntry({ name: params.wiki });\n    if (entry === null) {\n      throw new Error(`no registered wiki named \"${params.wiki}\"`);\n    }\n    if (!existsSync(join(entry.path, \".almanac\"))) {\n      throw new Error(\n        `wiki \"${params.wiki}\" path is unreachable (${entry.path})`,\n      );\n    }\n    return entry.path;\n  }\n\n  const nearest = findNearestAlmanacDir(params.cwd);\n  if (nearest === null) {\n    throw new Error(\n      \"no .almanac/ found in this directory or any parent; run `almanac bootstrap` first\",\n    );\n  }\n  return nearest;\n}\n","import 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-PDFS5VFE.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/commands/hook.ts","../src/commands/hook/script.ts"],"sourcesContent":["import { existsSync } from \"node:fs\";\nimport { mkdir, readFile, rename, writeFile } from \"node:fs/promises\";\nimport { homedir } from \"node:os\";\nimport path from \"node:path\";\n\nimport {\n  copyToStableHooksDir,\n  resolveHookScriptPath,\n  resolveSettingsPath,\n  type ScriptResolution,\n} from \"./hook/script.js\";\nimport { isCursorEnabled } from \"../update/config.js\";\n\n/**\n * `almanac hook install|uninstall|status` — wires the bundled\n * `hooks/almanac-capture.sh` into `~/.claude/settings.json` as a\n * `SessionEnd` hook.\n *\n * Design notes:\n *\n * - **Schema.** Claude Code validates `settings.json` against a strict\n *   schema: each entry in an event array (like `SessionEnd`) is a\n *   `{matcher, hooks: [...]}` container, and the actual command objects\n *   live in the nested `hooks` array. v0.1.0–v0.1.4 wrote command objects\n *   directly at the event-array level; newer Claude Code versions now\n *   reject that shape. We produce the wrapped form on install, and when\n *   encountering a legacy unwrapped entry that we recognize as ours (by\n *   `command` ending in `almanac-capture.sh`) we migrate it on next\n *   install. `SessionEnd` never uses the `matcher` field to discriminate\n *   anything — we always emit an empty `matcher: \"\"` (matches\n *   everything, which is what session-end lifecycle hooks want).\n *\n * - **Idempotent.** `install` twice leaves one entry, not two. We match by\n *   `command` string equality on the inner `hooks[]` entries. If the user\n *   replaces our absolute path with a symlink pointing at the same\n *   script, we'll treat it as foreign. That's acceptable; the `status`\n *   output shows the path we'd use, so the user can reconcile manually.\n *\n * - **Refuse foreign entries.** If `SessionEnd` is already populated with\n *   a command we don't recognize, we print the existing value and exit\n *   non-zero. Claude Code lets users wire their own hooks (notifications,\n *   git autocommit scripts, etc.) and silently replacing them would be\n *   rude. Foreign wrapped containers that don't reference our script are\n *   preserved byte-for-byte.\n *\n * - **Atomic write.** `settings.json` is small but heavily touched by\n *   Claude Code. Writing via tmp-file + rename avoids corrupting the file\n *   if we crash mid-write.\n *\n * - **Non-interactive.** No prompts, no confirmations. The caller is\n *   already making an intentional choice by running `almanac hook\n *   install`.\n */\n\nexport interface HookCommandOptions {\n  /** Which agent app to install hooks for. Default keeps legacy Claude behavior. */\n  source?: \"claude\" | \"codex\" | \"cursor\" | \"all\";\n  /**\n   * Override the hook script path. Production code leaves this undefined\n   * and we resolve the bundled `hooks/almanac-capture.sh`. Tests pass a\n   * fixture path to avoid depending on the runtime-install layout.\n   */\n  hookScriptPath?: string;\n  /**\n   * Override `~/.claude/settings.json`. Tests sandbox this to a tmpdir;\n   * production code leaves it undefined.\n   */\n  settingsPath?: string;\n  /**\n   * Override the stable hooks directory where we copy the script.\n   * Defaults to `~/.claude/hooks/`. Tests sandbox this to a tmpdir.\n   *\n   * Bug #1 fix: we always copy the bundled script to this stable path\n   * before writing it into settings.json. This way the settings entry\n   * points at a user-owned location that survives npm version bumps,\n   * npx cache evictions, and nvm version switches — instead of an\n   * ephemeral path inside ~/.npm/_npx/<sha>/... or the nvm-versioned\n   * node_modules/.\n   */\n  stableHooksDir?: string;\n}\n\nexport interface HookCommandResult {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\nconst HOOK_TIMEOUT_SECONDS = 10;\n\n/** A single command invocation inside a wrapper's `hooks[]` array. */\ninterface HookCommand {\n  type: \"command\";\n  command: string;\n  timeout?: number;\n}\n\n/** A wrapped SessionEnd entry per Claude Code's schema. */\ninterface WrappedEntry {\n  matcher: string;\n  hooks: HookCommand[];\n}\n\n/**\n * What we read from `settings.hooks.SessionEnd`. During a read we may\n * encounter the legacy unwrapped shape (`HookCommand` directly) written\n * by v0.1.0–v0.1.4 — we recognize and migrate it. Unknown entries we\n * can't classify are preserved as-is via `unknown`.\n */\ntype RawEntry = WrappedEntry | HookCommand | unknown;\n\n/**\n * Claude Code's `settings.json` is a free-form JSON object; we only care\n * about the `hooks.SessionEnd` array. Preserve everything else verbatim\n * so we don't drop user settings when we write the file back.\n */\ntype SettingsJson = Record<string, unknown> & {\n  hooks?: Record<string, RawEntry[] | undefined>;\n};\n\n/**\n * Heuristic: does this command path look like one we installed?\n *\n * We match on the filename `almanac-capture.sh` regardless of the parent\n * directory. This covers:\n *   - the stable path: `~/.claude/hooks/almanac-capture.sh`\n *   - legacy paths from v0.1.0–v0.1.5: inside the nvm node_modules or\n *     npx cache\n * The stable path is what new installs produce; legacy paths are what\n * we migrate when the user runs `almanac hook install` again.\n */\nfunction isOurCommandPath(command: string): boolean {\n  return command.endsWith(\"almanac-capture.sh\");\n}\n\n/**\n * Classify a raw SessionEnd entry. Wrapped entries are the canonical\n * shape; unwrapped-command entries are legacy output from v0.1.0–v0.1.4.\n * Anything else (random user JSON) is `unknown` and we leave it alone.\n */\ntype Classified =\n  | { kind: \"wrapped\"; entry: WrappedEntry }\n  | { kind: \"legacy\"; entry: HookCommand }\n  | { kind: \"unknown\"; entry: unknown };\n\nfunction classifyEntry(raw: RawEntry): Classified {\n  if (raw === null || typeof raw !== \"object\") {\n    return { kind: \"unknown\", entry: raw };\n  }\n  const obj = raw as Record<string, unknown>;\n  if (Array.isArray(obj.hooks)) {\n    // Wrapped shape. `matcher` may be absent in hand-edited files; treat\n    // absent as \"\" so we don't throw on slightly malformed input.\n    const matcher = typeof obj.matcher === \"string\" ? obj.matcher : \"\";\n    const hooks: HookCommand[] = [];\n    for (const h of obj.hooks as unknown[]) {\n      if (h !== null && typeof h === \"object\") {\n        const ho = h as Record<string, unknown>;\n        if (ho.type === \"command\" && typeof ho.command === \"string\") {\n          const cmd: HookCommand = {\n            type: \"command\",\n            command: ho.command,\n          };\n          if (typeof ho.timeout === \"number\") cmd.timeout = ho.timeout;\n          hooks.push(cmd);\n        }\n      }\n    }\n    return { kind: \"wrapped\", entry: { matcher, hooks } };\n  }\n  if (obj.type === \"command\" && typeof obj.command === \"string\") {\n    // Legacy unwrapped shape — v0.1.0–v0.1.4 wrote this form.\n    const cmd: HookCommand = {\n      type: \"command\",\n      command: obj.command as string,\n    };\n    if (typeof obj.timeout === \"number\") cmd.timeout = obj.timeout;\n    return { kind: \"legacy\", entry: cmd };\n  }\n  return { kind: \"unknown\", entry: raw };\n}\n\n/** True when the entry references our script and is safely ours to manage. */\nfunction isOurWrapped(entry: WrappedEntry): boolean {\n  return entry.hooks.some((h) => isOurCommandPath(h.command));\n}\n\nexport async function runHookInstall(\n  options: HookCommandOptions = {},\n): Promise<HookCommandResult> {\n  const bundled = resolveHookScriptPath(options);\n  if (!bundled.ok) {\n    return { stdout: \"\", stderr: `almanac: ${bundled.error}\\n`, exitCode: 1 };\n  }\n\n  // Copy the bundled hook script to a stable user-owned location before\n  // writing that path into settings.json. This is the Bug #1 fix:\n  //\n  //   OLD behavior: settings.json pointed at the bundled path (inside\n  //   ~/.nvm/versions/node/<ver>/lib/node_modules/codealmanac/hooks/... or\n  //   ~/.npm/_npx/<sha>/node_modules/codealmanac/hooks/...). When the user\n  //   switches Node versions or the npx cache is evicted, the path breaks\n  //   silently and captures stop firing.\n  //\n  //   NEW behavior: we copy almanac-capture.sh to ~/.claude/hooks/ (same\n  //   directory Claude Code uses for its own built-in hooks, always present)\n  //   and point settings.json there. The stable path is independent of\n  //   Node version and npm cache state. When the user upgrades codealmanac,\n  //   `almanac hook install` copies a fresh script and updates settings.json\n  //   if the path changed.\n  //\n  // When `hookScriptPath` is explicitly provided (test injection), the\n  // caller has already specified the destination path — skip the copy and\n  // use that path directly. The stable-copy concern only applies to the\n  // production flow where we resolved from the bundled package layout.\n  const script: ScriptResolution = options.hookScriptPath !== undefined\n    ? bundled // already the caller-provided path, no copy needed\n    : await copyToStableHooksDir(bundled.path, options);\n  if (!script.ok) {\n    return { stdout: \"\", stderr: `almanac: ${script.error}\\n`, exitCode: 1 };\n  }\n\n  const source = options.source ?? \"claude\";\n  if (source === \"all\") {\n    const results = [\n      await installClaudeHook(options, script.path),\n      await installGenericHook({\n        label: \"Codex Stop\",\n        settingsPath: path.join(homedir(), \".codex\", \"hooks.json\"),\n        eventName: \"Stop\",\n        shape: \"wrapped\",\n        scriptPath: script.path,\n      }),\n    ];\n    if (isCursorEnabled()) {\n      results.push(await installGenericHook({\n        label: \"Cursor sessionEnd\",\n        settingsPath: path.join(homedir(), \".cursor\", \"hooks.json\"),\n        eventName: \"sessionEnd\",\n        shape: \"flat\",\n        scriptPath: script.path,\n      }));\n    }\n    const failed = results.find((r) => r.exitCode !== 0);\n    if (failed !== undefined) return failed;\n    return {\n      stdout: results.map((r) => r.stdout.trimEnd()).join(\"\\n\") + \"\\n\",\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n  if (source === \"codex\") {\n    return await installGenericHook({\n      label: \"Codex Stop\",\n      settingsPath: path.join(homedir(), \".codex\", \"hooks.json\"),\n      eventName: \"Stop\",\n      shape: \"wrapped\",\n      scriptPath: script.path,\n    });\n  }\n  if (source === \"cursor\") {\n    if (!isCursorEnabled()) {\n      return {\n        stdout: \"\",\n        stderr:\n          \"almanac: cursor hooks are disabled. Set CODEALMANAC_ENABLE_CURSOR=1 to enable experimental Cursor support.\\n\",\n        exitCode: 1,\n      };\n    }\n    return await installGenericHook({\n      label: \"Cursor sessionEnd\",\n      settingsPath: path.join(homedir(), \".cursor\", \"hooks.json\"),\n      eventName: \"sessionEnd\",\n      shape: \"flat\",\n      scriptPath: script.path,\n    });\n  }\n\n  return await installClaudeHook(options, script.path);\n}\n\nasync function installClaudeHook(\n  options: HookCommandOptions,\n  scriptPath: string,\n): Promise<HookCommandResult> {\n\n  const settingsPath = resolveSettingsPath(options);\n  const settings = await readSettings(settingsPath);\n  const existing = (settings.hooks?.SessionEnd ?? []).slice();\n\n  // Walk existing entries and split them into buckets:\n  //   - `preserved`  — foreign wrapped/unknown entries we leave alone.\n  //   - `oursAlready` — a wrapped entry that already points at OUR exact\n  //                     script path (makes install a no-op).\n  //   - `oursStale`   — a wrapped or legacy entry that references our\n  //                     capture script but at a different absolute path\n  //                     (old install, `npm i` moved us) or in the legacy\n  //                     unwrapped shape. We'll collapse these into a\n  //                     single fresh entry at the new path.\n  const preserved: RawEntry[] = [];\n  let oursAlready: WrappedEntry | null = null;\n  const staleCount = { n: 0 };\n\n  for (const raw of existing) {\n    const c = classifyEntry(raw);\n    if (c.kind === \"wrapped\") {\n      if (!isOurWrapped(c.entry)) {\n        preserved.push(raw);\n        continue;\n      }\n      // Entry belongs to us. Does it already point at the exact script\n      // path? If every command in its `hooks[]` that looks like ours is\n      // already at `script.path`, it's up to date.\n      const exactMatch = c.entry.hooks.some(\n        (h) => h.command === scriptPath,\n      );\n      if (exactMatch && oursAlready === null) {\n        oursAlready = c.entry;\n      } else {\n        staleCount.n += 1;\n      }\n    } else if (c.kind === \"legacy\") {\n      if (isOurCommandPath(c.entry.command)) {\n        // Legacy unwrapped entry of ours — always migrate to wrapped.\n        staleCount.n += 1;\n      } else {\n        // Foreign legacy entry (user had their own script before\n        // settings.json required wrapping). Leave it alone.\n        preserved.push(raw);\n      }\n    } else {\n      // Unknown shape — we can't classify it. Preserve verbatim.\n      preserved.push(raw);\n    }\n  }\n\n  // If every non-ours entry is a foreign unwrapped command (not a\n  // wrapped one) we refuse to touch the file — Claude Code's newer\n  // schema will already reject such files, but surfacing it here lets\n  // the user clean up before we stack our entry on top. Wrapped foreign\n  // entries are fine to leave alongside ours.\n  const foreignLegacy = preserved.filter((raw) => {\n    const c = classifyEntry(raw);\n    return c.kind === \"legacy\";\n  });\n  if (foreignLegacy.length > 0) {\n    const lines = foreignLegacy\n      .map((raw) => {\n        const c = classifyEntry(raw);\n        if (c.kind === \"legacy\") return `  - ${c.entry.command}`;\n        return \"  - <unrecognized>\";\n      })\n      .join(\"\\n\");\n    return {\n      stdout: \"\",\n      stderr:\n        `almanac: SessionEnd has a foreign legacy entry:\\n${lines}\\n` +\n        `Remove or rewrap it manually in ${settingsPath} before installing.\\n`,\n      exitCode: 1,\n    };\n  }\n\n  if (oursAlready !== null && staleCount.n === 0) {\n    return {\n      stdout: `almanac: SessionEnd hook already installed at ${scriptPath}\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  // Build the fresh wrapped entry and append to preserved foreign\n  // entries. Stale entries of ours are dropped (we only ever want a\n  // single active entry; multiple copies of the capture hook would\n  // double-fire on session end).\n  const fresh: WrappedEntry = {\n    matcher: \"\",\n    hooks: [\n        {\n          type: \"command\",\n          command: scriptPath,\n          timeout: HOOK_TIMEOUT_SECONDS,\n        },\n    ],\n  };\n\n  const newEntries: RawEntry[] = [...preserved, fresh];\n\n  settings.hooks = { ...(settings.hooks ?? {}), SessionEnd: newEntries };\n  await writeSettings(settingsPath, settings);\n\n  return {\n    stdout:\n      `almanac: SessionEnd hook installed\\n` +\n      `  script: ${scriptPath}\\n` +\n      `  settings: ${settingsPath}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\nasync function installGenericHook(args: {\n  label: string;\n  settingsPath: string;\n  eventName: string;\n  shape: \"flat\" | \"wrapped\";\n  scriptPath: string;\n}): Promise<HookCommandResult> {\n  const settings = await readSettings(args.settingsPath);\n  const hooksObj =\n    settings.hooks !== undefined &&\n    settings.hooks !== null &&\n    typeof settings.hooks === \"object\"\n      ? settings.hooks\n      : {};\n  const existing = Array.isArray(hooksObj[args.eventName])\n    ? (hooksObj[args.eventName] as RawEntry[])\n    : [];\n  const kept = existing.filter((entry) => !entryHasOurCommand(entry));\n  const already = existing.some((entry) =>\n    entryHasExactCommand(entry, args.scriptPath),\n  );\n  if (already && kept.length === existing.length - 1) {\n    return {\n      stdout: `almanac: ${args.label} hook already installed at ${args.scriptPath}\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n  const fresh =\n    args.shape === \"wrapped\"\n      ? {\n          hooks: [\n            {\n              type: \"command\",\n              command: args.scriptPath,\n              timeout: HOOK_TIMEOUT_SECONDS,\n            },\n          ],\n        }\n      : {\n          command: args.scriptPath,\n          timeout: HOOK_TIMEOUT_SECONDS,\n        };\n  hooksObj[args.eventName] = [\n    ...kept,\n    fresh,\n  ];\n  settings.hooks = hooksObj;\n  await writeSettings(args.settingsPath, settings);\n  if (args.label.startsWith(\"Codex \")) {\n    await ensureCodexHooksFeature(path.join(homedir(), \".codex\", \"config.toml\"));\n  }\n  return {\n    stdout:\n      `almanac: ${args.label} hook installed\\n` +\n      `  script: ${args.scriptPath}\\n` +\n      `  settings: ${args.settingsPath}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\nfunction entryHasOurCommand(entry: unknown): boolean {\n  return collectHookCommands(entry).some(isOurCommandPath);\n}\n\nfunction entryHasExactCommand(entry: unknown, command: string): boolean {\n  return collectHookCommands(entry).some((candidate) => candidate === command);\n}\n\nfunction collectHookCommands(entry: unknown): string[] {\n  if (entry === null || typeof entry !== \"object\") return [];\n  const obj = entry as Record<string, unknown>;\n  const direct = typeof obj.command === \"string\" ? [obj.command] : [];\n  const nested = Array.isArray(obj.hooks)\n    ? obj.hooks.flatMap((hook) => collectHookCommands(hook))\n    : [];\n  return [...direct, ...nested];\n}\n\nasync function ensureCodexHooksFeature(configPath: string): Promise<void> {\n  let body = \"\";\n  if (existsSync(configPath)) {\n    body = await readFile(configPath, \"utf8\");\n  }\n  if (/^\\s*codex_hooks\\s*=\\s*true\\s*$/m.test(body)) return;\n\n  const next = setTomlFeatureFlag(body, \"codex_hooks\", true);\n  await mkdir(path.dirname(configPath), { recursive: true });\n  const tmp = `${configPath}.almanac-tmp-${process.pid}`;\n  await writeFile(tmp, next.endsWith(\"\\n\") ? next : `${next}\\n`, \"utf8\");\n  await rename(tmp, configPath);\n}\n\nfunction setTomlFeatureFlag(\n  body: string,\n  key: string,\n  value: boolean,\n): string {\n  const desired = `${key} = ${value ? \"true\" : \"false\"}`;\n  const lines = body.split(/\\r?\\n/);\n  let featuresStart = -1;\n  let featuresEnd = lines.length;\n\n  for (let i = 0; i < lines.length; i++) {\n    if (/^\\s*\\[features\\]\\s*$/.test(lines[i] ?? \"\")) {\n      featuresStart = i;\n      continue;\n    }\n    if (featuresStart !== -1 && i > featuresStart && /^\\s*\\[.*\\]\\s*$/.test(lines[i] ?? \"\")) {\n      featuresEnd = i;\n      break;\n    }\n  }\n\n  if (featuresStart === -1) {\n    const prefix = body.trim().length === 0 ? \"\" : `${body.trimEnd()}\\n\\n`;\n    return `${prefix}[features]\\n${desired}\\n`;\n  }\n\n  const keyPattern = new RegExp(`^\\\\s*${escapeRegex(key)}\\\\s*=`);\n  for (let i = featuresStart + 1; i < featuresEnd; i++) {\n    if (keyPattern.test(lines[i] ?? \"\")) {\n      lines[i] = desired;\n      return lines.join(\"\\n\");\n    }\n  }\n\n  lines.splice(featuresStart + 1, 0, desired);\n  return lines.join(\"\\n\");\n}\n\nfunction escapeRegex(value: string): string {\n  return value.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n}\n\nexport async function runHookUninstall(\n  options: HookCommandOptions = {},\n): Promise<HookCommandResult> {\n  const settingsPath = resolveSettingsPath(options);\n\n  if (!existsSync(settingsPath)) {\n    return {\n      stdout: `almanac: SessionEnd hook not installed (no settings file)\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  const settings = await readSettings(settingsPath);\n  const existing = (settings.hooks?.SessionEnd ?? []).slice();\n\n  const kept: RawEntry[] = [];\n  let removed = 0;\n\n  for (const raw of existing) {\n    const c = classifyEntry(raw);\n    if (c.kind === \"wrapped\") {\n      // Filter out our command(s) from the inner hooks array. Keep\n      // anything else in the array intact — a foreign wrapper that\n      // happened to include our script alongside its own commands\n      // (unusual, but survivable) loses our entry and keeps theirs.\n      const innerKept = c.entry.hooks.filter(\n        (h) => !isOurCommandPath(h.command),\n      );\n      const innerRemoved = c.entry.hooks.length - innerKept.length;\n      removed += innerRemoved;\n      if (innerKept.length === 0) {\n        // Only drop the outer wrapper when it was entirely ours. A\n        // foreign wrapper that never contained our script stays verbatim\n        // below (handled by `innerRemoved === 0`, which leaves\n        // `innerKept.length === c.entry.hooks.length`, hence we fall\n        // through to the else-branch).\n        if (innerRemoved === 0) kept.push(raw);\n        // else: fully owned by us, drop the container.\n      } else if (innerRemoved === 0) {\n        // Untouched foreign wrapper — preserve the raw object to keep\n        // any fields (like matcher) byte-for-byte.\n        kept.push(raw);\n      } else {\n        // Partial: rebuild with just the kept inner entries, preserving\n        // the original matcher string.\n        kept.push({ matcher: c.entry.matcher, hooks: innerKept });\n      }\n    } else if (c.kind === \"legacy\") {\n      if (isOurCommandPath(c.entry.command)) {\n        removed += 1;\n      } else {\n        kept.push(raw);\n      }\n    } else {\n      kept.push(raw);\n    }\n  }\n\n  if (removed === 0) {\n    return {\n      stdout: `almanac: SessionEnd hook not installed\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  if (settings.hooks !== undefined) {\n    if (kept.length === 0) {\n      // Empty SessionEnd array confuses some linters; drop the key when\n      // nothing's left.\n      const { SessionEnd: _dropped, ...rest } = settings.hooks;\n      void _dropped;\n      settings.hooks = rest;\n    } else {\n      settings.hooks = { ...settings.hooks, SessionEnd: kept };\n    }\n\n    // If `hooks` itself is now empty (user had only our SessionEnd entry\n    // and no other hook categories), drop the `hooks` key entirely so\n    // uninstall leaves the settings file in the same shape it would be\n    // in had we never run install. An empty `\"hooks\": {}` is an obvious\n    // breadcrumb in commit diffs.\n    if (Object.keys(settings.hooks).length === 0) {\n      delete settings.hooks;\n    }\n  }\n\n  await writeSettings(settingsPath, settings);\n\n  return {\n    stdout: `almanac: SessionEnd hook removed\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\nexport async function runHookStatus(\n  options: HookCommandOptions = {},\n): Promise<HookCommandResult> {\n  const script = resolveHookScriptPath(options);\n  const settingsPath = resolveSettingsPath(options);\n\n  if (!existsSync(settingsPath)) {\n    return {\n      stdout:\n        `SessionEnd hook: not installed\\n` +\n        `settings: ${settingsPath} (does not exist)\\n` +\n        (script.ok ? `script would be: ${script.path}\\n` : \"\"),\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  const settings = await readSettings(settingsPath);\n  const existing = settings.hooks?.SessionEnd ?? [];\n\n  // Walk the array looking for any entry (wrapped or legacy) that\n  // references our capture script. Gathering foreign entries separately\n  // lets us show them to the user if nothing of ours was found.\n  let ourCommand: string | null = null;\n  const foreignSummary: string[] = [];\n  for (const raw of existing) {\n    const c = classifyEntry(raw);\n    if (c.kind === \"wrapped\") {\n      for (const h of c.entry.hooks) {\n        if (isOurCommandPath(h.command)) {\n          ourCommand ??= h.command;\n        } else {\n          foreignSummary.push(h.command);\n        }\n      }\n    } else if (c.kind === \"legacy\") {\n      if (isOurCommandPath(c.entry.command)) {\n        ourCommand ??= c.entry.command;\n      } else {\n        foreignSummary.push(c.entry.command);\n      }\n    }\n  }\n\n  if (ourCommand === null) {\n    const foreignLines = foreignSummary\n      .map((c) => `  - ${c}`)\n      .join(\"\\n\");\n    return {\n      stdout:\n        `SessionEnd hook: not installed\\n` +\n        `settings: ${settingsPath}\\n` +\n        (foreignSummary.length > 0\n          ? `(${foreignSummary.length} foreign entr${foreignSummary.length === 1 ? \"y\" : \"ies\"} present:\\n${foreignLines})\\n`\n          : \"\") +\n        (script.ok ? `script would be: ${script.path}\\n` : \"\"),\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  return {\n    stdout:\n      `SessionEnd hook: installed\\n` +\n      `script: ${ourCommand}\\n` +\n      `settings: ${settingsPath}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\n// ─── Settings JSON helpers ───────────────────────────────────────────\n\nasync function readSettings(settingsPath: string): Promise<SettingsJson> {\n  if (!existsSync(settingsPath)) return {};\n  try {\n    const raw = await readFile(settingsPath, \"utf8\");\n    if (raw.trim().length === 0) return {};\n    const parsed = JSON.parse(raw) as unknown;\n    if (parsed === null || typeof parsed !== \"object\") return {};\n    return parsed as SettingsJson;\n  } catch (err: unknown) {\n    const msg = err instanceof Error ? err.message : String(err);\n    throw new Error(`failed to read ${settingsPath}: ${msg}`);\n  }\n}\n\nasync function writeSettings(\n  settingsPath: string,\n  settings: SettingsJson,\n): Promise<void> {\n  const dir = path.dirname(settingsPath);\n  await mkdir(dir, { recursive: true });\n\n  // Atomic write: JSON.stringify → tmp file → rename. `rename` within the\n  // same filesystem is atomic on POSIX; Claude Code never sees a partial\n  // file. Formatted with 2-space indent to match the existing settings.\n  const tmp = `${settingsPath}.almanac-tmp-${process.pid}`;\n  const body = `${JSON.stringify(settings, null, 2)}\\n`;\n  await writeFile(tmp, body, \"utf8\");\n  await rename(tmp, settingsPath);\n}\n","import { existsSync } from \"node:fs\";\nimport { copyFile, mkdir, readFile } from \"node:fs/promises\";\nimport { homedir } from \"node:os\";\nimport path from \"node:path\";\nimport { fileURLToPath } from \"node:url\";\n\nexport interface HookPathOptions {\n  hookScriptPath?: string;\n  settingsPath?: string;\n  stableHooksDir?: string;\n}\n\nexport type ScriptResolution =\n  | { ok: true; path: string }\n  | { ok: false; error: string };\n\nexport function resolveSettingsPath(options: HookPathOptions): string {\n  if (options.settingsPath !== undefined) return options.settingsPath;\n  return path.join(homedir(), \".claude\", \"settings.json\");\n}\n\n/**\n * Copy the bundled hook script to `~/.claude/hooks/almanac-capture.sh`.\n *\n * This stable, user-owned destination survives Node version switches and\n * npm/npx cache evictions. The copy is idempotent: if bytes already match\n * we skip writing so repeated setup runs do not bump mtimes.\n */\nexport async function copyToStableHooksDir(\n  bundledPath: string,\n  options: HookPathOptions,\n): Promise<ScriptResolution> {\n  const stableHooksDir =\n    options.stableHooksDir ?? path.join(homedir(), \".claude\", \"hooks\");\n  const dest = path.join(stableHooksDir, \"almanac-capture.sh\");\n\n  try {\n    await mkdir(stableHooksDir, { recursive: true });\n    const srcBytes = await readFile(bundledPath);\n    let needsCopy = true;\n    if (existsSync(dest)) {\n      try {\n        const destBytes = await readFile(dest);\n        if (srcBytes.equals(destBytes)) needsCopy = false;\n      } catch {\n        // Can't read dest — overwrite.\n      }\n    }\n    if (needsCopy) {\n      await copyFile(bundledPath, dest);\n    }\n    return { ok: true, path: dest };\n  } catch (err: unknown) {\n    const msg = err instanceof Error ? err.message : String(err);\n    return {\n      ok: false,\n      error: `could not copy hook script to ${dest}: ${msg}`,\n    };\n  }\n}\n\n/**\n * Locate the bundled `hooks/almanac-capture.sh`. 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