codealmanac 0.2.5 → 0.2.7

package/dist/register-commands-LULZUSPO.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/topics/frontmatter-rewrite.ts","../src/topics/paths.ts","../src/commands/tag.ts","../src/commands/topics/workspace.ts","../src/commands/topics/create.ts","../src/commands/topics/page-rewrite.ts","../src/commands/topics/delete.ts","../src/commands/topics/describe.ts","../src/commands/topics/link.ts","../src/commands/topics/list.ts","../src/commands/topics/rename.ts","../src/commands/topics/read.ts","../src/commands/topics/show.ts","../src/commands/topics/unlink.ts","../src/registry/autoregister.ts","../src/cli/register-edit-commands.ts","../src/commands/list.ts","../src/commands/search.ts","../src/commands/show.ts","../src/cli/register-query-commands.ts","../src/cli/register-setup-commands.ts","../src/commands/jobs.ts","../src/cli/outcome.ts","../src/commands/operations.ts","../src/agent/prompts.ts","../src/operations/run.ts","../src/operations/absorb.ts","../src/operations/build.ts","../src/commands/init.ts","../src/operations/garden.ts","../src/commands/session-transcripts.ts","../src/commands/reindex.ts","../src/cli/register-wiki-lifecycle-commands.ts","../src/cli/register-commands.ts"],"sourcesContent":["import { readFile, rename, writeFile } from \"node:fs/promises\";\n\nimport yaml from \"js-yaml\";\n\n/**\n * Rewrite the `topics:` field in a markdown file's YAML frontmatter.\n *\n * The absolute requirement is **body byte-preservation**. Tag/untag/\n * rename commands touch only the frontmatter; everything after the\n * closing `---` must be byte-identical to the input (same line endings,\n * same trailing whitespace, same final-newline-or-not). We lean on a\n * precise split rather than re-serializing the whole file so any\n * incidental bytes in the body (literal `\\r\\n`, unusual trailing\n * whitespace, triple-hyphen rulers) are left alone.\n *\n * For the frontmatter itself we do a **surgical rewrite of the `topics:`\n * field only** — not a full YAML roundtrip. Reasons:\n *   - `js-yaml` normalizes quoting, re-orders keys alphabetically by\n *     default, and can drop comments. Any of those would surprise a user\n *     who hand-edited their own frontmatter and expects their formatting\n *     preserved byte-for-byte.\n *   - We only care about one field. Replacing just that field lets the\n *     rest of the YAML survive verbatim.\n *\n * The strategy:\n *   1. Find the exact span of the `topics:` key (whether flow\n *      `topics: [a, b]` or block `topics:\\n  - a\\n  - b\\n`) using a\n *      small line scanner.\n *   2. Compute the new topics list from the caller's transform.\n *   3. Replace the span with a freshly-emitted `topics: [a, b, c]` line\n *      (flow style — compact, readable, and what most authors write).\n *   4. If no `topics:` key exists and the new list is non-empty, append\n *      a line to the end of the frontmatter block.\n *   5. If `topics:` exists but the new list is empty, drop the line\n *      entirely rather than leaving `topics: []` around.\n *\n * The transform function gets the current deduplicated topic list and\n * returns the new list. Returning an empty array means \"remove the\n * `topics:` key entirely\".\n */\n\nexport interface RewriteResult {\n  /** The page's topics before the rewrite (possibly empty). */\n  before: string[];\n  /** The page's topics after the rewrite (possibly empty). */\n  after: string[];\n  /** True iff the file content actually changed. */\n  changed: boolean;\n}\n\n/**\n * Read `filePath`, compute the new topics via `transform`, and\n * atomically rewrite if the result differs.\n *\n * Atomic per file: write to `<path>.tmp` then rename, same pattern as\n * the registry and topics.yaml writers. A half-written page would\n * corrupt committed user content, so this is non-negotiable.\n */\nexport async function rewritePageTopics(\n  filePath: string,\n  transform: (current: string[]) => string[],\n): Promise<RewriteResult> {\n  const raw = await readFile(filePath, \"utf8\");\n  const { before, after, output, changed } = applyTopicsTransform(\n    raw,\n    transform,\n  );\n  if (changed) {\n    const tmp = `${filePath}.tmp`;\n    await writeFile(tmp, output, \"utf8\");\n    await rename(tmp, filePath);\n  }\n  return { before, after, changed };\n}\n\ninterface TransformApplied {\n  before: string[];\n  after: string[];\n  output: string;\n  changed: boolean;\n}\n\n/**\n * Pure-string version of `rewritePageTopics`. Useful for tests and for\n * the few places (rename, delete) where we loop many files and want to\n * short-circuit no-op writes cheaply.\n */\nexport function applyTopicsTransform(\n  raw: string,\n  transform: (current: string[]) => string[],\n): TransformApplied {\n  const parsed = splitFrontmatter(raw);\n  if (parsed === null) {\n    // No frontmatter at all. Tagging a topic on such a page means\n    // creating a frontmatter block. We keep the body untouched and\n    // prepend `---\\ntopics: [...]\\n---\\n\\n`. If the transform yields\n    // an empty list, this is a no-op. Line endings: default to LF for a\n    // brand-new frontmatter — we can't infer intent from a file that\n    // doesn't have frontmatter yet, and LF is the committed default in\n    // most modern repos.\n    const next = dedupeSlugs(transform([]));\n    if (next.length === 0) {\n      return { before: [], after: [], output: raw, changed: false };\n    }\n    const fm = `---\\ntopics: ${flowList(next)}\\n---\\n\\n`;\n    return {\n      before: [],\n      after: next,\n      output: `${fm}${raw}`,\n      changed: true,\n    };\n  }\n\n  const { opener, fmLines, closer, body, eol } = parsed;\n  const { before, existingRange } = readTopicsFromLines(fmLines);\n  const beforeDeduped = dedupeSlugs(before);\n  const after = dedupeSlugs(transform(beforeDeduped));\n\n  if (arraysEqual(beforeDeduped, after)) {\n    return { before: beforeDeduped, after, output: raw, changed: false };\n  }\n\n  let nextFmLines: string[];\n  if (existingRange === null) {\n    // No `topics:` key currently present. Add one (only if non-empty).\n    if (after.length === 0) {\n      return { before: beforeDeduped, after, output: raw, changed: false };\n    }\n    nextFmLines = [...fmLines, `topics: ${flowList(after)}`];\n  } else {\n    const replacement =\n      after.length === 0 ? null : `topics: ${flowList(after)}`;\n    // Interleaved comments/blank lines from a block-style list are\n    // re-emitted BELOW the new flow-style `topics:` line so the\n    // author's commentary sticks around. Flow/scalar inputs produce an\n    // empty `preserved` array, so this collapses to the old behavior\n    // for the common case. When we fully delete the key (empty after)\n    // the preserved lines go too — without a `topics:` key to anchor\n    // them to, trailing \"# below the topics list\" comments become\n    // orphans that no longer mean what they said.\n    const preservedTail =\n      replacement === null ? [] : existingRange.preserved;\n    nextFmLines = [\n      ...fmLines.slice(0, existingRange.start),\n      ...(replacement === null ? [] : [replacement]),\n      ...preservedTail,\n      ...fmLines.slice(existingRange.end),\n    ];\n  }\n\n  // Rejoin with the same line ending the input frontmatter used so a\n  // CRLF-authored file comes out CRLF end-to-end. `splitFrontmatter`\n  // sniffed the dominant separator for us.\n  const fmBlock =\n    nextFmLines.length === 0 ? \"\" : `${nextFmLines.join(eol)}${eol}`;\n  const output = `${opener}${fmBlock}${closer}${body}`;\n  return {\n    before: beforeDeduped,\n    after,\n    output,\n    changed: true,\n  };\n}\n\ninterface SplitFrontmatter {\n  /** The opening `---\\n` or `---\\r\\n`. */\n  opener: string;\n  /** Frontmatter lines (no line-ending character included). */\n  fmLines: string[];\n  /** The closing `---\\n` (or `---\\r\\n`, possibly without trailing newline if EOF). */\n  closer: string;\n  /** Everything after the closing fence, byte-for-byte. */\n  body: string;\n  /**\n   * Dominant line ending inside the frontmatter block. CRLF-authored\n   * files stay CRLF on write; LF stays LF. We sniff once at split time\n   * so rewriting doesn't have to re-inspect every line.\n   */\n  eol: \"\\n\" | \"\\r\\n\";\n}\n\n/**\n * Split a file into (opener, frontmatter lines, closer, body). The\n * regex mirrors `parseFrontmatter` in `indexer/frontmatter.ts` so the\n * indexer and the rewriter agree on what \"has frontmatter\" means.\n *\n * Returns `null` when the file doesn't start with a `---` fence or\n * lacks a matching closer — both cases are legal (a page with only\n * body content) and the caller treats them as \"no frontmatter to\n * rewrite\".\n */\nfunction splitFrontmatter(raw: string): SplitFrontmatter | null {\n  if (!raw.startsWith(\"---\")) return null;\n  // Match the exact opener (with its line ending) so we can preserve\n  // it byte-for-byte.\n  const openerMatch = raw.match(/^---(\\r?\\n)/);\n  if (openerMatch === null) return null;\n  const opener = `---${openerMatch[1] ?? \"\\n\"}`;\n  const rest = raw.slice(opener.length);\n  // Find the closing `---` that begins at the start of a line. We\n  // also handle the edge case where the closer sits at position 0 of\n  // `rest` (frontmatter was empty).\n  let fenceIdx: number;\n  if (rest.startsWith(\"---\")) {\n    fenceIdx = 0;\n  } else {\n    const m = rest.match(/\\r?\\n---(\\r?\\n|$)/);\n    if (m === null || m.index === undefined) return null;\n    // `m.index` points at the `\\r?\\n` before `---`; skip that newline\n    // so fenceIdx lands exactly on the `-`.\n    const leadingNewlineLen = (m[0] ?? \"\").startsWith(\"\\r\\n\") ? 2 : 1;\n    fenceIdx = m.index + leadingNewlineLen;\n  }\n  const fmBlock = rest.slice(0, fenceIdx);\n  // Determine the closer's full span, including its trailing newline if any.\n  const afterDashes = rest.slice(fenceIdx + 3);\n  let closerTail = \"\";\n  if (afterDashes.startsWith(\"\\r\\n\")) {\n    closerTail = \"\\r\\n\";\n  } else if (afterDashes.startsWith(\"\\n\")) {\n    closerTail = \"\\n\";\n  }\n  const closer = `---${closerTail}`;\n  const body = afterDashes.slice(closerTail.length);\n  const fmLines =\n    fmBlock.length === 0 ? [] : fmBlock.replace(/\\r?\\n$/, \"\").split(/\\r?\\n/);\n  // Sniff the frontmatter's dominant line ending. We look at the\n  // opener first (most reliable signal — it's always present and\n  // always has an ending). Fall back to checking the fmBlock for any\n  // `\\r\\n` runs so a frontmatter with a single-line opener and\n  // multi-line body still gets classified right.\n  const eol: \"\\n\" | \"\\r\\n\" =\n    opener.endsWith(\"\\r\\n\") || /\\r\\n/.test(fmBlock) ? \"\\r\\n\" : \"\\n\";\n  return { opener, fmLines, closer, body, eol };\n}\n\ninterface ExistingRange {\n  /** Index in `fmLines` of the `topics:` key line (inclusive). */\n  start: number;\n  /** Index in `fmLines` one past the last line belonging to this key. */\n  end: number;\n  /**\n   * Lines inside `[start+1, end)` that aren't `- entry` lines — i.e.\n   * interleaved comments and blank lines a user wrote between entries.\n   * We preserve these verbatim when rewriting block-style lists to\n   * flow; otherwise a `tag` on a commented list would silently drop\n   * the commentary. Empty for flow/scalar shapes.\n   */\n  preserved: string[];\n}\n\n/**\n * Find `topics:` in a frontmatter-lines array and read the values.\n *\n * Handles three YAML shapes authors commonly write:\n *   - `topics: [a, b, c]`       (flow sequence, one line)\n *   - `topics:` followed by block entries like `  - a` (block sequence)\n *   - `topics: a` (a single scalar — treated as one element)\n *\n * Also handles the empty case `topics:` with nothing after it, and the\n * \"no topics key\" case (returns `existingRange: null`).\n *\n * This is NOT a general YAML parser — it's intentionally scoped to the\n * one key we mutate, because using `js-yaml` for a round-trip would\n * lose comments and re-quote strings the user picked a specific way.\n */\nfunction readTopicsFromLines(fmLines: string[]): {\n  before: string[];\n  existingRange: ExistingRange | null;\n} {\n  const keyLineIdx = findTopKey(fmLines, \"topics\");\n  if (keyLineIdx === -1) {\n    return { before: [], existingRange: null };\n  }\n  const keyLine = fmLines[keyLineIdx] ?? \"\";\n  const colonIdx = keyLine.indexOf(\":\");\n  // Everything to the right of the first colon, trimmed.\n  const after = keyLine.slice(colonIdx + 1).trim();\n  // Strip trailing `# ...` line-comment from a flow value so we don't\n  // parse comments as list contents. (A block list's sub-items have\n  // their own comments stripped in the block branch below.)\n  const afterNoComment = stripTrailingComment(after);\n\n  if (afterNoComment.length === 0) {\n    // Block sequence style: collect subsequent `- item` lines. Between\n    // entries a user may have written:\n    //   - interleaved `# comment` lines\n    //   - blank lines\n    // We must NOT break the scan on those — doing so would drop every\n    // entry after the first comment/blank when we rewrite (silent data\n    // loss: the original bug that triggered this fix). We skip them in\n    // the scan and stash them in `preserved` so the replacement step\n    // can re-emit them verbatim BETWEEN the new flow-style line and\n    // the rest of the frontmatter.\n    //\n    // Edge: comments/blanks that appear BEFORE the first `- entry` or\n    // AFTER the last `- entry` count as part of the block too — pulling\n    // them out keeps the author's commentary near the list it belongs\n    // to. We cap the scan when we hit a real non-entry line (e.g. the\n    // next top-level key), leaving everything from that line onward\n    // outside the range.\n    const values: string[] = [];\n    const preserved: string[] = [];\n    // Provisional scan cursor. `endIdx` only advances when we've seen\n    // something we're sure belongs to this block (an entry line), so\n    // trailing whitespace/comments that don't precede another entry\n    // stay OUTSIDE the range and aren't shuffled on rewrite.\n    let i = keyLineIdx + 1;\n    let endIdx = i;\n    // `pendingNonEntries` holds comments/blanks we've seen since the\n    // last confirmed entry. They're committed to `preserved` only\n    // when a subsequent `- entry` proves they live mid-list.\n    let pendingNonEntries: string[] = [];\n    while (i < fmLines.length) {\n      const line = fmLines[i] ?? \"\";\n      const trimmed = line.trim();\n      if (trimmed.length === 0 || trimmed.startsWith(\"#\")) {\n        pendingNonEntries.push(line);\n        i += 1;\n        continue;\n      }\n      const m = line.match(/^\\s*-\\s+(.*)$/);\n      if (m === null) break;\n      // Promote any pending comments/blanks — they're between entries\n      // (or before the first entry within the block).\n      if (pendingNonEntries.length > 0) {\n        preserved.push(...pendingNonEntries);\n        pendingNonEntries = [];\n      }\n      const raw = stripTrailingComment((m[1] ?? \"\").trim());\n      const parsed = parseScalar(raw);\n      if (parsed.length > 0) values.push(parsed);\n      i += 1;\n      endIdx = i;\n    }\n    return {\n      before: values,\n      existingRange: { start: keyLineIdx, end: endIdx, preserved },\n    };\n  }\n\n  // Flow / scalar shape on one line. Let js-yaml handle the value-parsing\n  // (quoting, escapes, etc.) for the RHS only.\n  let parsed: unknown;\n  try {\n    parsed = yaml.load(afterNoComment);\n  } catch {\n    parsed = null;\n  }\n  const values: string[] = [];\n  if (Array.isArray(parsed)) {\n    for (const v of parsed) {\n      if (typeof v === \"string\" && v.trim().length > 0) {\n        values.push(v.trim());\n      }\n    }\n  } else if (typeof parsed === \"string\" && parsed.trim().length > 0) {\n    values.push(parsed.trim());\n  }\n  return {\n    before: values,\n    existingRange: { start: keyLineIdx, end: keyLineIdx + 1, preserved: [] },\n  };\n}\n\n/**\n * Find a top-level key line. \"Top-level\" means no leading whitespace —\n * we don't walk into nested mappings. The indexer's frontmatter parser\n * only reads top-level keys too, so this matches.\n */\nfunction findTopKey(fmLines: string[], key: string): number {\n  const re = new RegExp(`^${escapeRegex(key)}\\\\s*:`);\n  for (let i = 0; i < fmLines.length; i += 1) {\n    if (re.test(fmLines[i] ?? \"\")) return i;\n  }\n  return -1;\n}\n\nfunction escapeRegex(s: string): string {\n  return s.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n}\n\nfunction stripTrailingComment(s: string): string {\n  // Only strip `#` outside of quotes. For the shapes we handle —\n  // slug-like kebab-case topics — quoted strings with `#` are rare, but\n  // be defensive.\n  let inSingle = false;\n  let inDouble = false;\n  for (let i = 0; i < s.length; i += 1) {\n    const ch = s[i];\n    if (ch === \"'\" && !inDouble) inSingle = !inSingle;\n    else if (ch === '\"' && !inSingle) inDouble = !inDouble;\n    else if (ch === \"#\" && !inSingle && !inDouble) {\n      return s.slice(0, i).trimEnd();\n    }\n  }\n  return s;\n}\n\n/**\n * Strip YAML quoting from a scalar. Block-sequence items might be\n * written as `- 'foo'` or `- \"foo\"` or bare `- foo`; we accept all\n * three and return the plain string.\n */\nfunction parseScalar(s: string): string {\n  if (s.length === 0) return s;\n  if (s.length >= 2 && s[0] === '\"' && s[s.length - 1] === '\"') {\n    return s.slice(1, -1);\n  }\n  if (s.length >= 2 && s[0] === \"'\" && s[s.length - 1] === \"'\") {\n    return s.slice(1, -1);\n  }\n  return s;\n}\n\n/**\n * Emit a flow-style YAML sequence like `[auth, jwt, security]`. We use\n * flow because it's the shape most authors write by hand and stays on\n * one line, which keeps diffs tight. Values are quoted only when\n * necessary — plain kebab-case slugs never need quoting.\n */\nfunction flowList(items: string[]): string {\n  return `[${items.map((t) => formatScalar(t)).join(\", \")}]`;\n}\n\nfunction formatScalar(s: string): string {\n  // If it's a bare kebab/alnum slug, no quotes. Otherwise fall back to\n  // js-yaml for correct escaping. We check against a conservative\n  // pattern — anything outside it gets YAML-quoted.\n  if (/^[a-z0-9][a-z0-9-]*$/.test(s)) return s;\n  return yaml\n    .dump(s, { flowLevel: 0, lineWidth: Number.MAX_SAFE_INTEGER })\n    .trimEnd();\n}\n\nfunction dedupeSlugs(list: string[]): string[] {\n  const seen = new Set<string>();\n  const out: string[] = [];\n  for (const raw of list) {\n    const s = raw.trim();\n    if (s.length === 0) continue;\n    if (seen.has(s)) continue;\n    seen.add(s);\n    out.push(s);\n  }\n  return out;\n}\n\nfunction arraysEqual(a: string[], b: string[]): boolean {\n  if (a.length !== b.length) return false;\n  for (let i = 0; i < a.length; i += 1) {\n    if (a[i] !== b[i]) return false;\n  }\n  return true;\n}\n","import { join } from \"node:path\";\n\n/**\n * `.almanac/topics.yaml` inside a given repo root. Single helper so no\n * caller has to remember where the file lives.\n */\nexport function topicsYamlPath(repoRoot: string): string {\n  return join(repoRoot, \".almanac\", \"topics.yaml\");\n}\n\n/**\n * `.almanac/index.db` inside a given repo root. Mirrors `topicsYamlPath`\n * so the topics commands don't have to import from scattered places.\n */\nexport function indexDbPath(repoRoot: string): string {\n  return join(repoRoot, \".almanac\", \"index.db\");\n}\n","import { ensureFreshIndex, runIndexer } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolve-wiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\nimport { toKebabCase } from \"../slug.js\";\nimport { rewritePageTopics } from \"../topics/frontmatter-rewrite.js\";\nimport { indexDbPath, topicsYamlPath } from \"../topics/paths.js\";\nimport {\n  ensureTopic,\n  loadTopicsFile,\n  writeTopicsFile,\n} from \"../topics/yaml.js\";\n\n/**\n * `almanac tag <page> <topic>...` and `almanac untag <page> <topic>`.\n *\n * These are the page-side of the topics system — `topics ...` manages\n * the DAG and metadata; `tag`/`untag` wires concrete pages into\n * topics. Both commands mutate page frontmatter atomically per file\n * and leave body bytes untouched.\n *\n * Auto-creation policy: if a topic passed to `tag` doesn't yet exist\n * in `topics.yaml`, we create a minimal entry for it (title-cased\n * title, no description, no parents). This matches the spec: \"Ensure\n * topic exists in topics.yaml; if not, create a minimal entry.\" We\n * don't silently create topics on `untag` — you can only untag\n * something that was already a topic.\n */\n\nexport interface TagCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\nexport interface TagOptions {\n  cwd: string;\n  wiki?: string;\n  page?: string;\n  topics: string[];\n  stdin?: boolean;\n  stdinInput?: string;\n}\n\nexport interface UntagOptions {\n  cwd: string;\n  wiki?: string;\n  page: string;\n  topic: string;\n}\n\nexport async function runTag(options: TagOptions): Promise<TagCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n\n  const topics = options.topics\n    .map((t) => toKebabCase(t))\n    .filter((t) => t.length > 0);\n  if (topics.length === 0) {\n    return {\n      stdout: \"\",\n      stderr: \"almanac: tag requires at least one topic\\n\",\n      exitCode: 1,\n    };\n  }\n\n  // Bulk mode reads slugs from stdin; single mode uses the positional.\n  const pages: string[] = [];\n  if (options.stdin === true) {\n    if (options.stdinInput === undefined) {\n      return {\n        stdout: \"\",\n        stderr: \"almanac: tag --stdin called without stdin input\\n\",\n        exitCode: 1,\n      };\n    }\n    for (const line of options.stdinInput.split(/\\r?\\n/)) {\n      const s = line.trim();\n      if (s.length > 0) pages.push(s);\n    }\n  } else if (options.page !== undefined && options.page.length > 0) {\n    pages.push(options.page);\n  } else {\n    return {\n      stdout: \"\",\n      stderr: \"almanac: tag requires a page slug (or --stdin)\\n\",\n      exitCode: 1,\n    };\n  }\n\n  // Resolve slugs to file paths from the DB. A stale index is fine for\n  // `tag` — we just need to find each page's file; `ensureFreshIndex`\n  // runs first so the common path is consistent.\n  await ensureFreshIndex({ repoRoot });\n  const db = openIndex(indexDbPath(repoRoot));\n\n  // Validate every requested page exists BEFORE touching topics.yaml.\n  // Previously we auto-created topics first, which meant\n  // `almanac tag does-not-exist brand-new` left `brand-new` in\n  // topics.yaml as a state leak even though the tag itself errored. We\n  // resolve rows up front, then short-circuit with an error (and no\n  // mutations) if none of the pages are valid.\n  const stmt = db.prepare<[string], { file_path: string }>(\n    \"SELECT file_path FROM pages WHERE slug = ?\",\n  );\n  const resolved: { page: string; filePath: string }[] = [];\n  const missing: string[] = [];\n  try {\n    for (const page of pages) {\n      const row = stmt.get(toKebabCase(page));\n      if (row === undefined) {\n        missing.push(page);\n      } else {\n        resolved.push({ page, filePath: row.file_path });\n      }\n    }\n  } finally {\n    db.close();\n  }\n\n  // Hard-fail when NO page resolved. We deliberately don't mutate\n  // topics.yaml on this path — the user's intent (tag page X) is\n  // inarguably unsatisfiable, so we shouldn't leave breadcrumbs.\n  //\n  // In bulk mode (`--stdin`) some pages might resolve and others\n  // won't; keeping the original partial-progress behavior for that case\n  // (topics get created, resolved pages get tagged, `missing` are\n  // reported on stderr with exitCode 1). The state leak only matters\n  // when NOTHING succeeds, and that's the case we're fixing.\n  if (resolved.length === 0) {\n    const stderr = missing.map((p) => `almanac: no such page \"${p}\"\\n`).join(\"\");\n    return {\n      stdout: \"\",\n      stderr,\n      exitCode: 1,\n    };\n  }\n\n  // Auto-create missing topics in topics.yaml. Safe to do now — we have\n  // at least one page that will actually end up tagged with them.\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n  let fileChanged = false;\n  for (const t of topics) {\n    // ensureTopic mutates the file; we check presence beforehand so\n    // we only write when something actually changes (skip a redundant\n    // atomic rewrite + mtime bump).\n    const before = file.topics.length;\n    ensureTopic(file, t);\n    if (file.topics.length > before) fileChanged = true;\n  }\n  if (fileChanged) {\n    await writeTopicsFile(yamlPath, file);\n  }\n\n  const summary: string[] = [];\n  let taggedPages = 0;\n  for (const { page, filePath } of resolved) {\n    const result = await rewritePageTopics(filePath, (current) => {\n      // Preserve existing order; append new topics in the order\n      // the caller supplied them. `applyTopicsTransform` will\n      // dedupe for us, but we skip redundant work here too.\n      const out = [...current];\n      for (const t of topics) if (!current.includes(t)) out.push(t);\n      return out;\n    });\n    if (result.changed) {\n      taggedPages += 1;\n      // Only surface the NEWLY ADDED topics — not the full request.\n      // Reporting every requested topic (including ones the page\n      // already had) reads like false positives in commit diffs.\n      const added = result.after.filter((t) => !result.before.includes(t));\n      summary.push(`tagged ${page}: ${added.join(\", \")}`);\n    } else {\n      summary.push(\n        `no change ${page} (already tagged with ${topics.join(\", \")})`,\n      );\n    }\n  }\n\n  if (taggedPages > 0 || fileChanged) {\n    // Trigger a reindex so downstream queries see the new rows\n    // immediately. Writes to page files bumped their mtimes; writes to\n    // topics.yaml are caught by `topicsYamlNewerThan`.\n    await runIndexer({ repoRoot });\n  }\n\n  const stderr = missing.map((p) => `almanac: no such page \"${p}\"\\n`).join(\"\");\n  return {\n    stdout: summary.length > 0 ? `${summary.join(\"\\n\")}\\n` : \"\",\n    stderr,\n    exitCode: missing.length > 0 ? 1 : 0,\n  };\n}\n\nexport async function runUntag(\n  options: UntagOptions,\n): Promise<TagCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  const page = toKebabCase(options.page);\n  const topic = toKebabCase(options.topic);\n  if (page.length === 0) {\n    return {\n      stdout: \"\",\n      stderr: \"almanac: untag requires a page slug\\n\",\n      exitCode: 1,\n    };\n  }\n  if (topic.length === 0) {\n    return {\n      stdout: \"\",\n      stderr: \"almanac: untag requires a topic\\n\",\n      exitCode: 1,\n    };\n  }\n\n  await ensureFreshIndex({ repoRoot });\n  const db = openIndex(indexDbPath(repoRoot));\n  let filePath: string;\n  try {\n    const row = db\n      .prepare<[string], { file_path: string }>(\n        \"SELECT file_path FROM pages WHERE slug = ?\",\n      )\n      .get(page);\n    if (row === undefined) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: no such page \"${page}\"\\n`,\n        exitCode: 1,\n      };\n    }\n    filePath = row.file_path;\n  } finally {\n    db.close();\n  }\n\n  const result = await rewritePageTopics(filePath, (current) =>\n    current.filter((t) => t !== topic),\n  );\n  if (result.changed) {\n    await runIndexer({ repoRoot });\n  }\n\n  return {\n    stdout: result.changed\n      ? `untagged ${page}: ${topic}\\n`\n      : `no change ${page} (not tagged with ${topic})\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n","import type Database from \"better-sqlite3\";\n\nimport { ensureFreshIndex } from \"../../indexer/index.js\";\nimport { resolveWikiRoot } from \"../../indexer/resolve-wiki.js\";\nimport { openIndex } from \"../../indexer/schema.js\";\nimport { indexDbPath, topicsYamlPath } from \"../../topics/paths.js\";\nimport {\n  findTopic,\n  loadTopicsFile,\n  type TopicsFile,\n} from \"../../topics/yaml.js\";\n\ninterface TopicsRepoOptions {\n  cwd: string;\n  wiki?: string;\n}\n\nexport interface TopicsWorkspace {\n  repoRoot: string;\n  yamlPath: string;\n  file: TopicsFile;\n  db: Database.Database;\n}\n\nexport function resolveTopicsRepo(options: TopicsRepoOptions): Promise<string> {\n  return resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n}\n\n/**\n * Shared setup path for mutating topic commands. These commands all need\n * a fresh DB view so ad-hoc topics from page frontmatter can be promoted\n * into `topics.yaml` before mutation.\n */\nexport async function openFreshTopicsWorkspace(\n  repoRoot: string,\n): Promise<TopicsWorkspace> {\n  await ensureFreshIndex({ repoRoot });\n\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n  const db = openIndex(indexDbPath(repoRoot));\n  return { repoRoot, yamlPath, file, db };\n}\n\nexport function closeWorkspace(workspace: TopicsWorkspace): void {\n  workspace.db.close();\n}\n\n/**\n * Is `slug` a known topic anywhere — in `topics.yaml`, or as an ad-hoc\n * slug that a page's frontmatter mentioned and the indexer seeded?\n */\nexport function topicExists(\n  file: TopicsFile,\n  db: Database.Database,\n  slug: string,\n): boolean {\n  if (findTopic(file, slug) !== null) return true;\n  const row = db\n    .prepare<[string], { slug: string }>(\n      \"SELECT slug FROM topics WHERE slug = ?\",\n    )\n    .get(slug);\n  return row !== undefined;\n}\n","import { runIndexer } from \"../../indexer/index.js\";\nimport { toKebabCase } from \"../../slug.js\";\nimport { ancestorsInFile } from \"../../topics/dag.js\";\nimport {\n  ensureTopic,\n  findTopic,\n  titleCase,\n  writeTopicsFile,\n  type TopicEntry,\n} from \"../../topics/yaml.js\";\nimport type { TopicsCommandOutput, TopicsCreateOptions } from \"./types.js\";\nimport {\n  closeWorkspace,\n  openFreshTopicsWorkspace,\n  resolveTopicsRepo,\n  topicExists,\n} from \"./workspace.js\";\n\n/**\n * `almanac topics create <name> [--parent <slug>]...`.\n *\n * Policy: `--parent <slug>` MUST refer to an existing topic (created\n * earlier in topics.yaml or indexed from page frontmatter). Auto-\n * creating parents silently would let typos cascade — `create JWT\n * --parent secuirty` would quietly spawn a \"secuirty\" topic. Better to\n * refuse and point the user at `almanac topics create <parent>` first.\n *\n * Already-exists is not an error if no new parents are being added —\n * rerunning the same `create` is a no-op. If new parents are introduced\n * we add them (respecting cycle prevention, just like `link`).\n */\nexport async function runTopicsCreate(\n  options: TopicsCreateOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveTopicsRepo(options);\n  const slug = toKebabCase(options.name);\n  if (slug.length === 0) {\n    return {\n      stdout: \"\",\n      stderr: `almanac: topic name \"${options.name}\" has no slug-able characters\\n`,\n      exitCode: 1,\n    };\n  }\n  const title = options.name.trim().length > 0 ? options.name.trim() : titleCase(slug);\n\n  const workspace = await openFreshTopicsWorkspace(repoRoot);\n  try {\n    const { repoRoot, yamlPath, file, db } = workspace;\n    // Resolve/validate parents BEFORE mutating the file. All-or-nothing.\n    const requestedParents = (options.parents ?? [])\n      .map((p) => toKebabCase(p))\n      .filter((p) => p.length > 0);\n    for (const p of requestedParents) {\n      if (p === slug) {\n        return {\n          stdout: \"\",\n          stderr: `almanac: topic cannot be its own parent\\n`,\n          exitCode: 1,\n        };\n      }\n      if (!topicExists(file, db, p)) {\n        return {\n          stdout: \"\",\n          stderr: `almanac: parent topic \"${p}\" does not exist; create it first with \\`almanac topics create ${p}\\`\\n`,\n          exitCode: 1,\n        };\n      }\n      if (findTopic(file, p) === null) {\n        // Topic exists only as an ad-hoc DB entry. Promote it into\n        // topics.yaml so it has a proper record. `ensureTopic` is\n        // idempotent so this is safe even if two loop iterations\n        // reference the same ad-hoc parent.\n        ensureTopic(file, p);\n      }\n    }\n\n    const existing = findTopic(file, slug);\n    if (existing === null) {\n      const entry: TopicEntry = {\n        slug,\n        title,\n        description: null,\n        parents: requestedParents,\n      };\n      file.topics.push(entry);\n    } else {\n      // Add any new parents, skipping ones that already exist or would\n      // create a cycle.\n      for (const p of requestedParents) {\n        if (existing.parents.includes(p)) continue;\n        const ancestors = ancestorsInFile(file, p);\n        if (ancestors.has(slug) || p === slug) {\n          return {\n            stdout: \"\",\n            stderr: `almanac: adding \"${p}\" as a parent of \"${slug}\" would create a cycle\\n`,\n            exitCode: 1,\n          };\n        }\n        existing.parents.push(p);\n      }\n      // Promote the user-supplied title only if the existing one was a\n      // title-cased default (i.e., they didn't describe it yet). Don't\n      // clobber a deliberate title silently.\n      if (\n        existing.title === titleCase(existing.slug) &&\n        title !== titleCase(slug) &&\n        title !== existing.title\n      ) {\n        existing.title = title;\n      }\n    }\n\n    await writeTopicsFile(yamlPath, file);\n    await runIndexer({ repoRoot });\n    return {\n      stdout: existing === null\n        ? `created topic \"${slug}\"\\n`\n        : `updated topic \"${slug}\"\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  } finally {\n    closeWorkspace(workspace);\n  }\n}\n","import { readFile } from \"node:fs/promises\";\nimport { join } from \"node:path\";\n\nimport fg from \"fast-glob\";\n\nimport {\n  applyTopicsTransform,\n  rewritePageTopics,\n} from \"../../topics/frontmatter-rewrite.js\";\n\n/**\n * Apply a `topic-list transform` to every `.almanac/pages/*.md` file\n * whose frontmatter contains a relevant topic. Returns the number of\n * files actually changed.\n *\n * We glob page files ourselves (not the DB) so this works even on a\n * stale index — `rename` and `delete` run the indexer AFTER mutation,\n * and we don't want the scan to miss a page that was just modified.\n */\nexport async function rewriteTopicOnPages(\n  repoRoot: string,\n  transform: (topics: string[]) => string[],\n): Promise<number> {\n  const pagesDir = join(repoRoot, \".almanac\", \"pages\");\n  const files = await fg(\"**/*.md\", {\n    cwd: pagesDir,\n    absolute: true,\n    onlyFiles: true,\n  });\n  let changed = 0;\n  for (const filePath of files) {\n    // Cheap read → in-memory check. Skip files that wouldn't be\n    // changed so we don't bump their mtime.\n    const raw = await readFile(filePath, \"utf8\");\n    const applied = applyTopicsTransform(raw, transform);\n    if (!applied.changed) continue;\n    await rewritePageTopics(filePath, transform);\n    changed += 1;\n  }\n  return changed;\n}\n","import { runIndexer } from \"../../indexer/index.js\";\nimport { toKebabCase } from \"../../slug.js\";\nimport { writeTopicsFile } from \"../../topics/yaml.js\";\nimport { rewriteTopicOnPages } from \"./page-rewrite.js\";\nimport type { TopicsCommandOutput, TopicsDeleteOptions } from \"./types.js\";\nimport {\n  closeWorkspace,\n  openFreshTopicsWorkspace,\n  resolveTopicsRepo,\n  topicExists,\n} from \"./workspace.js\";\n\n/**\n * `almanac topics delete <slug>`. Removes the topic from `topics.yaml`\n * (if present), scrubs any parent edges pointing at it, and untags\n * every page that had it. Pages themselves are left alone — deleting a\n * topic doesn't delete pages, just the relationship.\n */\nexport async function runTopicsDelete(\n  options: TopicsDeleteOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveTopicsRepo(options);\n  const slug = toKebabCase(options.slug);\n  if (slug.length === 0) {\n    return { stdout: \"\", stderr: `almanac: empty topic slug\\n`, exitCode: 1 };\n  }\n\n  const workspace = await openFreshTopicsWorkspace(repoRoot);\n  let pagesUpdated: number;\n  try {\n    const { repoRoot, yamlPath, file, db } = workspace;\n    if (!topicExists(file, db, slug)) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: no such topic \"${slug}\"\\n`,\n        exitCode: 1,\n      };\n    }\n\n    // Remove the entry and strip it from everyone else's `parents` list.\n    file.topics = file.topics.filter((t) => t.slug !== slug);\n    for (const t of file.topics) {\n      t.parents = t.parents.filter((p) => p !== slug);\n    }\n\n    // Same write ordering as rename: topics.yaml first (atomic), then\n    // pages. A crash between the two leaves topics.yaml already scrubbed\n    // and any remaining in-page references become ad-hoc topics — which\n    // the reindex will pick up as empty-topics on next health, and the\n    // user can re-run to finish untagging.\n    await writeTopicsFile(yamlPath, file);\n\n    pagesUpdated = await rewriteTopicOnPages(repoRoot, (topics) =>\n      topics.filter((t) => t !== slug),\n    );\n  } finally {\n    closeWorkspace(workspace);\n  }\n\n  await runIndexer({ repoRoot: workspace.repoRoot });\n  return {\n    stdout: `deleted topic \"${slug}\" (${pagesUpdated} page${pagesUpdated === 1 ? \"\" : \"s\"} untagged)\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n","import { runIndexer } from \"../../indexer/index.js\";\nimport { toKebabCase } from \"../../slug.js\";\nimport { ensureTopic, writeTopicsFile } from \"../../topics/yaml.js\";\nimport type { TopicsCommandOutput, TopicsDescribeOptions } from \"./types.js\";\nimport {\n  closeWorkspace,\n  openFreshTopicsWorkspace,\n  resolveTopicsRepo,\n  topicExists,\n} from \"./workspace.js\";\n\n/**\n * `almanac topics describe <slug> \"<text>\"`. Sets or updates the\n * one-liner description. An empty string clears it.\n */\nexport async function runTopicsDescribe(\n  options: TopicsDescribeOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveTopicsRepo(options);\n  const slug = toKebabCase(options.slug);\n  if (slug.length === 0) {\n    return { stdout: \"\", stderr: `almanac: empty topic slug\\n`, exitCode: 1 };\n  }\n\n  const workspace = await openFreshTopicsWorkspace(repoRoot);\n  try {\n    const { yamlPath, file, db } = workspace;\n    if (!topicExists(file, db, slug)) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: no such topic \"${slug}\"\\n`,\n        exitCode: 1,\n      };\n    }\n    // `ensureTopic` is idempotent — if the topic was DB-only it\n    // promotes into `file`; if already in `file` it returns the\n    // existing entry. Either way we get a concrete entry to mutate.\n    const entry = ensureTopic(file, slug);\n\n    const text = options.description.trim();\n    entry.description = text.length === 0 ? null : text;\n\n    await writeTopicsFile(yamlPath, file);\n  } finally {\n    closeWorkspace(workspace);\n  }\n\n  await runIndexer({ repoRoot: workspace.repoRoot });\n  return {\n    stdout: `described ${slug}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n","import { runIndexer } from \"../../indexer/index.js\";\nimport { toKebabCase } from \"../../slug.js\";\nimport { ancestorsInFile } from \"../../topics/dag.js\";\nimport {\n  ensureTopic,\n  findTopic,\n  writeTopicsFile,\n} from \"../../topics/yaml.js\";\nimport type { TopicsCommandOutput, TopicsLinkOptions } from \"./types.js\";\nimport {\n  closeWorkspace,\n  openFreshTopicsWorkspace,\n  resolveTopicsRepo,\n  topicExists,\n} from \"./workspace.js\";\n\n/**\n * `almanac topics link <child> <parent>`. Adds a DAG edge after\n * checking that it wouldn't close a cycle. Both topics must exist.\n */\nexport async function runTopicsLink(\n  options: TopicsLinkOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveTopicsRepo(options);\n  const child = toKebabCase(options.child);\n  const parent = toKebabCase(options.parent);\n  if (child.length === 0 || parent.length === 0) {\n    return { stdout: \"\", stderr: `almanac: empty topic slug\\n`, exitCode: 1 };\n  }\n  if (child === parent) {\n    return {\n      stdout: \"\",\n      stderr: `almanac: topic cannot be its own parent\\n`,\n      exitCode: 1,\n    };\n  }\n\n  const workspace = await openFreshTopicsWorkspace(repoRoot);\n  try {\n    const { repoRoot, yamlPath, file, db } = workspace;\n    for (const slug of [child, parent]) {\n      if (!topicExists(file, db, slug)) {\n        return {\n          stdout: \"\",\n          stderr: `almanac: topic \"${slug}\" does not exist\\n`,\n          exitCode: 1,\n        };\n      }\n      if (findTopic(file, slug) === null) {\n        // DB-only ad-hoc topic → promote it into topics.yaml so the\n        // new DAG edge has a concrete home.\n        ensureTopic(file, slug);\n      }\n    }\n\n    const childEntry = findTopic(file, child);\n    if (childEntry === null) {\n      // Shouldn't happen after ensureTopic above — defensive.\n      return {\n        stdout: \"\",\n        stderr: `almanac: topic \"${child}\" not found\\n`,\n        exitCode: 1,\n      };\n    }\n\n    if (childEntry.parents.includes(parent)) {\n      return {\n        stdout: `edge ${child} → ${parent} already exists\\n`,\n        stderr: \"\",\n        exitCode: 0,\n      };\n    }\n\n    // Cycle check BEFORE mutation. Uses the in-memory file so the check\n    // operates on the state we're about to write — no DB round-trip needed.\n    const parentAncestors = ancestorsInFile(file, parent);\n    if (parentAncestors.has(child) || parent === child) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: adding ${parent} as parent of ${child} would create a cycle\\n`,\n        exitCode: 1,\n      };\n    }\n\n    childEntry.parents.push(parent);\n    await writeTopicsFile(yamlPath, file);\n    await runIndexer({ repoRoot });\n    return {\n      stdout: `linked ${child} → ${parent}\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  } finally {\n    closeWorkspace(workspace);\n  }\n}\n","import { BLUE, DIM, RST } from \"../../ansi.js\";\nimport { ensureFreshIndex } from \"../../indexer/index.js\";\nimport { resolveWikiRoot } from \"../../indexer/resolve-wiki.js\";\nimport { openIndex } from \"../../indexer/schema.js\";\nimport { indexDbPath } from \"../../topics/paths.js\";\nimport type { TopicsCommandOutput, TopicsListOptions } from \"./types.js\";\n\n/**\n * `almanac topics` (and `almanac topics list`). Prints one line per\n * known topic — from the DB, which already unions topics.yaml with any\n * ad-hoc slugs found in page frontmatter. Page counts come straight\n * from `page_topics`, which the indexer rebuilt on entry.\n */\nexport async function runTopicsList(\n  options: TopicsListOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  await ensureFreshIndex({ repoRoot });\n\n  const db = openIndex(indexDbPath(repoRoot));\n  try {\n    const rows = db\n      .prepare<\n        [],\n        { slug: string; title: string | null; description: string | null; page_count: number }\n      >(\n        // page_count excludes archived pages — matches the policy used\n        // by `topics show` (see `pagesDirectlyTagged`) and by every\n        // page-scoped check in `health`. Pick one rule and apply it\n        // everywhere; a topic with \"5 pages\" in `topics list` and \"3\n        // pages\" in `topics show` is a trust-eroding inconsistency.\n        `SELECT t.slug, t.title, t.description,\n                (SELECT COUNT(*)\n                   FROM page_topics pt\n                   JOIN pages p ON p.slug = pt.page_slug\n                   WHERE pt.topic_slug = t.slug AND p.archived_at IS NULL\n                ) AS page_count\n         FROM topics t\n         ORDER BY t.slug`,\n      )\n      .all();\n\n    if (options.json === true) {\n      return {\n        stdout: `${JSON.stringify(rows, null, 2)}\\n`,\n        stderr: \"\",\n        exitCode: 0,\n      };\n    }\n\n    if (rows.length === 0) {\n      return {\n        stdout:\n          \"no topics. create one with `almanac topics create <name>` or tag a page.\\n\",\n        stderr: \"\",\n        exitCode: 0,\n      };\n    }\n\n    const slugWidth = rows.reduce((w, r) => Math.max(w, r.slug.length), 0);\n    const lines = rows.map((r) => {\n      const slug = r.slug.padEnd(slugWidth);\n      const count = `(${r.page_count} page${r.page_count === 1 ? \"\" : \"s\"})`;\n      return `${BLUE}${slug}${RST}  ${DIM}${count}${RST}`;\n    });\n    return { stdout: `${lines.join(\"\\n\")}\\n`, stderr: \"\", exitCode: 0 };\n  } finally {\n    db.close();\n  }\n}\n","import { runIndexer } from \"../../indexer/index.js\";\nimport { toKebabCase } from \"../../slug.js\";\nimport {\n  findTopic,\n  titleCase,\n  writeTopicsFile,\n} from \"../../topics/yaml.js\";\nimport { rewriteTopicOnPages } from \"./page-rewrite.js\";\nimport type { TopicsCommandOutput, TopicsRenameOptions } from \"./types.js\";\nimport {\n  closeWorkspace,\n  openFreshTopicsWorkspace,\n  resolveTopicsRepo,\n  topicExists,\n} from \"./workspace.js\";\n\n/**\n * `almanac topics rename <old> <new>`. Rewrites the slug both in\n * `topics.yaml` (as an entry key and in anyone who declared it as a\n * parent) and in every affected page's frontmatter.\n *\n * Refuses if `<new>` is already a distinct topic — \"merging\" two topics\n * should be explicit, not a silent side effect of a rename.\n */\nexport async function runTopicsRename(\n  options: TopicsRenameOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveTopicsRepo(options);\n  const oldSlug = toKebabCase(options.oldSlug);\n  const newSlug = toKebabCase(options.newSlug);\n  if (oldSlug.length === 0 || newSlug.length === 0) {\n    return { stdout: \"\", stderr: `almanac: empty topic slug\\n`, exitCode: 1 };\n  }\n  if (oldSlug === newSlug) {\n    return {\n      stdout: `topic \"${oldSlug}\" unchanged\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  const workspace = await openFreshTopicsWorkspace(repoRoot);\n  let pagesUpdated: number;\n  try {\n    const { repoRoot, yamlPath, file, db } = workspace;\n    // Fetch existence info. `oldInYaml` is kept as a direct reference\n    // because we mutate the entry; the DB check is only needed when\n    // the slug isn't in the file (ad-hoc-only).\n    const oldInYaml = findTopic(file, oldSlug);\n    if (!topicExists(file, db, oldSlug)) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: no such topic \"${oldSlug}\"\\n`,\n        exitCode: 1,\n      };\n    }\n\n    if (topicExists(file, db, newSlug)) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: topic \"${newSlug}\" already exists; delete it first if you intend to merge\\n`,\n        exitCode: 1,\n      };\n    }\n\n    // Rewrite `topics.yaml`: the entry itself (if present) plus any\n    // parent reference to `oldSlug`.\n    if (oldInYaml !== null) {\n      oldInYaml.slug = newSlug;\n      if (oldInYaml.title === titleCase(oldSlug)) {\n        // Title was the auto-generated default — refresh it to the new\n        // slug's title-case. A custom title stays as-is.\n        oldInYaml.title = titleCase(newSlug);\n      }\n    }\n    for (const t of file.topics) {\n      t.parents = t.parents.map((p) => (p === oldSlug ? newSlug : p));\n    }\n\n    // Write ordering matters: topics.yaml FIRST (atomic tmp+rename), THEN\n    // the page rewrites. If topics.yaml write fails, no page was touched.\n    // If a page rewrite fails midway, topics.yaml already reflects the\n    // rename so the next reindex picks up the ad-hoc state and the user\n    // can re-run to finish the remaining pages. The opposite ordering\n    // would leave half-rewritten pages referencing a slug that\n    // topics.yaml doesn't know about.\n    await writeTopicsFile(yamlPath, file);\n\n    // Rewrite every page that has `oldSlug` in `topics:` frontmatter.\n    pagesUpdated = await rewriteTopicOnPages(repoRoot, (topics) =>\n      topics.map((t) => (t === oldSlug ? newSlug : t)),\n    );\n  } finally {\n    closeWorkspace(workspace);\n  }\n\n  await runIndexer({ repoRoot: workspace.repoRoot });\n  return {\n    stdout: `renamed ${oldSlug} → ${newSlug} (${pagesUpdated} page${pagesUpdated === 1 ? \"\" : \"s\"} updated)\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n","import type Database from \"better-sqlite3\";\n\nimport { BLUE, DIM, RST } from \"../../ansi.js\";\nimport { descendantsInDb } from \"../../topics/dag.js\";\nimport { titleCase } from \"../../topics/yaml.js\";\n\nexport interface TopicsShowRecord {\n  slug: string;\n  title: string | null;\n  description: string | null;\n  parents: string[];\n  children: string[];\n  pages: string[];\n  descendants_used?: boolean;\n}\n\nexport function pagesDirectlyTagged(\n  db: Database.Database,\n  slug: string,\n): string[] {\n  return db\n    .prepare<[string], { page_slug: string }>(\n      `SELECT pt.page_slug\n       FROM page_topics pt\n       JOIN pages p ON p.slug = pt.page_slug\n       WHERE pt.topic_slug = ? AND p.archived_at IS NULL\n       ORDER BY pt.page_slug`,\n    )\n    .all(slug)\n    .map((r) => r.page_slug);\n}\n\nexport function pagesForSubtree(\n  db: Database.Database,\n  slug: string,\n): string[] {\n  const slugs = [slug, ...descendantsInDb(db, slug)];\n  // Deduplicate + preserve order via a Set — a page can belong to\n  // multiple topics in the subtree and we only want one row per page.\n  const placeholders = slugs.map(() => \"?\").join(\", \");\n  const rows = db\n    .prepare<unknown[], { page_slug: string }>(\n      `SELECT DISTINCT pt.page_slug\n       FROM page_topics pt\n       JOIN pages p ON p.slug = pt.page_slug\n       WHERE pt.topic_slug IN (${placeholders}) AND p.archived_at IS NULL\n       ORDER BY pt.page_slug`,\n    )\n    .all(...slugs);\n  return rows.map((r) => r.page_slug);\n}\n\nexport function formatShow(r: TopicsShowRecord): string {\n  const lines: string[] = [];\n  lines.push(`${DIM}slug:${RST}         ${BLUE}${r.slug}${RST}`);\n  lines.push(`${DIM}title:${RST}        ${r.title ?? titleCase(r.slug)}`);\n  lines.push(`${DIM}description:${RST}  ${r.description ?? \"—\"}`);\n  lines.push(\n    `${DIM}parents:${RST}      ${r.parents.length > 0 ? r.parents.join(\", \") : \"—\"}`,\n  );\n  lines.push(\n    `${DIM}children:${RST}     ${r.children.length > 0 ? r.children.join(\", \") : \"—\"}`,\n  );\n  const pagesLabel = r.descendants_used === true\n    ? \"pages (incl. descendants)\"\n    : \"pages\";\n  lines.push(`${DIM}${pagesLabel}:${RST}`);\n  if (r.pages.length === 0) {\n    lines.push(\"  —\");\n  } else {\n    for (const p of r.pages) lines.push(`  ${BLUE}${p}${RST}`);\n  }\n  return `${lines.join(\"\\n\")}\\n`;\n}\n","import { ensureFreshIndex } from \"../../indexer/index.js\";\nimport { resolveWikiRoot } from \"../../indexer/resolve-wiki.js\";\nimport { openIndex } from \"../../indexer/schema.js\";\nimport { toKebabCase } from \"../../slug.js\";\nimport { indexDbPath } from \"../../topics/paths.js\";\nimport {\n  formatShow,\n  pagesDirectlyTagged,\n  pagesForSubtree,\n  type TopicsShowRecord,\n} from \"./read.js\";\nimport type { TopicsCommandOutput, TopicsShowOptions } from \"./types.js\";\n\n/**\n * `almanac topics show <slug>`. Prints metadata + parents, children,\n * and the page list. `--descendants` widens the page list to include\n * pages tagged with any descendant topic (via the DAG).\n */\nexport async function runTopicsShow(\n  options: TopicsShowOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  await ensureFreshIndex({ repoRoot });\n\n  const slug = toKebabCase(options.slug);\n  if (slug.length === 0) {\n    return {\n      stdout: \"\",\n      stderr: `almanac: empty topic slug\\n`,\n      exitCode: 1,\n    };\n  }\n\n  const db = openIndex(indexDbPath(repoRoot));\n  try {\n    const row = db\n      .prepare<\n        [string],\n        { slug: string; title: string | null; description: string | null }\n      >(\"SELECT slug, title, description FROM topics WHERE slug = ?\")\n      .get(slug);\n    if (row === undefined) {\n      return {\n        stdout: \"\",\n        stderr: `almanac: no such topic \"${slug}\"\\n`,\n        exitCode: 1,\n      };\n    }\n\n    const parents = db\n      .prepare<[string], { parent_slug: string }>(\n        \"SELECT parent_slug FROM topic_parents WHERE child_slug = ? ORDER BY parent_slug\",\n      )\n      .all(slug)\n      .map((r) => r.parent_slug);\n\n    const children = db\n      .prepare<[string], { child_slug: string }>(\n        \"SELECT child_slug FROM topic_parents WHERE parent_slug = ? ORDER BY child_slug\",\n      )\n      .all(slug)\n      .map((r) => r.child_slug);\n\n    const pageSlugs = options.descendants === true\n      ? pagesForSubtree(db, slug)\n      : pagesDirectlyTagged(db, slug);\n\n    const record: TopicsShowRecord = {\n      slug: row.slug,\n      title: row.title,\n      description: row.description,\n      parents,\n      children,\n      pages: pageSlugs,\n      descendants_used: options.descendants === true,\n    };\n\n    if (options.json === true) {\n      return {\n        stdout: `${JSON.stringify(record, null, 2)}\\n`,\n        stderr: \"\",\n        exitCode: 0,\n      };\n    }\n    return { stdout: formatShow(record), stderr: \"\", exitCode: 0 };\n  } finally {\n    db.close();\n  }\n}\n","import { runIndexer } from \"../../indexer/index.js\";\nimport { resolveWikiRoot } from \"../../indexer/resolve-wiki.js\";\nimport { toKebabCase } from \"../../slug.js\";\nimport { topicsYamlPath } from \"../../topics/paths.js\";\nimport {\n  findTopic,\n  loadTopicsFile,\n  writeTopicsFile,\n} from \"../../topics/yaml.js\";\nimport type { TopicsCommandOutput, TopicsUnlinkOptions } from \"./types.js\";\n\n/**\n * `almanac topics unlink <child> <parent>`. Removes a DAG edge if it\n * exists. No-op (exit 0) if not. Never deletes topics.\n */\nexport async function runTopicsUnlink(\n  options: TopicsUnlinkOptions,\n): Promise<TopicsCommandOutput> {\n  const repoRoot = await resolveWikiRoot({ cwd: options.cwd, wiki: options.wiki });\n  const child = toKebabCase(options.child);\n  const parent = toKebabCase(options.parent);\n  if (child.length === 0 || parent.length === 0) {\n    return { stdout: \"\", stderr: `almanac: empty topic slug\\n`, exitCode: 1 };\n  }\n  const yamlPath = topicsYamlPath(repoRoot);\n  const file = await loadTopicsFile(yamlPath);\n  const childEntry = findTopic(file, child);\n  if (childEntry === null || !childEntry.parents.includes(parent)) {\n    return {\n      stdout: `no edge ${child} → ${parent}\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n  childEntry.parents = childEntry.parents.filter((p) => p !== parent);\n  await writeTopicsFile(yamlPath, file);\n  await runIndexer({ repoRoot });\n  return {\n    stdout: `unlinked ${child} → ${parent}\\n`,\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n","import { existsSync } from \"node:fs\";\nimport { basename } from \"node:path\";\n\nimport { findNearestAlmanacDir } from \"../paths.js\";\nimport { toKebabCase } from \"../slug.js\";\nimport {\n  addEntry,\n  readRegistry,\n  type RegistryEntry,\n} from \"./index.js\";\n\n/**\n * If the current working directory (or any parent) has a `.almanac/` that\n * isn't in the registry, silently add it. Runs as a side effect of every\n * command except `init` (which does its own registration) and `list --drop`\n * (which shouldn't resurrect the entry the user just removed).\n *\n * The contract is \"silent\" for environmental problems — missing home dir,\n * unreadable registry file, permission errors. Those shouldn't block the\n * real command from running. But a **malformed** registry IS surfaced: if\n * the JSON is corrupt, the user needs to know, not have auto-register\n * quietly pretend the registry was empty and start overwriting entries.\n */\nexport async function autoRegisterIfNeeded(\n  cwd: string,\n): Promise<RegistryEntry | null> {\n  try {\n    const repoRoot = findNearestAlmanacDir(cwd);\n    if (repoRoot === null) return null;\n\n    // Double-check the directory still exists — `findNearestAlmanacDir`\n    // already confirms this, but we're explicit about the precondition.\n    if (!existsSync(repoRoot)) return null;\n\n    // Read the registry ONCE. `resolveNameCollision` scans this snapshot\n    // in memory; re-reading per iteration would be O(N²) in collision\n    // count and needlessly hit the filesystem.\n    const entries = await readRegistry();\n\n    const existing = entries.find((e) => samePath(e.path, repoRoot));\n    if (existing !== undefined) return existing;\n\n    // Derive a kebab-case name from the directory. If the dir name is\n    // somehow empty (e.g. repo is at filesystem root), skip — we don't\n    // want to register a nameless entry.\n    const name = toKebabCase(basename(repoRoot));\n    if (name.length === 0) return null;\n\n    // Resolve collisions on name by falling back to a disambiguated form.\n    // Auto-registration should never overwrite an existing named entry\n    // that points elsewhere.\n    const finalName = resolveNameCollision(entries, name, repoRoot);\n    if (finalName === null) return null;\n\n    const entry: RegistryEntry = {\n      name: finalName,\n      description: \"\",\n      path: repoRoot,\n      registered_at: new Date().toISOString(),\n    };\n    await addEntry(entry);\n    return entry;\n  } catch (err: unknown) {\n    // Only swallow errors that mean \"registry state isn't readable right\n    // now\" — everything else (malformed JSON, programmer errors, bugs)\n    // should propagate so the user can see it.\n    if (\n      err instanceof Error &&\n      \"code\" in err &&\n      (err.code === \"ENOENT\" ||\n        err.code === \"EACCES\" ||\n        err.code === \"EPERM\")\n    ) {\n      return null;\n    }\n    throw err;\n  }\n}\n\n/**\n * If another repo already claims `name`, append `-2`, `-3`, ... until we\n * find an unused slug. Only relevant for auto-registration — `init` with\n * `--name` lets the user resolve collisions explicitly.\n *\n * Takes a snapshot of registry entries instead of re-reading the file per\n * iteration. Caps at 1000 attempts to prevent pathological loops if the\n * registry somehow contains every suffix (it can't, but we'd rather fail\n * explicitly than spin).\n */\nfunction resolveNameCollision(\n  entries: RegistryEntry[],\n  baseName: string,\n  repoPath: string,\n): string | null {\n  const owner = entries.find((e) => e.name === baseName);\n  if (owner === undefined || samePath(owner.path, repoPath)) {\n    return baseName;\n  }\n  const taken = new Set(entries.map((e) => e.name));\n  const MAX_ATTEMPTS = 1000;\n  for (let suffix = 2; suffix < MAX_ATTEMPTS + 2; suffix += 1) {\n    const candidate = `${baseName}-${suffix}`;\n    if (!taken.has(candidate)) return candidate;\n  }\n  return null;\n}\n\n/**\n * Mirror `pathsEqual` in `registry/index.ts` — case-insensitive on\n * macOS/Windows, case-sensitive on Linux. Duplicated here rather than\n * exported to keep the registry module's public surface small.\n */\nfunction samePath(a: string, b: string): boolean {\n  if (process.platform === \"darwin\" || process.platform === \"win32\") {\n    return a.toLowerCase() === b.toLowerCase();\n  }\n  return a === b;\n}\n","import { Command } from \"commander\";\n\nimport { runTag, runUntag } from \"../commands/tag.js\";\nimport {\n  runTopicsCreate,\n  runTopicsDelete,\n  runTopicsDescribe,\n  runTopicsLink,\n  runTopicsList,\n  runTopicsRename,\n  runTopicsShow,\n  runTopicsUnlink,\n} from \"../commands/topics.js\";\nimport { autoRegisterIfNeeded } from \"../registry/autoregister.js\";\nimport { collectOption, emit, readStdin } from \"./helpers.js\";\n\nexport function registerEditCommands(program: Command): void {\n  program\n    .command(\"tag [page] [topics...]\")\n    .description(\"add topics to a page (auto-creates missing topics)\")\n    .option(\"--stdin\", \"read page slugs from stdin (one per line)\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (\n        page: string | undefined,\n        topicsArg: string[],\n        opts: { stdin?: boolean; wiki?: string },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const resolvedTopics = opts.stdin === true\n          ? [page, ...topicsArg].filter(\n              (t): t is string => typeof t === \"string\" && t.length > 0,\n            )\n          : topicsArg;\n        const result = await runTag({\n          cwd: process.cwd(),\n          page: opts.stdin === true ? undefined : page,\n          topics: resolvedTopics,\n          stdin: opts.stdin,\n          stdinInput: opts.stdin === true ? await readStdin() : undefined,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  program\n    .command(\"untag <page> <topic>\")\n    .description(\"remove a topic from a page's frontmatter\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (page: string, topic: string, opts: { wiki?: string }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runUntag({\n          cwd: process.cwd(),\n          page,\n          topic,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  const topics = program\n    .command(\"topics\")\n    .description(\"manage the topic DAG\");\n\n  topics\n    .command(\"list\", { isDefault: true })\n    .description(\"list all topics with page counts\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .option(\"--json\", \"emit structured JSON\")\n    .action(async (opts: { wiki?: string; json?: boolean }) => {\n      await autoRegisterIfNeeded(process.cwd());\n      const result = await runTopicsList({\n        cwd: process.cwd(),\n        wiki: opts.wiki,\n        json: opts.json,\n      });\n      emit(result);\n    });\n\n  topics\n    .command(\"show <slug>\")\n    .description(\"print a topic's metadata, parents, children, and pages\")\n    .option(\"--descendants\", \"include pages tagged with descendant topics\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .option(\"--json\", \"emit structured JSON\")\n    .action(\n      async (\n        slug: string,\n        opts: { descendants?: boolean; wiki?: string; json?: boolean },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runTopicsShow({\n          cwd: process.cwd(),\n          slug,\n          descendants: opts.descendants,\n          wiki: opts.wiki,\n          json: opts.json,\n        });\n        emit(result);\n      },\n    );\n\n  topics\n    .command(\"create <name>\")\n    .description(\"create a topic (rejects if --parent slug does not exist)\")\n    .option(\"--parent <slug>\", \"parent topic slug (repeat for multiple parents)\", collectOption, [] as string[])\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (name: string, opts: { parent?: string[]; wiki?: string }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runTopicsCreate({\n          cwd: process.cwd(),\n          name,\n          parents: opts.parent,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  topics\n    .command(\"link <child> <parent>\")\n    .description(\"add a DAG edge (cycle-checked)\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(async (child: string, parent: string, opts: { wiki?: string }) => {\n      await autoRegisterIfNeeded(process.cwd());\n      const result = await runTopicsLink({\n        cwd: process.cwd(),\n        child,\n        parent,\n        wiki: opts.wiki,\n      });\n      emit(result);\n    });\n\n  topics\n    .command(\"unlink <child> <parent>\")\n    .description(\"remove a DAG edge\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(async (child: string, parent: string, opts: { wiki?: string }) => {\n      await autoRegisterIfNeeded(process.cwd());\n      const result = await runTopicsUnlink({\n        cwd: process.cwd(),\n        child,\n        parent,\n        wiki: opts.wiki,\n      });\n      emit(result);\n    });\n\n  topics\n    .command(\"rename <old> <new>\")\n    .description(\"rename a topic; rewrites every affected page's frontmatter\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(async (oldSlug: string, newSlug: string, opts: { wiki?: string }) => {\n      await autoRegisterIfNeeded(process.cwd());\n      const result = await runTopicsRename({\n        cwd: process.cwd(),\n        oldSlug,\n        newSlug,\n        wiki: opts.wiki,\n      });\n      emit(result);\n    });\n\n  topics\n    .command(\"delete <slug>\")\n    .description(\"delete a topic; untags every affected page\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(async (slug: string, opts: { wiki?: string }) => {\n      await autoRegisterIfNeeded(process.cwd());\n      const result = await runTopicsDelete({\n        cwd: process.cwd(),\n        slug,\n        wiki: opts.wiki,\n      });\n      emit(result);\n    });\n\n  topics\n    .command(\"describe <slug> <text>\")\n    .description(\"set a topic's one-line description\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(async (slug: string, text: string, opts: { wiki?: string }) => {\n      await autoRegisterIfNeeded(process.cwd());\n      const result = await runTopicsDescribe({\n        cwd: process.cwd(),\n        slug,\n        description: text,\n        wiki: opts.wiki,\n      });\n      emit(result);\n    });\n}\n","import { existsSync } from \"node:fs\";\n\nimport { BLUE, BOLD, DIM, RST } from \"../ansi.js\";\nimport {\n  dropEntry,\n  readRegistry,\n  type RegistryEntry,\n} from \"../registry/index.js\";\n\nexport interface ListOptions {\n  json?: boolean;\n  drop?: string;\n}\n\nexport interface ListCommandOutput {\n  stdout: string;\n  exitCode: number;\n}\n\n/**\n * `almanac list` — the global discovery surface. Three modes:\n *\n *  - default: pretty table of reachable wikis\n *  - `--json`: structured output (reachable wikis only, by default)\n *  - `--drop <name>`: explicit removal, then exits\n *\n * **Unreachable paths are silently skipped in the default output**, but\n * never auto-dropped. This is the registry hygiene rule from the design —\n * branch switches, unmounted drives, and VM-offline repos should not cost\n * the user a registration. Only `--drop` removes entries.\n */\nexport async function listWikis(\n  options: ListOptions,\n): Promise<ListCommandOutput> {\n  if (options.drop !== undefined) {\n    return handleDrop(options.drop);\n  }\n\n  const entries = await readRegistry();\n  const reachable = entries.filter((e) => isReachable(e));\n\n  if (options.json === true) {\n    return { stdout: `${JSON.stringify(reachable, null, 2)}\\n`, exitCode: 0 };\n  }\n\n  return { stdout: formatPretty(reachable), exitCode: 0 };\n}\n\nasync function handleDrop(name: string): Promise<ListCommandOutput> {\n  const removed = await dropEntry(name);\n  if (removed === null) {\n    return {\n      stdout: `no registry entry named \"${name}\"\\n`,\n      exitCode: 1,\n    };\n  }\n  return {\n    stdout: `removed \"${removed.name}\" (${removed.path})\\n`,\n    exitCode: 0,\n  };\n}\n\n/**\n * A registry path is \"reachable\" if something still exists at that path.\n * We use `existsSync` rather than `stat` — we don't care whether the path\n * is a directory or has a `.almanac/` inside; we only hide it from default\n * output when the path itself is gone (e.g., repo deleted, drive\n * unmounted).\n */\nfunction isReachable(entry: RegistryEntry): boolean {\n  if (entry.path.length === 0) return false;\n  return existsSync(entry.path);\n}\n\n/**\n * Human-readable listing. Empty state prints a gentle hint rather than a\n * blank screen, and entries render in registration order (chronological,\n * since `addEntry` appends).\n */\nfunction formatPretty(entries: RegistryEntry[]): string {\n  if (entries.length === 0) {\n    return `${DIM}no wikis registered. run \\`almanac init\\` in a repo to create one.${RST}\\n`;\n  }\n\n  // Column-width the name for alignment; cap at 30 so absurd names don't\n  // stretch the whole table.\n  const nameWidth = Math.min(\n    30,\n    entries.reduce((w, e) => Math.max(w, e.name.length), 0),\n  );\n\n  const lines: string[] = [];\n  for (const entry of entries) {\n    const name = entry.name.padEnd(nameWidth);\n    const desc = entry.description.length > 0 ? entry.description : \"—\";\n    lines.push(`${BLUE}${BOLD}${name}${RST}  ${desc}`);\n    lines.push(`${\" \".repeat(nameWidth)}  ${DIM}${entry.path}${RST}`);\n  }\n  return `${lines.join(\"\\n\")}\\n`;\n}\n","import { join } from \"node:path\";\n\nimport type Database from \"better-sqlite3\";\n\nimport { BLUE, RST } from \"../ansi.js\";\nimport { parseDuration } from \"../indexer/duration.js\";\nimport { ensureFreshIndex } from \"../indexer/index.js\";\nimport { looksLikeDir, normalizePath } from \"../indexer/paths.js\";\nimport { resolveWikiRoot } from \"../indexer/resolve-wiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\n\nexport interface SearchOptions {\n  cwd: string;\n  query?: string;\n  topics: string[];\n  mentions?: string;\n  since?: string;\n  stale?: string;\n  orphan?: boolean;\n  includeArchive?: boolean;\n  archived?: boolean;\n  wiki?: string;\n  json?: boolean;\n  limit?: number;\n}\n\nexport interface SearchResult {\n  slug: string;\n  title: string | null;\n  updated_at: number;\n  archived_at: number | null;\n  superseded_by: string | null;\n  topics: string[];\n}\n\nexport interface SearchCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * `almanac search` — the core query surface.\n *\n * Filters compose with AND logic. The implementation is deliberately\n * pedestrian: build a list of clauses + params, join them with `AND`,\n * intersect topic filters by requiring one subquery per `--topic`. No\n * clever query-planner tricks needed for the sizes we handle (<10k pages).\n *\n * All output ordering is stable: `updated_at DESC, slug ASC`. FTS5 rank\n * is layered on top when the user passed a text query — we ORDER BY rank\n * first, then fall through to the default.\n */\nexport async function runSearch(\n  options: SearchOptions,\n): Promise<SearchCommandOutput> {\n  const repoRoot = await resolveWikiRoot({\n    cwd: options.cwd,\n    wiki: options.wiki,\n  });\n  await ensureFreshIndex({ repoRoot });\n\n  const dbPath = join(repoRoot, \".almanac\", \"index.db\");\n  const db = openIndex(dbPath);\n\n  try {\n    const rows = executeQuery(db, options);\n    const limited =\n      options.limit !== undefined && options.limit >= 0\n        ? rows.slice(0, options.limit)\n        : rows;\n\n    const stdout = formatResults(limited, options);\n    const stderr = buildStderr(limited, options);\n    return { stdout, stderr, exitCode: 0 };\n  } finally {\n    db.close();\n  }\n}\n\ninterface PageRow {\n  slug: string;\n  title: string | null;\n  updated_at: number;\n  archived_at: number | null;\n  superseded_by: string | null;\n}\n\nfunction executeQuery(\n  db: Database.Database,\n  options: SearchOptions,\n): SearchResult[] {\n  const whereClauses: string[] = [];\n  const params: (string | number)[] = [];\n\n  // Archive scope. Three modes, mutually exclusive in practice:\n  //   - default            → active only\n  //   - --include-archive  → active + archived\n  //   - --archived         → archived only\n  // `--archived` wins over `--include-archive` when both are passed —\n  // being explicit about \"only archived\" is strictly narrower than\n  // \"include archived\", so intersecting them yields \"only archived\".\n  if (options.archived === true) {\n    whereClauses.push(\"p.archived_at IS NOT NULL\");\n  } else if (options.includeArchive !== true) {\n    whereClauses.push(\"p.archived_at IS NULL\");\n  }\n\n  // --topic foo --topic bar → page must have BOTH. We add one EXISTS\n  // subquery per topic rather than grouping, which keeps param order\n  // simple and the plan readable.\n  for (const rawTopic of options.topics) {\n    const topicSlug = slugForTopic(rawTopic);\n    if (topicSlug.length === 0) continue;\n    whereClauses.push(\n      \"EXISTS (SELECT 1 FROM page_topics pt WHERE pt.page_slug = p.slug AND pt.topic_slug = ?)\",\n    );\n    params.push(topicSlug);\n  }\n\n  // --mentions: look for a file_refs row on this page that either\n  // matches exactly, OR is a containing folder (is_dir=1 and the query\n  // path starts with the row's path), OR the row itself lives inside\n  // the queried folder. See spec → \"Graph querying → Query examples\".\n  //\n  // We deliberately avoid GLOB on the RHS of the comparison with stored\n  // `r.path`, because stored paths can legitimately contain GLOB\n  // metacharacters — Next.js dynamic routes like `src/[id]/page.tsx`\n  // store a literal `[id]`, and `[abc]` is a SQL GLOB character class.\n  // Concatenating `r.path || '*'` into a GLOB pattern would make\n  // `src/[id]/page.tsx*` match `src/i/page.tsx` (spurious hit on the\n  // character class).\n  //\n  // Instead we enumerate the prefix folders in JS and use parameterized\n  // equality. For `src/checkout/handler.ts` the prefixes are\n  // `['src/', 'src/checkout/']`; any file_refs row with is_dir=1 and\n  // a path in that list is a containing folder of the queried file.\n  // This also lets SQLite use `idx_file_refs_path` as an equality\n  // probe rather than a range scan.\n  if (options.mentions !== undefined && options.mentions.length > 0) {\n    const isDir = looksLikeDir(options.mentions);\n    const norm = normalizePath(options.mentions, isDir);\n    if (isDir) {\n      // Query is a folder. Match: the exact folder, OR any file/sub-\n      // folder whose path starts with the folder prefix. The prefix\n      // match is the one place we still need GLOB — but we escape any\n      // wildcard metacharacters in `norm` first so a user-supplied\n      // `src/[id]/` query is treated as a literal. Note: the query\n      // path comes from the caller, not from stored data, but a user\n      // typing `--mentions src/[id]/` should get the literal folder,\n      // not a character class.\n      const escaped = escapeGlobMeta(norm);\n      whereClauses.push(\n        `EXISTS (\n           SELECT 1 FROM file_refs r\n           WHERE r.page_slug = p.slug\n             AND (r.path = ? OR r.path GLOB ?)\n         )`,\n      );\n      params.push(norm, `${escaped}*`);\n    } else {\n      // Query is a file. Match: the exact file, OR any folder whose\n      // path is a prefix of this file. Build the prefix list in JS and\n      // probe file_refs with equality — no GLOB on stored values.\n      const prefixes = parentFolderPrefixes(norm);\n      if (prefixes.length === 0) {\n        whereClauses.push(\n          `EXISTS (\n             SELECT 1 FROM file_refs r\n             WHERE r.page_slug = p.slug AND r.path = ?\n           )`,\n        );\n        params.push(norm);\n      } else {\n        const placeholders = prefixes.map(() => \"?\").join(\", \");\n        whereClauses.push(\n          `EXISTS (\n             SELECT 1 FROM file_refs r\n             WHERE r.page_slug = p.slug\n               AND (\n                 r.path = ?\n                 OR (r.is_dir = 1 AND r.path IN (${placeholders}))\n               )\n           )`,\n        );\n        params.push(norm, ...prefixes);\n      }\n    }\n  }\n\n  const now = Math.floor(Date.now() / 1000);\n\n  if (options.since !== undefined) {\n    const seconds = parseDuration(options.since);\n    whereClauses.push(\"p.updated_at >= ?\");\n    params.push(now - seconds);\n  }\n\n  if (options.stale !== undefined) {\n    const seconds = parseDuration(options.stale);\n    whereClauses.push(\"p.updated_at < ?\");\n    params.push(now - seconds);\n  }\n\n  if (options.orphan === true) {\n    whereClauses.push(\n      \"NOT EXISTS (SELECT 1 FROM page_topics pt WHERE pt.page_slug = p.slug)\",\n    );\n  }\n\n  // FTS5 text query. When a text query is supplied we JOIN against\n  // `fts_pages` so we can ORDER BY its `rank` column — lower (more\n  // negative) ranks are better matches. Without a query we skip the\n  // join entirely.\n  let sql: string;\n  if (options.query !== undefined && options.query.trim().length > 0) {\n    const ftsExpr = buildFtsQuery(options.query);\n    sql = `\n      SELECT p.slug, p.title, p.updated_at, p.archived_at, p.superseded_by\n      FROM pages p\n      JOIN fts_pages f ON f.slug = p.slug\n      WHERE fts_pages MATCH ?\n        ${whereClauses.length > 0 ? `AND ${whereClauses.join(\" AND \")}` : \"\"}\n      ORDER BY f.rank ASC, p.updated_at DESC, p.slug ASC\n    `;\n    // MATCH param goes first (it's the first `?` in the compiled SQL).\n    params.unshift(ftsExpr);\n  } else {\n    sql = buildSql(whereClauses);\n  }\n\n  const rows = db.prepare<unknown[], PageRow>(sql).all(...params);\n\n  // Attach topics in a second pass — simpler than a correlated\n  // `GROUP_CONCAT`, and the output rows are small enough that N+1 on a\n  // single prepared statement is fine.\n  const topicStmt = db.prepare<[string], { topic_slug: string }>(\n    \"SELECT topic_slug FROM page_topics WHERE page_slug = ? ORDER BY topic_slug\",\n  );\n  const out: SearchResult[] = rows.map((row) => ({\n    slug: row.slug,\n    title: row.title,\n    updated_at: row.updated_at,\n    archived_at: row.archived_at,\n    superseded_by: row.superseded_by,\n    topics: topicStmt.all(row.slug).map((t) => t.topic_slug),\n  }));\n\n  return out;\n}\n\nfunction buildSql(whereClauses: string[]): string {\n  const where =\n    whereClauses.length > 0 ? `WHERE ${whereClauses.join(\" AND \")}` : \"\";\n  return `\n    SELECT p.slug, p.title, p.updated_at, p.archived_at, p.superseded_by\n    FROM pages p\n    ${where}\n    ORDER BY p.updated_at DESC, p.slug ASC\n  `;\n}\n\n/**\n * Turn a user query into an FTS5 MATCH expression. FTS5's default\n * grammar gets unhappy with punctuation (hyphens, colons, slashes), so\n * we tokenize into alphanumeric runs and emit a conjunction of prefixed\n * tokens. Each token is suffixed with `*` so \"stri\" matches \"stripe\".\n *\n * Quoted input (`\"stripe webhook\"`) is treated as an FTS5 phrase query\n * — tokens must appear contiguously in that order. This matches shell\n * conventions where quoting something means \"match it literally\". We\n * strip the surrounding quotes, collapse inner punctuation to spaces,\n * and re-wrap in quotes for FTS5's phrase syntax. Any embedded `\"` in\n * the user input is dropped (FTS5 phrase syntax has no escape).\n *\n * Anything that tokenizes to empty (e.g. pure punctuation) falls back\n * to an empty MATCH, which yields no rows — which is the right answer.\n */\nfunction buildFtsQuery(raw: string): string {\n  const trimmed = raw.trim();\n  if (\n    trimmed.length >= 2 &&\n    trimmed.startsWith(\"\\\"\") &&\n    trimmed.endsWith(\"\\\"\")\n  ) {\n    // Phrase mode. Strip outer quotes, lowercase, collapse non-alnum\n    // runs to a single space, trim. Any surviving inner `\"` are\n    // removed since FTS5 phrase syntax has no escape mechanism.\n    const inner = trimmed\n      .slice(1, -1)\n      .toLowerCase()\n      .replace(/[^a-z0-9]+/g, \" \")\n      .trim();\n    if (inner.length === 0) return \"\\\"\\\"\";\n    return `\"${inner}\"`;\n  }\n  const tokens = trimmed\n    .toLowerCase()\n    .split(/[^a-z0-9]+/)\n    .filter((t) => t.length > 0);\n  if (tokens.length === 0) return \"\\\"\\\"\";\n  return tokens.map((t) => `${t}*`).join(\" AND \");\n}\n\nfunction slugForTopic(raw: string): string {\n  return raw\n    .toLowerCase()\n    .replace(/[^a-z0-9]+/g, \"-\")\n    .replace(/^-+|-+$/g, \"\");\n}\n\n/**\n * For a normalized file path like `src/checkout/handler.ts`, enumerate\n * every containing folder in the form those folders are stored (trailing\n * slash): `['src/', 'src/checkout/']`. Empty for paths with no folder\n * separator (e.g. `README.md`) — a top-level file has no parent folder\n * recorded in `file_refs`.\n *\n * Used by the `--mentions <file>` path to let us probe `file_refs` with\n * equality instead of GLOB, sidestepping wildcard-escape bugs entirely.\n */\nfunction parentFolderPrefixes(filePath: string): string[] {\n  const out: string[] = [];\n  let cursor = 0;\n  while (true) {\n    const next = filePath.indexOf(\"/\", cursor);\n    if (next === -1) break;\n    // Slice includes the slash — matches how directories are stored.\n    out.push(filePath.slice(0, next + 1));\n    cursor = next + 1;\n  }\n  return out;\n}\n\n/**\n * Escape SQLite GLOB metacharacters (`*`, `?`, `[`) by wrapping each in\n * a single-character class. SQLite GLOB has no backslash-escape, so the\n * idiomatic trick is `[*]` → literal `*`, `[?]` → literal `?`, `[[]` →\n * literal `[`. `]` doesn't need escaping outside a class.\n *\n * We only need this on the *query* side — stored paths aren't\n * concatenated into GLOB patterns anymore (see --mentions handling).\n * But a user-typed `--mentions src/[id]/` should still match a stored\n * `src/[id]/` literally, not as a character class over `i` or `d`.\n */\nfunction escapeGlobMeta(s: string): string {\n  return s.replace(/[\\*\\?\\[]/g, (ch) => `[${ch}]`);\n}\n\nfunction formatResults(\n  rows: SearchResult[],\n  options: SearchOptions,\n): string {\n  if (options.json === true) {\n    return `${JSON.stringify(rows, null, 2)}\\n`;\n  }\n  // Default output: one slug per line. Empty result = empty output (not\n  // \"no results found\") — makes piping into xargs / subsequent commands\n  // degrade gracefully.\n  if (rows.length === 0) return \"\";\n  return `${rows.map((r) => `${BLUE}${r.slug}${RST}`).join(\"\\n\")}\\n`;\n}\n\nfunction buildStderr(rows: SearchResult[], options: SearchOptions): string {\n  // Spec: \"print warns if >50 when not --json\". The warning goes to\n  // stderr so it doesn't corrupt pipelines that filter stdout.\n  if (options.json === true) return \"\";\n  // Empty-result breadcrumb (v0.1.3). Interviews showed users saw blank\n  // stdout and concluded the wiki was broken rather than the query\n  // genuinely matched nothing. A single `# 0 results` line to stderr\n  // makes the outcome legible without corrupting stdout pipelines (the\n  // downstream command still sees zero lines). `--json` mode is silent\n  // because `[]` is the unambiguous empty signal there.\n  if (rows.length === 0) {\n    return \"# 0 results\\n\";\n  }\n  if (options.limit !== undefined) return \"\";\n  if (rows.length > 50) {\n    return `almanac: ${rows.length} results — consider --limit or a narrower query\\n`;\n  }\n  return \"\";\n}\n","import { readFile } from \"node:fs/promises\";\nimport { join } from \"node:path\";\n\nimport type Database from \"better-sqlite3\";\n\nimport { BLUE, DIM, RST } from \"../ansi.js\";\nimport { ensureFreshIndex } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolve-wiki.js\";\nimport { openIndex } from \"../indexer/schema.js\";\n\n/**\n * `almanac show <slug>` — structured view of a page.\n *\n * This file absorbs what used to be split across `show` (body), `info`\n * (metadata), and `path` (file path resolution). One command, multiple\n * view flags.\n *\n * Three output \"shapes\":\n *\n *   1. **Default** — metadata header + `\\n---\\n` separator + body. Useful\n *      to skim a page and still see its topics/files/links at a glance.\n *   2. **View flags** (mutually exclusive-ish):\n *        --json   structured JSON, overrides everything else\n *        --body   body only (`--raw` is a deprecated CLI alias)\n *        --meta   metadata only, no body\n *        --lead   first paragraph of body only (cheap preview)\n *   3. **Field flags** (composable). Each selects one \"field\" of the page:\n *        --title / --topics / --files / --links / --backlinks / --xwiki\n *        --lineage / --updated / --path\n *      A single field → bare, pipe-friendly output (one item per line).\n *      Multiple fields → labeled sections, one per flag.\n *\n * `--stdin` is always JSON Lines (one record per line). This avoids the\n * separator ambiguity with markdown `---` in bulk output: the old `info`\n * used a human-readable array; the old `show` used `\\n---\\n` which\n * collided with page frontmatter delimiters.\n */\nexport interface ShowOptions {\n  cwd: string;\n  slug?: string;\n  stdin?: boolean;\n  stdinInput?: string;\n  wiki?: string;\n\n  // View modes (mutually exclusive-ish — precedence: json > raw > meta > lead > default).\n  json?: boolean;\n  raw?: boolean; // alias: body\n  meta?: boolean;\n  lead?: boolean;\n\n  // Composable field flags.\n  title?: boolean;\n  topics?: boolean;\n  files?: boolean;\n  links?: boolean;\n  backlinks?: boolean;\n  xwiki?: boolean;\n  lineage?: boolean;\n  updated?: boolean;\n  path?: boolean;\n}\n\nexport interface ShowCommandOutput {\n  stdout: string;\n  stderr: string;\n  exitCode: number;\n}\n\n/**\n * The structured record emitted by `--json`. Also the shape we read into\n * in order to compose any other output. Keeping this a plain flat object\n * means callers can JSON.parse downstream tooling without chasing nested\n * subschemas.\n */\nexport interface ShowRecord {\n  slug: string;\n  title: string | null;\n  file_path: string;\n  updated_at: number;\n  archived_at: number | null;\n  superseded_by: string | null;\n  supersedes: string[];\n  topics: string[];\n  file_refs: Array<{ path: string; is_dir: boolean }>;\n  wikilinks_out: string[];\n  wikilinks_in: string[];\n  cross_wiki_links: Array<{ wiki: string; target: string }>;\n  body: string;\n}\n\nexport async function runShow(\n  options: ShowOptions,\n): Promise<ShowCommandOutput> {\n  const repoRoot = await resolveWikiRoot({\n    cwd: options.cwd,\n    wiki: options.wiki,\n  });\n  await ensureFreshIndex({ repoRoot });\n\n  const dbPath = join(repoRoot, \".almanac\", \"index.db\");\n  const db = openIndex(dbPath);\n\n  try {\n    const slugs = collectSlugs(options);\n    if (slugs.length === 0) {\n      return {\n        stdout: \"\",\n        stderr: \"almanac: show requires a slug (or --stdin)\\n\",\n        exitCode: 1,\n      };\n    }\n\n    const records: ShowRecord[] = [];\n    const missing: string[] = [];\n    for (const slug of slugs) {\n      const rec = await fetchRecord(db, slug);\n      if (rec === null) {\n        missing.push(slug);\n        continue;\n      }\n      records.push(rec);\n    }\n\n    const bulk = options.stdin === true;\n    const stdout = bulk\n      ? formatBulk(records)\n      : formatSingle(records, options);\n\n    const stderr = missing\n      .map((s) => `almanac: no such page \"${s}\"\\n`)\n      .join(\"\");\n\n    return {\n      stdout,\n      stderr,\n      exitCode: missing.length > 0 ? 1 : 0,\n    };\n  } finally {\n    db.close();\n  }\n}\n\n// ─── Record fetch ────────────────────────────────────────────────────\n\nasync function fetchRecord(\n  db: Database.Database,\n  slug: string,\n): Promise<ShowRecord | null> {\n  const pageRow = db\n    .prepare<\n      [string],\n      {\n        slug: string;\n        title: string | null;\n        file_path: string;\n        updated_at: number;\n        archived_at: number | null;\n        superseded_by: string | null;\n      }\n    >(\n      \"SELECT slug, title, file_path, updated_at, archived_at, superseded_by FROM pages WHERE slug = ?\",\n    )\n    .get(slug);\n  if (pageRow === undefined) return null;\n\n  const topics = db\n    .prepare<[string], { topic_slug: string }>(\n      \"SELECT topic_slug FROM page_topics WHERE page_slug = ? ORDER BY topic_slug\",\n    )\n    .all(slug)\n    .map((r) => r.topic_slug);\n\n  const refs = db\n    .prepare<[string], { original_path: string; is_dir: number }>(\n      \"SELECT original_path, is_dir FROM file_refs WHERE page_slug = ? ORDER BY original_path\",\n    )\n    .all(slug)\n    .map((r) => ({ path: r.original_path, is_dir: r.is_dir === 1 }));\n\n  const linksOut = db\n    .prepare<[string], { target_slug: string }>(\n      \"SELECT target_slug FROM wikilinks WHERE source_slug = ? ORDER BY target_slug\",\n    )\n    .all(slug)\n    .map((r) => r.target_slug);\n\n  const linksIn = db\n    .prepare<[string], { source_slug: string }>(\n      \"SELECT source_slug FROM wikilinks WHERE target_slug = ? ORDER BY source_slug\",\n    )\n    .all(slug)\n    .map((r) => r.source_slug);\n\n  const xwiki = db\n    .prepare<[string], { target_wiki: string; target_slug: string }>(\n      \"SELECT target_wiki, target_slug FROM cross_wiki_links WHERE source_slug = ? ORDER BY target_wiki, target_slug\",\n    )\n    .all(slug)\n    .map((r) => ({ wiki: r.target_wiki, target: r.target_slug }));\n\n  const supersedesRows = db\n    .prepare<[string], { slug: string }>(\n      \"SELECT slug FROM pages WHERE superseded_by = ? ORDER BY slug\",\n    )\n    .all(slug)\n    .map((r) => r.slug);\n\n  // Read body (strip YAML frontmatter). `show` is the only command\n  // permitted to read page content, per the spec.\n  let body = \"\";\n  try {\n    body = stripFrontmatter(await readFile(pageRow.file_path, \"utf8\"));\n  } catch {\n    // If the page row exists but the file is unreadable (race with `git\n    // mv`, permission change, …) we keep the record — everything else we\n    // have is sourced from the index. Body renders as empty. The missing\n    // view flags still work.\n  }\n\n  return {\n    slug: pageRow.slug,\n    title: pageRow.title,\n    file_path: pageRow.file_path,\n    updated_at: pageRow.updated_at,\n    archived_at: pageRow.archived_at,\n    superseded_by: pageRow.superseded_by,\n    supersedes: supersedesRows,\n    topics,\n    file_refs: refs,\n    wikilinks_out: linksOut,\n    wikilinks_in: linksIn,\n    cross_wiki_links: xwiki,\n    body,\n  };\n}\n\n// ─── Formatting ──────────────────────────────────────────────────────\n\nfunction formatBulk(records: ShowRecord[]): string {\n  // JSON Lines. One record per line, trailing newline when non-empty.\n  // Consumers split on `\\n` and `JSON.parse` each line.\n  if (records.length === 0) return \"\";\n  return records.map((r) => JSON.stringify(r)).join(\"\\n\") + \"\\n\";\n}\n\nfunction formatSingle(\n  records: ShowRecord[],\n  options: ShowOptions,\n): string {\n  if (options.json === true) {\n    // JSON always wins. Positional mode emits a single object (never an\n    // array) for a found page, `null` for a missing one — matches the\n    // shape contract from the old `info --json`.\n    const only = records[0] ?? null;\n    return `${JSON.stringify(only, null, 2)}\\n`;\n  }\n  return records.map((r) => formatRecord(r, options)).join(\"\");\n}\n\n/**\n * Figure out which fields the user asked for. Precedence:\n *   1. Body-only mode — everything else is ignored.\n *   2. `--meta` — metadata only, no body. Ignores `--lead`.\n *   3. `--lead` — first paragraph only.\n *   4. Any field flag (`--title`, `--topics`, …) set → those fields only.\n *   5. Nothing set → full view (metadata header + body).\n */\ntype FieldName =\n  | \"title\"\n  | \"topics\"\n  | \"files\"\n  | \"links\"\n  | \"backlinks\"\n  | \"xwiki\"\n  | \"lineage\"\n  | \"updated\"\n  | \"path\";\n\nconst FIELD_ORDER: FieldName[] = [\n  \"title\",\n  \"topics\",\n  \"files\",\n  \"links\",\n  \"backlinks\",\n  \"xwiki\",\n  \"lineage\",\n  \"updated\",\n  \"path\",\n];\n\nfunction selectedFields(options: ShowOptions): FieldName[] {\n  const selected: FieldName[] = [];\n  for (const f of FIELD_ORDER) {\n    if (options[f] === true) selected.push(f);\n  }\n  return selected;\n}\n\nfunction formatRecord(rec: ShowRecord, options: ShowOptions): string {\n  // 1. raw / body\n  if (options.raw === true) {\n    // Guarantee exactly one trailing newline. Without it, shell redirects\n    // (`almanac show foo --body > foo.md`) produce files missing a final\n    // newline, which confuses concatenation and diff tools. We don't\n    // collapse multiple trailing newlines — a page that ends with a\n    // blank line is intentional.\n    if (rec.body.length === 0) return \"\";\n    return rec.body.endsWith(\"\\n\") ? rec.body : `${rec.body}\\n`;\n  }\n\n  // 4. Field flags (check before meta/lead so --meta + --title is unambiguous).\n  const fields = selectedFields(options);\n  if (fields.length > 0) {\n    if (fields.length === 1) {\n      return bareField(rec, fields[0]!);\n    }\n    return labeledFields(rec, fields);\n  }\n\n  // 2. meta only\n  if (options.meta === true) {\n    return metadataHeader(rec) + \"\\n\";\n  }\n\n  // 3. lead only\n  if (options.lead === true) {\n    return firstParagraph(rec.body) + \"\\n\";\n  }\n\n  // 5. Default — metadata header + separator + body.\n  const header = metadataHeader(rec);\n  const body = rec.body;\n  const sep = body.length > 0 ? `\\n\\n${DIM}---${RST}\\n\\n` : \"\\n\";\n  return header + sep + body;\n}\n\n/**\n * Single-field bare output. One item per line, no labels, no colons —\n * designed to be piped directly into another command. The exact format\n * per field tries to preserve \"scriptable by default\":\n *\n *   --title      → the title (or empty if null)\n *   --topics     → one topic slug per line\n *   --files      → one file ref per line; trailing slash for folders\n *   --links      → one outgoing slug per line\n *   --backlinks  → one incoming slug per line\n *   --xwiki      → one `wiki:slug` per line\n *   --lineage    → archived_at / supersedes / superseded_by, one per line\n *                  (only the ones that exist — silent when all absent)\n *   --updated    → ISO-8601 UTC timestamp\n *   --path       → absolute file path (replaces the old `almanac path`)\n */\nfunction bareField(rec: ShowRecord, field: FieldName): string {\n  switch (field) {\n    case \"title\":\n      return (rec.title ?? \"\") + \"\\n\";\n    case \"topics\":\n      return rec.topics.map((t) => `${t}\\n`).join(\"\");\n    case \"files\":\n      return rec.file_refs\n        .map((r) => `${r.path}\\n`)\n        .join(\"\");\n    case \"links\":\n      return rec.wikilinks_out.map((t) => `${t}\\n`).join(\"\");\n    case \"backlinks\":\n      return rec.wikilinks_in.map((t) => `${t}\\n`).join(\"\");\n    case \"xwiki\":\n      return rec.cross_wiki_links\n        .map((x) => `${x.wiki}:${x.target}\\n`)\n        .join(\"\");\n    case \"lineage\": {\n      const lines: string[] = [];\n      if (rec.archived_at !== null) {\n        lines.push(\n          `archived_at: ${new Date(rec.archived_at * 1000).toISOString()}`,\n        );\n      }\n      if (rec.superseded_by !== null) {\n        lines.push(`superseded_by: ${rec.superseded_by}`);\n      }\n      if (rec.supersedes.length > 0) {\n        lines.push(`supersedes: ${rec.supersedes.join(\", \")}`);\n      }\n      return lines.length > 0 ? `${lines.join(\"\\n\")}\\n` : \"\";\n    }\n    case \"updated\":\n      return `${new Date(rec.updated_at * 1000).toISOString()}\\n`;\n    case \"path\":\n      return `${rec.file_path}\\n`;\n  }\n}\n\n/**\n * Multi-field labeled output. Each requested field renders as a labeled\n * section, in canonical order (the order of `FIELD_ORDER`, not the order\n * flags appeared on the command line). Sections are separated by blank\n * lines to make grep-by-label reliable.\n */\nfunction labeledFields(rec: ShowRecord, fields: FieldName[]): string {\n  const parts: string[] = [];\n  for (const f of fields) {\n    parts.push(labeledSection(rec, f));\n  }\n  return parts.join(\"\\n\");\n}\n\nfunction labeledSection(rec: ShowRecord, field: FieldName): string {\n  switch (field) {\n    case \"title\":\n      return `${DIM}title:${RST} ${rec.title ?? \"—\"}\\n`;\n    case \"topics\":\n      return rec.topics.length > 0\n        ? `${DIM}topics:${RST} ${rec.topics.join(\", \")}\\n`\n        : `${DIM}topics:${RST} —\\n`;\n    case \"files\":\n      return formatListSection(\n        \"files\",\n        rec.file_refs.map((r) => `${r.path}`),\n      );\n    case \"links\":\n      return formatListSection(\"links\", rec.wikilinks_out);\n    case \"backlinks\":\n      return formatListSection(\"backlinks\", rec.wikilinks_in);\n    case \"xwiki\":\n      return formatListSection(\n        \"xwiki\",\n        rec.cross_wiki_links.map((x) => `${x.wiki}:${x.target}`),\n      );\n    case \"lineage\": {\n      const lines: string[] = [`${DIM}lineage:${RST}`];\n      if (rec.archived_at !== null) {\n        lines.push(\n          `  ${DIM}archived_at:${RST} ${new Date(rec.archived_at * 1000).toISOString()}`,\n        );\n      }\n      if (rec.superseded_by !== null) {\n        lines.push(`  ${DIM}superseded_by:${RST} ${rec.superseded_by}`);\n      }\n      if (rec.supersedes.length > 0) {\n        lines.push(`  ${DIM}supersedes:${RST} ${rec.supersedes.join(\", \")}`);\n      }\n      if (lines.length === 1) lines.push(\"  —\");\n      return lines.join(\"\\n\") + \"\\n\";\n    }\n    case \"updated\":\n      return `${DIM}updated:${RST} ${new Date(rec.updated_at * 1000).toISOString()}\\n`;\n    case \"path\":\n      return `${DIM}path:${RST} ${rec.file_path}\\n`;\n  }\n}\n\nfunction formatListSection(label: string, items: string[]): string {\n  if (items.length === 0) return `${DIM}${label}:${RST} —\\n`;\n  if (items.length <= 3) return `${DIM}${label}:${RST} ${items.join(\", \")}\\n`;\n  return `${DIM}${label}:${RST}\\n${items.map((i) => `  ${i}`).join(\"\\n\")}\\n`;\n}\n\n/**\n * Metadata header rendered for default and `--meta` views. Single-line\n * fields for short lists; indented block form for long lists. This is\n * the human-readable counterpart to the JSON dump — labeled, column-\n * aligned, skimmable.\n */\nfunction metadataHeader(rec: ShowRecord): string {\n  const lines: string[] = [];\n  lines.push(`${DIM}slug:${RST}       ${BLUE}${rec.slug}${RST}`);\n  lines.push(`${DIM}title:${RST}      ${rec.title ?? \"—\"}`);\n  lines.push(\n    `${DIM}topics:${RST}     ${rec.topics.length > 0 ? rec.topics.join(\", \") : \"—\"}`,\n  );\n\n  if (rec.file_refs.length > 0) {\n    const parts = rec.file_refs.map(\n      (r) => `${r.path}`,\n    );\n    lines.push(`${DIM}files:${RST}      ${parts.join(\", \")}`);\n  }\n\n  lines.push(\n    `${DIM}updated:${RST}    ${new Date(rec.updated_at * 1000).toISOString()}`,\n  );\n\n  if (rec.wikilinks_out.length > 0) {\n    lines.push(`${DIM}links:${RST}      ${rec.wikilinks_out.join(\", \")}`);\n  }\n  if (rec.wikilinks_in.length > 0) {\n    lines.push(`${DIM}backlinks:${RST}  ${rec.wikilinks_in.join(\", \")}`);\n  }\n  if (rec.cross_wiki_links.length > 0) {\n    lines.push(\n      `${DIM}xwiki:${RST}      ${rec.cross_wiki_links\n        .map((x) => `${x.wiki}:${x.target}`)\n        .join(\", \")}`,\n    );\n  }\n  if (rec.archived_at !== null) {\n    lines.push(\n      `${DIM}archived:${RST}   ${new Date(rec.archived_at * 1000).toISOString()}`,\n    );\n  }\n  if (rec.superseded_by !== null) {\n    lines.push(`${DIM}superseded_by:${RST} ${rec.superseded_by}`);\n  }\n  if (rec.supersedes.length > 0) {\n    lines.push(`${DIM}supersedes:${RST} ${rec.supersedes.join(\", \")}`);\n  }\n\n  return lines.join(\"\\n\");\n}\n\n// ─── Helpers ─────────────────────────────────────────────────────────\n\n/**\n * Strip a leading YAML frontmatter block (fenced by `---` on its own\n * lines). Everything between the opening `---\\n` and the next `---\\n` is\n * dropped, along with the surrounding fence. If no opening fence is\n * present we return the source unchanged.\n *\n * Hand-rolled rather than pulling in gray-matter because the CLI's only\n * goal here is \"show the body without the YAML header\" — we don't need\n * the parsed fields, the indexer already has them.\n */\nfunction stripFrontmatter(src: string): string {\n  if (!src.startsWith(\"---\\n\") && !src.startsWith(\"---\\r\\n\")) return src;\n  // Strip the opening fence. A regex replace handles both LF and CRLF\n  // line endings without the off-by-one that `src.indexOf(\"\\n\") + 1`\n  // suffered on CRLF files — `indexOf(\"\\n\")` landed AFTER the `\\r`, so\n  // the `\\r` survived as a prefix on the first body byte.\n  const afterOpen = src.replace(/^---\\r?\\n/, \"\");\n  const endMatch = afterOpen.match(/^---[ \\t]*\\r?\\n/m);\n  if (endMatch === null || endMatch.index === undefined) return src;\n  // Slice after the closing fence's line.\n  return afterOpen.slice(endMatch.index + endMatch[0].length);\n}\n\n/**\n * First paragraph of the body, where \"paragraph\" is everything up to (but\n * not including) the first blank line. Skips a leading `# Title` line if\n * present so `--lead` previews the first real sentence, not the heading.\n */\nfunction firstParagraph(body: string): string {\n  let src = body.trimStart();\n  if (src.startsWith(\"# \")) {\n    const nl = src.indexOf(\"\\n\");\n    src = nl === -1 ? \"\" : src.slice(nl + 1).trimStart();\n  }\n  const blank = src.search(/\\n[ \\t]*\\n/);\n  if (blank === -1) return src.trimEnd();\n  return src.slice(0, blank).trimEnd();\n}\n\nfunction collectSlugs(options: ShowOptions): string[] {\n  if (options.stdin === true && options.stdinInput !== undefined) {\n    return options.stdinInput\n      .split(/\\r?\\n/)\n      .map((s) => s.trim())\n      .filter((s) => s.length > 0);\n  }\n  if (options.slug !== undefined && options.slug.length > 0) {\n    return [options.slug];\n  }\n  return [];\n}\n","import { Command } from \"commander\";\n\nimport { runHealth } from \"../commands/health.js\";\nimport { listWikis } from \"../commands/list.js\";\nimport { runSearch } from \"../commands/search.js\";\nimport { runShow } from \"../commands/show.js\";\nimport { autoRegisterIfNeeded } from \"../registry/autoregister.js\";\nimport {\n  collectOption,\n  deprecationWarning,\n  emit,\n  parsePositiveInt,\n  readStdin,\n  withWarning,\n} from \"./helpers.js\";\n\nexport function registerQueryCommands(program: Command): void {\n  program\n    .command(\"search [query]\")\n    .description(\"find pages by text, topic, file mentions, freshness\")\n    .option(\n      \"--topic <name...>\",\n      \"filter by topic (repeat for intersection)\",\n      collectOption,\n      [] as string[],\n    )\n    .option(\n      \"--mentions <path>\",\n      \"pages referencing this path; matches exact file, trailing-slash folders, and any file under a folder prefix\",\n    )\n    .option(\"--since <duration>\", \"updated within duration, by file mtime (e.g. 2w, 30d)\")\n    .option(\"--stale <duration>\", \"NOT updated within duration, by file mtime\")\n    .option(\"--orphan\", \"pages with no topics\")\n    .option(\"--include-archive\", \"include archived pages\")\n    .option(\"--archived\", \"archived pages only\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .option(\"--json\", \"emit structured JSON\")\n    .option(\"--limit <n>\", \"cap results\", parsePositiveInt)\n    .action(\n      async (\n        query: string | undefined,\n        opts: {\n          topic?: string[];\n          mentions?: string;\n          since?: string;\n          stale?: string;\n          orphan?: boolean;\n          includeArchive?: boolean;\n          archived?: boolean;\n          wiki?: string;\n          json?: boolean;\n          limit?: number;\n        },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runSearch({\n          cwd: process.cwd(),\n          query,\n          topics: opts.topic ?? [],\n          mentions: opts.mentions,\n          since: opts.since,\n          stale: opts.stale,\n          orphan: opts.orphan,\n          includeArchive: opts.includeArchive,\n          archived: opts.archived,\n          wiki: opts.wiki,\n          json: opts.json,\n          limit: opts.limit,\n        });\n        emit(result);\n      },\n    );\n\n  program\n    .command(\"show [slug]\")\n    .description(\"print a page (metadata + body; flags to narrow)\")\n    .option(\"--stdin\", \"read slugs from stdin (one per line)\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .option(\"--json\", \"structured JSON (overrides other view/field flags)\")\n    .option(\"--body\", \"body only\")\n    .option(\"--raw\", \"deprecated alias for --body\")\n    .option(\"--meta\", \"metadata only, no body\")\n    .option(\"--lead\", \"first paragraph of the body only\")\n    .option(\"--title\", \"print title\")\n    .option(\"--topics\", \"print topics\")\n    .option(\"--files\", \"print file refs\")\n    .option(\"--links\", \"print outgoing wikilinks\")\n    .option(\"--backlinks\", \"print incoming wikilinks\")\n    .option(\"--xwiki\", \"print cross-wiki links\")\n    .option(\"--lineage\", \"print archived_at / supersedes / superseded_by\")\n    .option(\"--updated\", \"print updated timestamp\")\n    .option(\"--path\", \"print absolute file path\")\n    .action(\n      async (\n        slug: string | undefined,\n        opts: {\n          stdin?: boolean;\n          wiki?: string;\n          json?: boolean;\n          raw?: boolean;\n          body?: boolean;\n          meta?: boolean;\n          lead?: boolean;\n          title?: boolean;\n          topics?: boolean;\n          files?: boolean;\n          links?: boolean;\n          backlinks?: boolean;\n          xwiki?: boolean;\n          lineage?: boolean;\n          updated?: boolean;\n          path?: boolean;\n        },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runShow({\n          cwd: process.cwd(),\n          slug,\n          stdin: opts.stdin,\n          stdinInput: opts.stdin === true ? await readStdin() : undefined,\n          wiki: opts.wiki,\n          json: opts.json,\n          raw: opts.raw === true || opts.body === true,\n          meta: opts.meta,\n          lead: opts.lead,\n          title: opts.title,\n          topics: opts.topics,\n          files: opts.files,\n          links: opts.links,\n          backlinks: opts.backlinks,\n          xwiki: opts.xwiki,\n          lineage: opts.lineage,\n          updated: opts.updated,\n          path: opts.path,\n        });\n        emit(opts.raw === true\n          ? withWarning(\n            result,\n            deprecationWarning(\"almanac show <slug> --raw\", \"almanac show <slug> --body\"),\n          )\n          : result);\n      },\n    );\n\n  program\n    .command(\"health\")\n    .description(\"report graph integrity problems\")\n    .option(\"--topic <name>\", \"scope to a topic + its descendants\")\n    .option(\"--stale <duration>\", \"stale threshold (default 90d)\")\n    .option(\"--stdin\", \"read page slugs from stdin (limit to these pages)\")\n    .option(\"--json\", \"emit structured JSON\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(\n      async (opts: {\n        topic?: string;\n        stale?: string;\n        stdin?: boolean;\n        json?: boolean;\n        wiki?: string;\n      }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runHealth({\n          cwd: process.cwd(),\n          topic: opts.topic,\n          stale: opts.stale,\n          stdin: opts.stdin,\n          stdinInput: opts.stdin === true ? await readStdin() : undefined,\n          json: opts.json,\n          wiki: opts.wiki,\n        });\n        emit(result);\n      },\n    );\n\n  program\n    .command(\"list\")\n    .description(\"list registered wikis\")\n    .option(\"--json\", \"emit structured JSON\")\n    .option(\n      \"--drop <name>\",\n      \"remove a wiki from the registry (the only way entries are ever removed)\",\n    )\n    .action(async (opts: { json?: boolean; drop?: string }) => {\n      if (opts.drop === undefined) {\n        await autoRegisterIfNeeded(process.cwd());\n      }\n      const result = await listWikis(opts);\n      process.stdout.write(result.stdout);\n      if (result.exitCode !== 0) {\n        process.exitCode = result.exitCode;\n      }\n    });\n}\n","import { Command } from \"commander\";\n\nimport {\n  runAgentsDoctor,\n  runAgentsList,\n  runAgentsModel,\n  runAgentsUse,\n  runDeprecatedSetAgentModel,\n  runDeprecatedSetDefaultAgent,\n} from \"../commands/agents.js\";\nimport {\n  runConfigGet,\n  runConfigList,\n  runConfigSet,\n  runConfigUnset,\n} from \"../commands/config.js\";\nimport { runDoctor } from \"../commands/doctor.js\";\nimport { runSetup } from \"../commands/setup.js\";\nimport { runUninstall } from \"../commands/uninstall.js\";\nimport { runUpdate } from \"../commands/update.js\";\nimport { emit } from \"./helpers.js\";\n\nexport function registerSetupCommands(program: Command): void {\n  const agents = program\n    .command(\"agents\")\n    .description(\"list supported AI agent providers and readiness\");\n\n  agents\n    .command(\"list\")\n    .description(\"show Claude, Codex, and Cursor provider status\")\n    .action(async () => {\n      emit(await runAgentsList());\n    });\n\n  agents\n    .command(\"doctor\")\n    .description(\"diagnose supported AI agent providers\")\n    .action(async () => {\n      emit(await runAgentsDoctor());\n    });\n\n  agents\n    .command(\"use\")\n    .description(\"set the default AI agent provider\")\n    .argument(\"<provider>\", \"claude, codex, cursor, or claude/<model>\")\n    .action(async (provider: string) => {\n      emit(await runAgentsUse({ provider }));\n    });\n\n  agents\n    .command(\"model\")\n    .description(\"set or reset a provider model\")\n    .argument(\"<provider>\", \"claude, codex, or cursor\")\n    .argument(\"[model]\", \"provider-specific model id\")\n    .option(\"--default\", \"reset to provider default\")\n    .action(async (\n      provider: string,\n      model: string | undefined,\n      opts: { default?: boolean },\n    ) => {\n      emit(await runAgentsModel({\n        provider,\n        model,\n        defaultModel: opts.default,\n      }));\n    });\n\n  const config = program\n    .command(\"config\")\n    .description(\"read and write codealmanac settings\");\n\n  config\n    .command(\"list\")\n    .description(\"show supported config keys\")\n    .option(\"--json\", \"emit structured JSON\")\n    .option(\"--show-origin\", \"show whether each value came from file or default\")\n    .action(async (opts: { json?: boolean; showOrigin?: boolean }) => {\n      emit(await runConfigList(opts));\n    });\n\n  config\n    .command(\"get\")\n    .description(\"print one config value\")\n    .argument(\"<key>\", \"config key\")\n    .option(\"--json\", \"emit structured JSON\")\n    .option(\"--show-origin\", \"show whether the value came from file or default\")\n    .action(async (\n      key: string,\n      opts: { json?: boolean; showOrigin?: boolean },\n    ) => {\n      emit(await runConfigGet({ key, ...opts }));\n    });\n\n  config\n    .command(\"set\")\n    .description(\"set one config value\")\n    .argument(\"<key>\", \"config key\")\n    .argument(\"<value>\", \"config value\")\n    .option(\"--project\", \"write .almanac/config.toml for this repo\")\n    .action(async (\n      key: string,\n      value: string,\n      opts: { project?: boolean },\n    ) => {\n      emit(await runConfigSet({ key, value, project: opts.project }));\n    });\n\n  config\n    .command(\"unset\")\n    .description(\"restore one config value to default\")\n    .argument(\"<key>\", \"config key\")\n    .option(\"--project\", \"remove from .almanac/config.toml for this repo\")\n    .action(async (key: string, opts: { project?: boolean }) => {\n      emit(await runConfigUnset({ key, project: opts.project }));\n    });\n\n  program\n    .command(\"set\")\n    .description(\"configure codealmanac defaults\")\n    .argument(\"<key>\", \"setting key, e.g. default-agent or model\")\n    .argument(\"[value...]\", \"setting value\")\n    .action(async (key: string, value: string[]) => {\n      if (key === \"default-agent\") {\n        emit(await runDeprecatedSetDefaultAgent({ provider: value[0] ?? \"\" }));\n        return;\n      }\n      if (key === \"model\") {\n        emit(await runDeprecatedSetAgentModel({\n          provider: value[0] ?? \"\",\n          model: value[1],\n        }));\n        return;\n      }\n      emit({\n        stdout: \"\",\n        stderr:\n          \"almanac: unknown setting. Use `default-agent` or `model`.\\n\",\n        exitCode: 1,\n      });\n    });\n\n  program\n    .command(\"setup\")\n    .description(\"install the hook + CLAUDE.md guides (bare codealmanac alias)\")\n    .option(\"-y, --yes\", \"skip prompts; install everything\")\n    .option(\"--agent <agent>\", \"default agent: claude, codex, or cursor\")\n    .option(\"--model <model>\", \"default model for the selected agent\")\n    .option(\"--skip-hook\", \"opt out of the SessionEnd hook\")\n    .option(\"--skip-guides\", \"opt out of the CLAUDE.md guides\")\n    .action(\n      async (opts: {\n        yes?: boolean;\n        agent?: string;\n        model?: string;\n        skipHook?: boolean;\n        skipGuides?: boolean;\n      }) => {\n        const result = await runSetup({\n          yes: opts.yes,\n          agent: opts.agent,\n          model: opts.model,\n          skipHook: opts.skipHook,\n          skipGuides: opts.skipGuides,\n        });\n        emit(result);\n      },\n    );\n\n  program\n    .command(\"doctor\")\n    .description(\"report on the codealmanac install + current wiki health\")\n    .option(\"--json\", \"emit structured JSON\")\n    .option(\"--install-only\", \"report only on the install (skip wiki checks)\")\n    .option(\"--wiki-only\", \"report only on the current wiki (skip install checks)\")\n    .action(\n      async (opts: {\n        json?: boolean;\n        installOnly?: boolean;\n        wikiOnly?: boolean;\n      }) => {\n        const result = await runDoctor({\n          cwd: process.cwd(),\n          json: opts.json,\n          installOnly: opts.installOnly,\n          wikiOnly: opts.wikiOnly,\n        });\n        emit(result);\n      },\n    );\n\n  program\n    .command(\"update\")\n    .description(\"install the latest codealmanac (synchronous foreground `npm i -g`)\")\n    .option(\n      \"--dismiss\",\n      \"silence the update banner for the current `latest_version` without installing\",\n    )\n    .option(\"--check\", \"force a registry check now (bypasses the 24h cache); no install\")\n    .option(\n      \"--enable-notifier\",\n      \"deprecated: use `almanac config set update_notifier true`\",\n    )\n    .option(\n      \"--disable-notifier\",\n      \"deprecated: use `almanac config set update_notifier false`\",\n    )\n    .action(\n      async (opts: {\n        dismiss?: boolean;\n        check?: boolean;\n        enableNotifier?: boolean;\n        disableNotifier?: boolean;\n      }) => {\n        const result = await runUpdate({\n          dismiss: opts.dismiss,\n          check: opts.check,\n          enableNotifier: opts.enableNotifier,\n          disableNotifier: opts.disableNotifier,\n        });\n        emit(result);\n      },\n    );\n\n  program\n    .command(\"uninstall\")\n    .description(\"remove the hook + guides + import line\")\n    .option(\"-y, --yes\", \"skip confirmations; remove everything\")\n    .option(\"--keep-hook\", \"don't remove the SessionEnd hook (guides still prompted unless --yes)\")\n    .option(\n      \"--keep-guides\",\n      \"don't remove the guides or CLAUDE.md import (hook still prompted unless --yes)\",\n    )\n    .action(\n      async (opts: {\n        yes?: boolean;\n        keepHook?: boolean;\n        keepGuides?: boolean;\n      }) => {\n        const result = await runUninstall({\n          yes: opts.yes,\n          keepHook: opts.keepHook,\n          keepGuides: opts.keepGuides,\n        });\n        emit(result);\n      },\n    );\n}\n","import { readFile } from \"node:fs/promises\";\n\nimport type { CommandResult } from \"../cli/helpers.js\";\nimport { renderOutcome } from \"../cli/outcome.js\";\nimport { findNearestAlmanacDir } from \"../paths.js\";\nimport {\n  finishRunRecord,\n  markRunCancelled,\n  listRunRecords,\n  readRunRecord,\n  runRecordPath,\n  toRunView,\n  writeRunRecord,\n} from \"../process/index.js\";\nimport type { RunView } from \"../process/index.js\";\n\nexport interface JobsOptions {\n  cwd: string;\n  json?: boolean;\n  now?: () => Date;\n  isPidAlive?: (pid: number) => boolean;\n}\n\nexport interface JobByIdOptions extends JobsOptions {\n  runId: string;\n}\n\nexport interface JobAttachStreamOptions extends JobByIdOptions {\n  write?: (chunk: string) => void;\n  pollMs?: number;\n}\n\nexport async function runJobsList(\n  options: JobsOptions,\n): Promise<CommandResult> {\n  const repoRoot = resolveWikiOrResult(options.cwd, options.json);\n  if (typeof repoRoot !== \"string\") return repoRoot;\n\n  const views = await listRunViews(repoRoot, options);\n  if (options.json === true) {\n    return {\n      stdout: `${JSON.stringify({ runs: views }, null, 2)}\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  if (views.length === 0) {\n    return { stdout: \"Jobs\\n\\nNo jobs found.\\n\", stderr: \"\", exitCode: 0 };\n  }\n  const lines = [\"Jobs\", \"\"];\n  for (const view of views) {\n    lines.push(\n      `${view.id}  ${view.operation}  ${view.displayStatus}  ${formatMs(view.elapsedMs)}`,\n    );\n  }\n  return { stdout: `${lines.join(\"\\n\")}\\n`, stderr: \"\", exitCode: 0 };\n}\n\nexport async function runJobsShow(\n  options: JobByIdOptions,\n): Promise<CommandResult> {\n  const repoRoot = resolveWikiOrResult(options.cwd, options.json);\n  if (typeof repoRoot !== \"string\") return repoRoot;\n  const view = await readRunView(repoRoot, options);\n  if (view === null) return missingRun(options.runId, options.json);\n\n  if (options.json === true) {\n    return {\n      stdout: `${JSON.stringify(view, null, 2)}\\n`,\n      stderr: \"\",\n      exitCode: 0,\n    };\n  }\n\n  return {\n    stdout:\n      [\n        `Run: ${view.id}`,\n        `Operation: ${view.operation}`,\n        `Status: ${view.displayStatus}`,\n        `Provider: ${view.provider}${view.model !== undefined ? `/${view.model}` : \"\"}`,\n        `Elapsed: ${formatMs(view.elapsedMs)}`,\n        `Log: ${view.logPath}`,\n        view.failure !== undefined\n          ? `Reason: ${view.failure.message}`\n          : view.error !== undefined\n            ? `Error: ${view.error}`\n            : undefined,\n        view.failure?.fix !== undefined ? `Fix: ${view.failure.fix}` : undefined,\n      ].filter((line): line is string => line !== undefined).join(\"\\n\") + \"\\n\",\n    stderr: \"\",\n    exitCode: 0,\n  };\n}\n\nexport async function runJobsLogs(\n  options: JobByIdOptions,\n): Promise<CommandResult> {\n  const repoRoot = resolveWikiOrResult(options.cwd, options.json);\n  if (typeof repoRoot !== \"string\") return repoRoot;\n  const record = await readRunRecord(runRecordPath(repoRoot, options.runId));\n  if (record === null) return missingRun(options.runId, options.json);\n  try {\n    return {\n      stdout: await readFile(record.logPath, \"utf8\"),\n      stderr: \"\",\n      exitCode: 0,\n    };\n  } catch (err: unknown) {\n    return renderOutcome(\n      {\n        type: \"error\",\n        message: err instanceof Error ? err.message : String(err),\n      },\n      { json: options.json },\n    );\n  }\n}\n\nexport async function runJobsAttach(\n  options: JobByIdOptions,\n): Promise<CommandResult> {\n  const logs = await runJobsLogs(options);\n  if (logs.exitCode !== 0 || options.json === true) return logs;\n  return {\n    ...logs,\n    stdout:\n      logs.stdout.length > 0\n        ? logs.stdout\n        : \"No log events have been written yet.\\n\",\n  };\n}\n\nexport async function streamJobsAttach(\n  options: JobAttachStreamOptions,\n): Promise<CommandResult> {\n  const repoRoot = resolveWikiOrResult(options.cwd, options.json);\n  if (typeof repoRoot !== \"string\") return repoRoot;\n  const initial = await readRunRecord(runRecordPath(repoRoot, options.runId));\n  if (initial === null) return missingRun(options.runId, options.json);\n\n  const write = options.write ?? ((chunk: string) => process.stdout.write(chunk));\n  let offset = 0;\n  while (true) {\n    const record = await readRunRecord(runRecordPath(repoRoot, options.runId));\n    if (record === null) return missingRun(options.runId, options.json);\n    offset = await writeLogChunk(record.logPath, offset, write);\n    const view = toRunView({\n      record,\n      now: options.now?.() ?? new Date(),\n      isPidAlive: options.isPidAlive ?? isPidAlive,\n    });\n    if (\n      view.displayStatus === \"done\" ||\n      view.displayStatus === \"failed\" ||\n      view.displayStatus === \"cancelled\" ||\n      view.displayStatus === \"stale\"\n    ) {\n      const summary = terminalAttachSummary(view);\n      if (summary.length > 0) write(summary);\n      return { stdout: \"\", stderr: \"\", exitCode: 0 };\n    }\n    await sleep(options.pollMs ?? 500);\n  }\n}\n\nexport async function runJobsCancel(\n  options: JobByIdOptions,\n): Promise<CommandResult> {\n  const repoRoot = resolveWikiOrResult(options.cwd, options.json);\n  if (typeof repoRoot !== \"string\") return repoRoot;\n  const path = runRecordPath(repoRoot, options.runId);\n  const record = await readRunRecord(path);\n  if (record === null) return missingRun(options.runId, options.json);\n  if (record.status === \"done\" || record.status === \"failed\" || record.status === \"cancelled\") {\n    return renderOutcome(\n      {\n        type: \"noop\",\n        message: `job already ${record.status}: ${record.id}`,\n        data: { runId: record.id, status: record.status },\n      },\n      { json: options.json },\n    );\n  }\n\n  await markRunCancelled(repoRoot, record.id);\n\n  if (record.pid > 0) {\n    try {\n      process.kill(record.pid, \"SIGTERM\");\n    } catch {\n      // The final record still becomes cancelled; stale detection covers\n      // processes that already exited.\n    }\n  }\n\n  const cancelled = finishRunRecord({\n    record,\n    status: \"cancelled\",\n    finishedAt: options.now?.() ?? new Date(),\n  });\n  await writeRunRecord(path, cancelled);\n  return renderOutcome(\n    {\n      type: \"success\",\n      message: `cancelled job: ${record.id}`,\n      data: { runId: record.id, status: \"cancelled\" },\n    },\n    { json: options.json },\n  );\n}\n\nasync function listRunViews(\n  repoRoot: string,\n  options: JobsOptions,\n): Promise<RunView[]> {\n  const records = await listRunRecords(repoRoot);\n  return records.map((record) =>\n    toRunView({\n      record,\n      now: options.now?.() ?? new Date(),\n      isPidAlive: options.isPidAlive ?? isPidAlive,\n    }),\n  );\n}\n\nasync function readRunView(\n  repoRoot: string,\n  options: JobByIdOptions,\n): Promise<RunView | null> {\n  const record = await readRunRecord(runRecordPath(repoRoot, options.runId));\n  if (record === null) return null;\n  return toRunView({\n    record,\n    now: options.now?.() ?? new Date(),\n    isPidAlive: options.isPidAlive ?? isPidAlive,\n  });\n}\n\nfunction resolveWikiOrResult(\n  cwd: string,\n  json: boolean | undefined,\n): string | CommandResult {\n  const repoRoot = findNearestAlmanacDir(cwd);\n  if (repoRoot !== null) return repoRoot;\n  return renderOutcome(\n    {\n      type: \"needs-action\",\n      message: \"no .almanac/ found in this directory or any parent\",\n      fix: \"run: almanac init\",\n    },\n    { json },\n  );\n}\n\nfunction missingRun(runId: string, json: boolean | undefined): CommandResult {\n  return renderOutcome(\n    { type: \"error\", message: `run not found: ${runId}` },\n    { json },\n  );\n}\n\nasync function writeLogChunk(\n  path: string,\n  offset: number,\n  write: (chunk: string) => void,\n): Promise<number> {\n  let text = \"\";\n  try {\n    text = await readFile(path, \"utf8\");\n  } catch {\n    return offset;\n  }\n  if (text.length <= offset) return offset;\n  const chunk = text.slice(offset);\n  write(chunk);\n  return text.length;\n}\n\nfunction sleep(ms: number): Promise<void> {\n  return new Promise((resolve) => setTimeout(resolve, ms));\n}\n\nfunction isPidAlive(pid: number): boolean {\n  if (pid <= 0) return false;\n  try {\n    process.kill(pid, 0);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\nfunction formatMs(ms: number): string {\n  if (ms < 1_000) return `${ms}ms`;\n  const seconds = Math.round(ms / 1_000);\n  if (seconds < 60) return `${seconds}s`;\n  const minutes = Math.round(seconds / 60);\n  if (minutes < 60) return `${minutes}m`;\n  return `${Math.round(minutes / 60)}h`;\n}\n\nfunction terminalAttachSummary(view: RunView): string {\n  if (view.displayStatus !== \"failed\" && view.displayStatus !== \"stale\") {\n    return \"\";\n  }\n  const lines = [`job ${view.displayStatus}: ${view.id}`];\n  if (view.failure !== undefined) {\n    lines.push(`Reason: ${view.failure.message}`);\n    if (view.failure.fix !== undefined) lines.push(`Fix: ${view.failure.fix}`);\n  } else if (view.error !== undefined) {\n    lines.push(`Error: ${view.error}`);\n  }\n  return `${lines.join(\"\\n\")}\\n`;\n}\n","import type { CommandResult } from \"./helpers.js\";\n\nexport type CommandOutcome =\n  | {\n      type: \"success\";\n      message: string;\n      data?: Record<string, unknown>;\n    }\n  | {\n      type: \"noop\";\n      message: string;\n      data?: Record<string, unknown>;\n    }\n  | {\n      type: \"needs-action\";\n      message: string;\n      fix: string;\n      data?: Record<string, unknown>;\n    }\n  | {\n      type: \"error\";\n      message: string;\n      data?: Record<string, unknown>;\n    };\n\nexport function renderOutcome(\n  outcome: CommandOutcome,\n  opts: { json?: boolean; exitCode?: number; stdout?: string } = {},\n): CommandResult {\n  const exitCode = opts.exitCode ?? defaultExitCode(outcome);\n  if (opts.json === true) {\n    return {\n      stdout: `${JSON.stringify(outcome, null, 2)}\\n`,\n      stderr: \"\",\n      exitCode,\n    };\n  }\n  if (outcome.type === \"needs-action\") {\n    return {\n      stdout: opts.stdout ?? \"\",\n      stderr: `almanac: ${outcome.message}\\n${outcome.fix}\\n`,\n      exitCode,\n    };\n  }\n  if (outcome.type === \"error\") {\n    return {\n      stdout: opts.stdout ?? \"\",\n      stderr: `almanac: ${outcome.message}\\n`,\n      exitCode,\n    };\n  }\n  return {\n    stdout: opts.stdout ?? `${outcome.message}\\n`,\n    stderr: \"\",\n    exitCode,\n  };\n}\n\nfunction defaultExitCode(outcome: CommandOutcome): number {\n  switch (outcome.type) {\n    case \"success\":\n    case \"noop\":\n      return 0;\n    case \"needs-action\":\n    case \"error\":\n      return 1;\n  }\n}\n","import { resolve } from \"node:path\";\n\nimport type { CommandResult } from \"../cli/helpers.js\";\nimport { renderOutcome } from \"../cli/outcome.js\";\nimport type { HarnessEvent } from \"../harness/events.js\";\nimport type { HarnessProviderId } from \"../harness/types.js\";\nimport { runAbsorbOperation } from \"../operations/absorb.js\";\nimport { runBuildOperation } from \"../operations/build.js\";\nimport { runGardenOperation } from \"../operations/garden.js\";\nimport { readConfig } from \"../update/config.js\";\nimport { resolveCaptureTranscripts } from \"./session-transcripts.js\";\nimport type {\n  OperationProviderSelection,\n  OperationRunResult,\n  StartBackgroundProcess,\n  StartForegroundProcess,\n} from \"../operations/types.js\";\n\nexport interface OperationCommandDeps {\n  startForeground?: StartForegroundProcess;\n  startBackground?: StartBackgroundProcess;\n  onEvent?: (event: HarnessEvent) => void | Promise<void>;\n}\n\nexport interface InitCommandOptions extends OperationCommandDeps {\n  cwd: string;\n  using?: string;\n  background?: boolean;\n  json?: boolean;\n  force?: boolean;\n  yes?: boolean;\n}\n\nexport interface CaptureCommandOptions extends OperationCommandDeps {\n  cwd: string;\n  sessionFiles?: string[];\n  app?: string;\n  session?: string;\n  since?: string;\n  limit?: number;\n  all?: boolean;\n  allApps?: boolean;\n  using?: string;\n  foreground?: boolean;\n  json?: boolean;\n  yes?: boolean;\n  claudeProjectsDir?: string;\n}\n\nexport interface IngestCommandOptions extends OperationCommandDeps {\n  cwd: string;\n  paths: string[];\n  using?: string;\n  foreground?: boolean;\n  json?: boolean;\n  yes?: boolean;\n}\n\nexport interface GardenCommandOptions extends OperationCommandDeps {\n  cwd: string;\n  using?: string;\n  foreground?: boolean;\n  json?: boolean;\n  yes?: boolean;\n}\n\nexport async function runInitCommand(\n  options: InitCommandOptions,\n): Promise<CommandResult> {\n  const provider = await resolveProviderOrOutcome(options);\n  if (\"error\" in provider) return provider.error;\n  const background = options.background === true;\n  if (options.json === true && !background) return jsonForegroundError(options.json);\n\n  try {\n    const result = await runBuildOperation({\n      cwd: options.cwd,\n      provider: provider.value,\n      background,\n      context: initContext(options),\n      force: options.force,\n      onEvent: options.onEvent,\n      startForeground: options.startForeground,\n      startBackground: options.startBackground,\n    });\n    return renderOperationResult(\"init\", result, options.json);\n  } catch (err: unknown) {\n    return renderOperationError(err, options.json);\n  }\n}\n\nexport async function runCaptureCommand(\n  options: CaptureCommandOptions,\n): Promise<CommandResult> {\n  const provider = await resolveProviderOrOutcome(options);\n  if (\"error\" in provider) return provider.error;\n  if (options.json === true && options.foreground === true) {\n    return jsonForegroundError(options.json);\n  }\n\n  try {\n    const repoRoot = await resolveCaptureRepoRoot(options.cwd, options.json);\n    if (typeof repoRoot !== \"string\") return repoRoot;\n    const resolved = await resolveCaptureTranscripts({\n      repoRoot,\n      cwd: options.cwd,\n      files: options.sessionFiles,\n      app: options.app,\n      session: options.session,\n      since: options.since,\n      limit: options.limit,\n      all: options.all,\n      allApps: options.allApps,\n      claudeProjectsDir: options.claudeProjectsDir,\n    });\n    if (!resolved.ok) {\n      return renderOutcome(\n        {\n          type: \"needs-action\",\n          message: resolved.error,\n          fix: resolved.fix,\n          data: {\n            app: options.app,\n            session: options.session,\n            since: options.since,\n            limit: options.limit,\n            all: options.all,\n            allApps: options.allApps,\n          },\n        },\n        { json: options.json },\n      );\n    }\n    const paths = resolved.paths;\n    const result = await runAbsorbOperation({\n      cwd: options.cwd,\n      provider: provider.value,\n      background: options.foreground !== true,\n      context: captureContext({ ...options, sessionFiles: paths }),\n      targetKind: \"session\",\n      targetPaths: paths,\n      onEvent: options.onEvent,\n      startForeground: options.startForeground,\n      startBackground: options.startBackground,\n    });\n    return renderOperationResult(\"capture\", result, options.json);\n  } catch (err: unknown) {\n    return renderOperationError(err, options.json);\n  }\n}\n\nexport async function runIngestCommand(\n  options: IngestCommandOptions,\n): Promise<CommandResult> {\n  const provider = await resolveProviderOrOutcome(options);\n  if (\"error\" in provider) return provider.error;\n  if (options.paths.length === 0) {\n    return renderOutcome(\n      { type: \"error\", message: \"ingest requires at least one file or folder\" },\n      { json: options.json },\n    );\n  }\n  if (options.json === true && options.foreground === true) {\n    return jsonForegroundError(options.json);\n  }\n\n  try {\n    const paths = options.paths.map((path) => resolve(options.cwd, path));\n    const result = await runAbsorbOperation({\n      cwd: options.cwd,\n      provider: provider.value,\n      background: options.foreground !== true,\n      context: ingestContext(paths),\n      targetKind: \"path\",\n      targetPaths: paths,\n      onEvent: options.onEvent,\n      startForeground: options.startForeground,\n      startBackground: options.startBackground,\n    });\n    return renderOperationResult(\"ingest\", result, options.json);\n  } catch (err: unknown) {\n    return renderOperationError(err, options.json);\n  }\n}\n\nexport async function runGardenCommand(\n  options: GardenCommandOptions,\n): Promise<CommandResult> {\n  const provider = await resolveProviderOrOutcome(options);\n  if (\"error\" in provider) return provider.error;\n  if (options.json === true && options.foreground === true) {\n    return jsonForegroundError(options.json);\n  }\n\n  try {\n    const result = await runGardenOperation({\n      cwd: options.cwd,\n      provider: provider.value,\n      background: options.foreground !== true,\n      onEvent: options.onEvent,\n      startForeground: options.startForeground,\n      startBackground: options.startBackground,\n    });\n    return renderOperationResult(\"garden\", result, options.json);\n  } catch (err: unknown) {\n    return renderOperationError(err, options.json);\n  }\n}\n\nexport function parseUsing(value: string | undefined): OperationProviderSelection {\n  if (value === undefined || value.trim().length === 0) {\n    return { id: \"claude\" };\n  }\n  const [rawProvider, ...modelParts] = value.split(\"/\");\n  if (!isProviderId(rawProvider)) {\n    throw new Error(\n      `invalid --using \"${value}\" (expected claude, codex, or cursor)`,\n    );\n  }\n  const model = modelParts.join(\"/\");\n  return {\n    id: rawProvider,\n    model: model.length > 0 ? model : undefined,\n  };\n}\n\nasync function resolveProviderOrOutcome(\n  options: {\n    cwd: string;\n    using?: string;\n    json?: boolean;\n  },\n): Promise<{ value: OperationProviderSelection } | { error: CommandResult }> {\n  try {\n    if (options.using !== undefined) {\n      return { value: parseUsing(options.using) };\n    }\n    const config = await readConfig({ cwd: options.cwd });\n    const id = config.agent.default;\n    const model = config.agent.models[id] ?? undefined;\n    return { value: { id, model: model ?? undefined } };\n  } catch (err: unknown) {\n    return {\n      error: renderOutcome(\n        { type: \"error\", message: err instanceof Error ? err.message : String(err) },\n        { json: options.json },\n      ),\n    };\n  }\n}\n\nfunction isProviderId(value: string | undefined): value is HarnessProviderId {\n  return value === \"claude\" || value === \"codex\" || value === \"cursor\";\n}\n\nfunction renderOperationResult(\n  operation: string,\n  result: OperationRunResult,\n  json: boolean | undefined,\n): CommandResult {\n  const record = result.background?.record ?? result.foreground?.record;\n  const status = record?.status;\n  const foregroundResult = result.foreground?.result;\n  if (\n    result.mode === \"foreground\" &&\n    (foregroundResult?.success === false || status === \"failed\")\n  ) {\n    const failure = foregroundResult?.failure ?? record?.failure;\n    return renderOutcome(\n      {\n        type: \"error\",\n        message: renderOperationFailureMessage({\n          operation,\n          runId: result.runId,\n          error: foregroundResult?.error,\n          failure,\n        }),\n        data: {\n          operation,\n          runId: result.runId,\n          mode: result.mode,\n          status,\n          pid: record?.pid,\n          logPath: record?.logPath,\n          error: foregroundResult?.error,\n          failure,\n        },\n      },\n      { json },\n    );\n  }\n  return renderOutcome(\n    {\n      type: \"success\",\n      message:\n        result.mode === \"background\"\n          ? `${operation} started: ${result.runId}`\n          : `${operation} finished: ${result.runId}`,\n      data: {\n        operation,\n        runId: result.runId,\n        mode: result.mode,\n        status,\n        pid: record?.pid,\n        logPath: record?.logPath,\n      },\n    },\n    { json },\n  );\n}\n\nfunction renderOperationFailureMessage(args: {\n  operation: string;\n  runId: string;\n  error?: string;\n  failure?: import(\"../harness/events.js\").HarnessFailure;\n}): string {\n  const lines = [`${args.operation} failed: ${args.runId}`];\n  if (args.failure !== undefined) {\n    lines.push(`Reason: ${args.failure.message}`);\n    if (args.failure.fix !== undefined) lines.push(`Fix: ${args.failure.fix}`);\n    return lines.join(\"\\n\");\n  }\n  if (args.error !== undefined) lines[0] += `: ${args.error}`;\n  return lines.join(\"\\n\");\n}\n\nfunction renderOperationError(\n  err: unknown,\n  json: boolean | undefined,\n): CommandResult {\n  const message = err instanceof Error ? err.message : String(err);\n  if (message.includes(\"no .almanac/\")) {\n    return renderOutcome(\n      {\n        type: \"needs-action\",\n        message,\n        fix: \"run: almanac init\",\n      },\n      { json },\n    );\n  }\n  return renderOutcome({ type: \"error\", message }, { json });\n}\n\nasync function resolveCaptureRepoRoot(\n  cwd: string,\n  json: boolean | undefined,\n): Promise<string | CommandResult> {\n  const { findNearestAlmanacDir } = await import(\"../paths.js\");\n  const repoRoot = findNearestAlmanacDir(cwd);\n  if (repoRoot !== null) return repoRoot;\n  return renderOutcome(\n    {\n      type: \"needs-action\",\n      message: \"no .almanac/ found in this directory or any parent\",\n      fix: \"run: almanac init\",\n    },\n    { json },\n  );\n}\n\nfunction jsonForegroundError(json: boolean | undefined): CommandResult {\n  return renderOutcome({\n    type: \"error\",\n    message: \"--json is only supported for background job start responses\",\n  }, { json });\n}\n\nfunction initContext(options: InitCommandOptions): string {\n  return [\n    \"Command context:\",\n    `- Command: init`,\n    `- Force requested: ${options.force === true ? \"yes\" : \"no\"}`,\n    `- Non-interactive confirmation: ${options.yes === true ? \"yes\" : \"no\"}`,\n  ].join(\"\\n\");\n}\n\nfunction captureContext(options: CaptureCommandOptions): string {\n  const lines = [\"Command context:\", \"- Command: capture\"];\n  if (options.app !== undefined) lines.push(`- App: ${options.app}`);\n  if (options.session !== undefined) lines.push(`- Session id: ${options.session}`);\n  if (options.since !== undefined) lines.push(`- Since: ${options.since}`);\n  if (options.limit !== undefined) lines.push(`- Limit: ${options.limit}`);\n  if (options.all === true) lines.push(\"- Capture all matching sessions\");\n  if (options.allApps === true) lines.push(\"- Capture all supported apps\");\n  const paths = options.sessionFiles ?? [];\n  if (paths.length > 0) {\n    lines.push(\"- Session/transcript files:\");\n    for (const path of paths) lines.push(`  - ${path}`);\n  }\n  if (paths.length === 0 && options.session === undefined) {\n    lines.push(\"- No explicit session file or session id was provided.\");\n  }\n  return lines.join(\"\\n\");\n}\n\nfunction ingestContext(paths: string[]): string {\n  return [\n    \"Command context:\",\n    \"- Command: ingest\",\n    \"- Paths:\",\n    ...paths.map((path) => `  - ${path}`),\n  ].join(\"\\n\");\n}\n","import { existsSync } from \"node:fs\";\nimport { readFile } from \"node:fs/promises\";\nimport path from \"node:path\";\nimport { fileURLToPath } from \"node:url\";\n\n/**\n * Loads bundled prompt text from the `prompts/` directory that ships with\n * the npm package. V1 prompts are split into shared base modules and\n * operation-specific instructions.\n *\n * ## Why not embed the prompts as TS string literals?\n *\n * The non-negotiable from the spec (see CLAUDE.md → \"Non-negotiables\"):\n * \"Prompts are shipped from the npm package. They live in `prompts/` at\n * repo root, are bundled into `files` in `package.json`, and the agent\n * harness reads them from the package install path at runtime.\"\n *\n * Keeping them as separate files means they can be reviewed as prose,\n * diffed meaningfully, and (in the future) edited by users without\n * rebuilding the package.\n *\n * ## Path resolution\n *\n * Two runtime layouts need to work:\n *\n *   1. **Installed (`npm i -g codealmanac`).** The entry point lives at\n *      `dist/codealmanac.js`; prompts at `prompts/*.md`. Walking up from\n *      `import.meta.url` (`.../<pkg>/dist/codealmanac.js`) one level and\n *      into `prompts/` hits the right directory.\n *\n *   2. **Source dev.** During `npm run dev`, tsup emits to `dist/` just\n *      like in production, so case 1 applies. Tests import\n *      `src/agent/prompts.ts` directly via tsx/vitest; `import.meta.url`\n *      points at `src/agent/prompts.ts`. Walking up two levels from there\n *      lands at the repo root, where `prompts/` also lives.\n *\n * We probe a small list of candidates in order and use the first that\n * contains the required prompt files. This keeps a single source of truth —\n * the `prompts/` directory on disk — without baking in whether\n * we're running from `dist/` or `src/`.\n */\n\nexport type PromptName =\n  | \"base/purpose\"\n  | \"base/notability\"\n  | \"base/syntax\"\n  | \"operations/build\"\n  | \"operations/absorb\"\n  | \"operations/garden\";\n\nconst PROMPT_NAMES: readonly PromptName[] = [\n  \"base/purpose\",\n  \"base/notability\",\n  \"base/syntax\",\n  \"operations/build\",\n  \"operations/absorb\",\n  \"operations/garden\",\n];\n\n/**\n * Override the prompts directory, for tests. Production code should never\n * call this — the auto-resolution handles both installed + source layouts.\n */\nlet overrideDir: string | null = null;\n\nexport function setPromptsDirForTesting(dir: string | null): void {\n  overrideDir = dir;\n}\n\n/**\n * Resolve the prompts directory by probing candidate locations. Cached\n * after the first call so repeated `loadPrompt()` calls don't stat the\n * filesystem more than once per process.\n */\nlet resolvedDir: string | null = null;\n\nexport function resolvePromptsDir(): string {\n  if (overrideDir !== null) return overrideDir;\n  if (resolvedDir !== null) return resolvedDir;\n\n  const here = path.dirname(fileURLToPath(import.meta.url));\n\n  // Candidates, most-specific first. Each path is where `prompts/` MIGHT\n  // live given some plausible bundle layout. The first one that exists\n  // and contains our expected prompt files wins.\n  const candidates = [\n    // Bundled dist layout: `.../<pkg>/dist/codealmanac.js` → `../prompts`\n    path.resolve(here, \"..\", \"prompts\"),\n    // Source layout: `.../<pkg>/src/agent/prompts.ts` → `../../prompts`\n    path.resolve(here, \"..\", \"..\", \"prompts\"),\n    // Defensive fallback: if tsup someday emits a nested `dist/src/agent`,\n    // walk up three levels.\n    path.resolve(here, \"..\", \"..\", \"..\", \"prompts\"),\n  ];\n\n  for (const dir of candidates) {\n    if (isPromptsDir(dir)) {\n      resolvedDir = dir;\n      return dir;\n    }\n  }\n\n  // If none matched, give a helpful error with the candidates we tried.\n  // This typically means the package was installed without the `prompts/`\n  // dir included — shouldn't happen unless someone broke `files` in\n  // package.json.\n  throw new Error(\n    \"could not locate bundled prompts/ directory. Tried:\\n\" +\n      candidates.map((c) => `  - ${c}`).join(\"\\n\"),\n  );\n}\n\nfunction isPromptsDir(dir: string): boolean {\n  if (!existsSync(dir)) return false;\n  // Require all base and operation prompts to be present. A half-populated\n  // directory is worse than not finding one — we'd rather error early.\n  return PROMPT_NAMES.every((name) =>\n    existsSync(path.join(dir, `${name}.md`)),\n  );\n}\n\nexport async function loadPrompt(name: PromptName | string): Promise<string> {\n  const dir = resolvePromptsDir();\n  return readFile(resolvePromptPath(dir, name), \"utf8\");\n}\n\nfunction resolvePromptPath(dir: string, name: string): string {\n  if (\n    name.length === 0 ||\n    path.isAbsolute(name) ||\n    name.includes(\"\\\\\") ||\n    name.split(\"/\").some((part) => part === \"\" || part === \".\" || part === \"..\")\n  ) {\n    throw new Error(`invalid prompt name: ${name}`);\n  }\n  const file = path.resolve(dir, `${name}.md`);\n  const relative = path.relative(dir, file);\n  if (relative.startsWith(\"..\") || path.isAbsolute(relative)) {\n    throw new Error(`invalid prompt name: ${name}`);\n  }\n  return file;\n}\n\nexport function joinPrompts(\n  parts: Array<string | null | undefined>,\n): string {\n  return parts\n    .map((part) => part?.trim())\n    .filter((part): part is string => part !== undefined && part.length > 0)\n    .join(\"\\n\\n---\\n\\n\");\n}\n","import { joinPrompts, loadPrompt } from \"../agent/prompts.js\";\nimport type { HarnessEvent } from \"../harness/events.js\";\nimport type { AgentRunSpec, OperationKind } from \"../harness/types.js\";\nimport type { ToolRequest } from \"../harness/tools.js\";\nimport {\n  startBackgroundProcess,\n  startForegroundProcess,\n} from \"../process/index.js\";\nimport type {\n  OperationProviderSelection,\n  OperationRunResult,\n  StartBackgroundProcess,\n  StartForegroundProcess,\n} from \"./types.js\";\n\nconst DEFAULT_MAX_TURNS = 150;\n\nconst BASE_OPERATION_TOOLS: ToolRequest[] = [\n  { id: \"read\" },\n  { id: \"write\" },\n  { id: \"edit\" },\n  { id: \"search\" },\n  { id: \"shell\" },\n];\n\nconst BASE_PROMPTS = [\n  \"base/purpose\",\n  \"base/notability\",\n  \"base/syntax\",\n] as const;\n\nexport async function createOperationRunSpec(args: {\n  operation: OperationKind;\n  promptName: string;\n  repoRoot: string;\n  provider?: OperationProviderSelection;\n  context?: string;\n  targetKind?: string;\n  targetPaths?: string[];\n}): Promise<AgentRunSpec> {\n  const basePrompts = await Promise.all(\n    BASE_PROMPTS.map((name) => loadPrompt(name)),\n  );\n  const operationPrompt = await loadPrompt(args.promptName);\n  const prompt = joinPrompts([\n    ...basePrompts,\n    operationPrompt,\n    operationRuntimeContext(args.repoRoot),\n    args.context,\n  ]);\n\n  return {\n    provider: args.provider ?? { id: \"claude\" },\n    cwd: args.repoRoot,\n    prompt,\n    tools: BASE_OPERATION_TOOLS,\n    limits: {\n      maxTurns: DEFAULT_MAX_TURNS,\n    },\n    metadata: {\n      operation: args.operation,\n      targetKind: args.targetKind,\n      targetPaths: args.targetPaths,\n    },\n  };\n}\n\nexport async function runOperationProcess(args: {\n  repoRoot: string;\n  spec: AgentRunSpec;\n  background: boolean;\n  runId?: string;\n  onEvent?: (event: HarnessEvent) => void | Promise<void>;\n  startForeground?: StartForegroundProcess;\n  startBackground?: StartBackgroundProcess;\n}): Promise<OperationRunResult> {\n  if (args.background) {\n    const background = await (args.startBackground ?? startBackgroundProcess)({\n      repoRoot: args.repoRoot,\n      spec: args.spec,\n      runId: args.runId,\n    });\n    return { mode: \"background\", runId: background.runId, background };\n  }\n\n  const foreground = await (args.startForeground ?? startForegroundProcess)({\n    repoRoot: args.repoRoot,\n    spec: args.spec,\n    runId: args.runId,\n    onEvent: args.onEvent,\n  });\n  return { mode: \"foreground\", runId: foreground.runId, foreground };\n}\n\nfunction operationRuntimeContext(repoRoot: string): string {\n  return [\n    \"Runtime context:\",\n    `- Repository root: ${repoRoot}`,\n    `- Almanac directory: ${repoRoot}/.almanac`,\n    `- Wiki pages directory: ${repoRoot}/.almanac/pages`,\n  ].join(\"\\n\");\n}\n","import type { AgentRunSpec } from \"../harness/types.js\";\nimport { findNearestAlmanacDir } from \"../paths.js\";\nimport type {\n  OperationProviderSelection,\n  OperationRunResult,\n  StartBackgroundProcess,\n  StartForegroundProcess,\n} from \"./types.js\";\nimport { createOperationRunSpec, runOperationProcess } from \"./run.js\";\n\nexport interface AbsorbOperationOptions {\n  cwd: string;\n  context: string;\n  provider?: OperationProviderSelection;\n  background?: boolean;\n  targetKind?: string;\n  targetPaths?: string[];\n  runId?: string;\n  onEvent?: (event: import(\"../harness/events.js\").HarnessEvent) => void | Promise<void>;\n  startForeground?: StartForegroundProcess;\n  startBackground?: StartBackgroundProcess;\n}\n\nexport async function createAbsorbRunSpec(args: {\n  repoRoot: string;\n  context: string;\n  provider?: OperationProviderSelection;\n  targetKind?: string;\n  targetPaths?: string[];\n}): Promise<AgentRunSpec> {\n  return createOperationRunSpec({\n    operation: \"absorb\",\n    promptName: \"operations/absorb\",\n    provider: args.provider ?? { id: \"claude\" },\n    repoRoot: args.repoRoot,\n    context: args.context,\n    targetKind: args.targetKind,\n    targetPaths: args.targetPaths,\n  });\n}\n\nexport async function runAbsorbOperation(\n  options: AbsorbOperationOptions,\n): Promise<OperationRunResult> {\n  const repoRoot = findNearestAlmanacDir(options.cwd);\n  if (repoRoot === null) {\n    throw new Error(\"no .almanac/ found in this directory or any parent\");\n  }\n  const spec = await createAbsorbRunSpec({\n    repoRoot,\n    provider: options.provider,\n    context: options.context,\n    targetKind: options.targetKind,\n    targetPaths: options.targetPaths,\n  });\n\n  return runOperationProcess({\n    repoRoot,\n    spec,\n    background: options.background !== false,\n    runId: options.runId,\n    onEvent: options.onEvent,\n    startForeground: options.startForeground,\n    startBackground: options.startBackground,\n  });\n}\n","import { existsSync } from \"node:fs\";\nimport { readdir } from \"node:fs/promises\";\nimport { join } from \"node:path\";\n\nimport type { AgentRunSpec } from \"../harness/types.js\";\nimport { initWiki } from \"../commands/init.js\";\nimport type {\n  OperationProviderSelection,\n  OperationRunResult,\n  StartBackgroundProcess,\n  StartForegroundProcess,\n} from \"./types.js\";\nimport { createOperationRunSpec, runOperationProcess } from \"./run.js\";\n\nexport interface BuildOperationOptions {\n  cwd: string;\n  provider?: OperationProviderSelection;\n  background?: boolean;\n  context?: string;\n  force?: boolean;\n  runId?: string;\n  onEvent?: (event: import(\"../harness/events.js\").HarnessEvent) => void | Promise<void>;\n  startForeground?: StartForegroundProcess;\n  startBackground?: StartBackgroundProcess;\n}\n\nexport async function createBuildRunSpec(args: {\n  repoRoot: string;\n  provider?: OperationProviderSelection;\n  context?: string;\n}): Promise<AgentRunSpec> {\n  return createOperationRunSpec({\n    operation: \"build\",\n    promptName: \"operations/build\",\n    provider: args.provider ?? { id: \"claude\" },\n    repoRoot: args.repoRoot,\n    context: args.context,\n    targetKind: \"repo\",\n    targetPaths: [args.repoRoot],\n  });\n}\n\nexport async function runBuildOperation(\n  options: BuildOperationOptions,\n): Promise<OperationRunResult> {\n  const init = await initWiki({ cwd: options.cwd });\n  const repoRoot = init.entry.path;\n  const pageCount = await countWikiPages(repoRoot);\n  if (pageCount > 0 && options.force !== true) {\n    throw new Error(\n      `.almanac/ already initialized with ${pageCount} page${pageCount === 1 ? \"\" : \"s\"}; pass --force to rebuild`,\n    );\n  }\n  const spec = await createBuildRunSpec({\n    repoRoot,\n    provider: options.provider,\n    context: options.context,\n  });\n\n  return runOperationProcess({\n    repoRoot,\n    spec,\n    background: options.background === true,\n    runId: options.runId,\n    onEvent: options.onEvent,\n    startForeground: options.startForeground,\n    startBackground: options.startBackground,\n  });\n}\n\nasync function countWikiPages(repoRoot: string): Promise<number> {\n  const pagesDir = join(repoRoot, \".almanac\", \"pages\");\n  if (!existsSync(pagesDir)) return 0;\n  const entries = await readdir(pagesDir);\n  return entries.filter((entry) => entry.endsWith(\".md\")).length;\n}\n","import { existsSync } from \"node:fs\";\nimport { mkdir, readFile, writeFile } from \"node:fs/promises\";\nimport { basename, join } from \"node:path\";\n\nimport { findNearestAlmanacDir, getRepoAlmanacDir } from \"../paths.js\";\nimport { toKebabCase } from \"../slug.js\";\nimport {\n  addEntry,\n  ensureGlobalDir,\n  type RegistryEntry,\n} from \"../registry/index.js\";\n\nexport interface InitOptions {\n  cwd: string;\n  name?: string;\n  description?: string;\n}\n\nexport interface InitResult {\n  entry: RegistryEntry;\n  almanacDir: string;\n  created: boolean; // false if .almanac/ already existed (idempotent re-init)\n}\n\n/**\n * Scaffold `.almanac/` in the repo and register it globally.\n *\n * Idempotent: running `init` on a repo that already has `.almanac/` is\n * fine — we re-register (refreshing the name/description) and skip\n * anything that already exists. We never overwrite a user-authored\n * `README.md` or touch existing pages.\n *\n * If `cwd` lives inside a subdirectory of an existing wiki, we walk up to\n * the wiki root and operate there. `almanac init` from `src/nested/`\n * should update the enclosing wiki, not create a nested one at\n * `src/nested/.almanac/` (which would fragment the registry and leave a\n * confusing orphan `.almanac/` on disk).\n */\nexport async function initWiki(options: InitOptions): Promise<InitResult> {\n  // If cwd is already inside a wiki, prefer that root. Otherwise treat\n  // cwd as the new wiki root.\n  const repoRoot = findNearestAlmanacDir(options.cwd) ?? options.cwd;\n\n  const almanacDir = getRepoAlmanacDir(repoRoot);\n  const pagesDir = join(almanacDir, \"pages\");\n  const readmePath = join(almanacDir, \"README.md\");\n\n  const alreadyExisted = existsSync(almanacDir);\n\n  await mkdir(pagesDir, { recursive: true });\n\n  if (!existsSync(readmePath)) {\n    await writeFile(readmePath, starterReadme(), \"utf8\");\n  }\n\n  await ensureGitignoreHasRuntimeArtifacts(repoRoot);\n\n  const name = toKebabCase(options.name ?? basename(repoRoot));\n  if (name.length === 0) {\n    throw new Error(\n      \"could not derive a wiki name from the current directory; pass --name\",\n    );\n  }\n\n  const description = (options.description ?? \"\").trim();\n\n  await ensureGlobalDir();\n  const entry: RegistryEntry = {\n    name,\n    description,\n    path: repoRoot,\n    registered_at: new Date().toISOString(),\n  };\n  await addEntry(entry);\n\n  return { entry, almanacDir, created: !alreadyExisted };\n}\n\n/**\n * Ensure `.gitignore` in the repo root contains the CodeAlmanac-derived\n * runtime files that should never be committed.\n *\n * The SQLite index is derived from markdown pages. Run records are local\n * process state and JSONL event logs; they can be large and are not wiki\n * content.\n *\n * We add the block regardless of whether the file exists (creating\n * `.gitignore` if needed), and we add any target lines that aren't\n * already present. Existing targets are left alone. If none of the\n * target lines need adding, the file is not touched at all.\n *\n * Formatting: when we do append, we guarantee exactly one blank line\n * between the prior content and our appended block. If the `# codealmanac`\n * header is already present but new targets need adding, we just append\n * the missing lines (no duplicate header).\n */\nasync function ensureGitignoreHasRuntimeArtifacts(cwd: string): Promise<void> {\n  const path = join(cwd, \".gitignore\");\n  const targets = [\n    \".almanac/index.db\",\n    \".almanac/index.db-wal\",\n    \".almanac/index.db-shm\",\n    \".almanac/runs/\",\n  ];\n\n  let existing = \"\";\n  if (existsSync(path)) {\n    existing = await readFile(path, \"utf8\");\n  }\n\n  // Normalize to line comparison to avoid false negatives on trailing\n  // whitespace or CRLF line endings.\n  const lines = existing.split(/\\r?\\n/).map((l) => l.trim());\n  const missing = targets.filter((t) => !lines.includes(t));\n  if (missing.length === 0) return;\n\n  const hasHeader = lines.includes(\"# codealmanac\");\n  const block = hasHeader\n    ? missing.join(\"\\n\") + \"\\n\"\n    : `# codealmanac\\n${missing.join(\"\\n\")}\\n`;\n\n  // Three cases for the separator before the appended block:\n  //  - empty file: no separator needed\n  //  - ends with newline: one more newline produces a single blank line\n  //  - no trailing newline: two newlines (one to terminate the last line,\n  //    one for the blank separator)\n  const sep =\n    existing.length === 0 ? \"\" : existing.endsWith(\"\\n\") ? \"\\n\" : \"\\n\\n\";\n  await writeFile(path, `${existing}${sep}${block}`, \"utf8\");\n}\n\n/**\n * The starter `.almanac/README.md` content. Based on the \"Wiki README\" and\n * \"Notability bar\" sections of the design spec. Kept opinionated but short\n * (~70 lines) — the user is expected to edit it to fit the repo.\n */\nfunction starterReadme(): string {\n  return `# Wiki\n\nThis is the codealmanac wiki for this repository. It captures the knowledge\nthe code itself can't say — decisions, flows, invariants, gotchas, incidents.\n\nThe primary reader is an AI coding agent. The secondary reader is a human\nskimming to understand the shape of the codebase. Write accordingly: dense,\nfactual, linked.\n\n## Notability bar\n\nWrite a page when there is **non-obvious knowledge that will help a future\nagent**. Specifically:\n\n- A decision that took discussion, research, or trial-and-error\n- A gotcha discovered through failure\n- A cross-cutting flow that spans multiple files and isn't obvious from any\n  one of them\n- A constraint or invariant not visible from the code\n- An entity (technology, service, system) referenced by multiple pages\n\nDo not write pages that restate what the code does. Do not write pages of\ninference — only of observation. Silence is an acceptable outcome.\n\n## Topic taxonomy\n\nTopics form a DAG; pages can belong to multiple topics. Start with these and\ngrow as the wiki does:\n\n- \\`stack\\` — technologies and services we use (frameworks, databases, APIs)\n- \\`systems\\` — custom systems we built (auth, billing, search)\n- \\`flows\\` — multi-file processes end-to-end (checkout-flow, publish-flow)\n- \\`decisions\\` — \"why X over Y\"\n- \\`incidents\\` — recorded failures and their fixes\n- \\`concepts\\` — shared vocabulary specific to this codebase\n\nDomain topics (\\`auth\\`, \\`payments\\`, \\`frontend\\`, \\`backend\\`) live alongside\nthese. A page about JWT rotation belongs to both \\`auth\\` and \\`decisions\\`.\n\n## Page shapes\n\nFour shapes cover most of what gets written. They are suggestions, not a\nschema — a page that fits none of them is fine.\n\n- **Entity** — a stable named thing (Supabase, Stripe, the search service)\n- **Decision** — why we chose X over Y\n- **Flow** — how a multi-file process works end-to-end\n- **Gotcha** — a specific surprise, failure, or constraint\n\n## Writing conventions\n\n- Every sentence contains a specific fact. If it doesn't, cut it.\n- Neutral tone. \"is\", not \"serves as\". No \"plays a pivotal role\", no\n  interpretive \"-ing\" clauses, no vague attribution (\"experts argue\").\n- No hedging or knowledge-gap disclaimers. If you don't know, don't write\n  the sentence.\n- Prose first. Bullets for genuine lists. Tables only for structured\n  comparison.\n- No formulaic conclusions. End with the last substantive fact.\n\n## Linking\n\nOne \\`[[...]]\\` syntax for everything, disambiguated by content:\n\n- \\`[[checkout-flow]]\\` — page slug\n- \\`[[src/checkout/handler.ts]]\\` — file reference\n- \\`[[src/checkout/]]\\` — folder reference (trailing slash)\n- \\`[[other-wiki:slug]]\\` — cross-wiki reference\n\nEvery page should link to at least one entity when possible. A page with no\nentity link is suspect.\n\n## Pages live in \\`.almanac/pages/\\`\n\nOne markdown file per page, kebab-case slug. Frontmatter carries \\`topics:\\`\nand optional \\`files:\\`. The rest is prose.\n`;\n}\n","import type { AgentRunSpec } from \"../harness/types.js\";\nimport { findNearestAlmanacDir } from \"../paths.js\";\nimport type {\n  OperationProviderSelection,\n  OperationRunResult,\n  StartBackgroundProcess,\n  StartForegroundProcess,\n} from \"./types.js\";\nimport { createOperationRunSpec, runOperationProcess } from \"./run.js\";\n\nexport interface GardenOperationOptions {\n  cwd: string;\n  provider?: OperationProviderSelection;\n  background?: boolean;\n  context?: string;\n  runId?: string;\n  onEvent?: (event: import(\"../harness/events.js\").HarnessEvent) => void | Promise<void>;\n  startForeground?: StartForegroundProcess;\n  startBackground?: StartBackgroundProcess;\n}\n\nexport async function createGardenRunSpec(args: {\n  repoRoot: string;\n  provider?: OperationProviderSelection;\n  context?: string;\n}): Promise<AgentRunSpec> {\n  return createOperationRunSpec({\n    operation: \"garden\",\n    promptName: \"operations/garden\",\n    provider: args.provider ?? { id: \"claude\" },\n    repoRoot: args.repoRoot,\n    context: args.context,\n    targetKind: \"wiki\",\n    targetPaths: [`${args.repoRoot}/.almanac`],\n  });\n}\n\nexport async function runGardenOperation(\n  options: GardenOperationOptions,\n): Promise<OperationRunResult> {\n  const repoRoot = findNearestAlmanacDir(options.cwd);\n  if (repoRoot === null) {\n    throw new Error(\"no .almanac/ found in this directory or any parent\");\n  }\n  const spec = await createGardenRunSpec({\n    repoRoot,\n    provider: options.provider,\n    context: options.context,\n  });\n\n  return runOperationProcess({\n    repoRoot,\n    spec,\n    background: options.background !== false,\n    runId: options.runId,\n    onEvent: options.onEvent,\n    startForeground: options.startForeground,\n    startBackground: options.startBackground,\n  });\n}\n","import { existsSync } from \"node:fs\";\nimport { readFile, readdir, stat } from \"node:fs/promises\";\nimport { homedir } from \"node:os\";\nimport { basename, join, resolve } from \"node:path\";\n\nimport { parseDuration } from \"../indexer/duration.js\";\n\nexport interface ResolveCaptureTranscriptsOptions {\n  repoRoot: string;\n  cwd: string;\n  files?: string[];\n  app?: string;\n  session?: string;\n  since?: string;\n  limit?: number;\n  all?: boolean;\n  allApps?: boolean;\n  now?: () => Date;\n  claudeProjectsDir?: string;\n}\n\nexport type ResolveCaptureTranscriptsResult =\n  | { ok: true; paths: string[]; app: \"claude\" | \"file\" }\n  | { ok: false; error: string; fix: string };\n\ninterface TranscriptEntry {\n  path: string;\n  mtime: number;\n}\n\nexport async function resolveCaptureTranscripts(\n  options: ResolveCaptureTranscriptsOptions,\n): Promise<ResolveCaptureTranscriptsResult> {\n  const explicit = options.files ?? [];\n  if (explicit.length > 0) {\n    const paths = explicit.map((path) => resolve(options.cwd, path));\n    const missing = paths.find((path) => !existsSync(path));\n    if (missing !== undefined) {\n      return {\n        ok: false,\n        error: `transcript not found: ${missing}`,\n        fix: \"pass an existing transcript file\",\n      };\n    }\n    return { ok: true, paths, app: \"file\" };\n  }\n\n  const app = options.app ?? \"claude\";\n  if (options.allApps === true) {\n    return {\n      ok: false,\n      error: \"capture --all-apps discovery is not implemented yet\",\n      fix: \"run capture per app, pass transcript files explicitly, or use almanac ingest <file-or-folder>\",\n    };\n  }\n  if (app !== \"claude\") {\n    return {\n      ok: false,\n      error: `capture discovery for ${app} sessions is not implemented yet`,\n      fix: \"pass one or more transcript files, or use almanac ingest <file-or-folder>\",\n    };\n  }\n\n  const projectsDir =\n    options.claudeProjectsDir ?? join(homedir(), \".claude\", \"projects\");\n  if (!existsSync(projectsDir)) {\n    return {\n      ok: false,\n      error:\n        `could not auto-resolve Claude transcript; ${projectsDir} does not exist`,\n      fix: \"pass --session <id> with a Claude transcript available, or pass a transcript file\",\n    };\n  }\n\n  const transcripts = await collectTranscripts(projectsDir);\n  if (options.session !== undefined && options.session.length > 0) {\n    if (hasBulkScope(options)) {\n      return {\n        ok: false,\n        error: \"capture --session cannot be combined with --since, --limit, --all, or --all-apps\",\n        fix: \"use --session for one transcript, or remove --session to capture a filtered set\",\n      };\n    }\n    const expected = `${options.session}.jsonl`;\n    const match = transcripts.find((entry) => basename(entry.path) === expected);\n    if (match === undefined) {\n      return {\n        ok: false,\n        error: `no Claude transcript found for session ${options.session}`,\n        fix: \"pass an existing transcript file\",\n      };\n    }\n    return { ok: true, paths: [match.path], app: \"claude\" };\n  }\n\n  let matches = await filterTranscriptsByCwd(transcripts, options.repoRoot);\n  const cutoff = parseSinceCutoff(options.since, options.now?.() ?? new Date());\n  if (!cutoff.ok) return cutoff;\n  const cutoffMtime = cutoff.mtime;\n  if (cutoffMtime !== undefined) {\n    matches = matches.filter((entry) => entry.mtime >= cutoffMtime);\n  }\n  if (matches.length === 0) {\n    return {\n      ok: false,\n      error:\n        `could not auto-resolve Claude transcript for cwd ${options.repoRoot}`,\n      fix: \"pass --session <id> or a transcript file\",\n    };\n  }\n  matches.sort((a, b) => b.mtime - a.mtime);\n  const limit = normalizeLimit(options.limit);\n  if (!limit.ok) return limit;\n  const count = options.all === true ? limit.value ?? matches.length : limit.value ?? 1;\n  return {\n    ok: true,\n    paths: matches.slice(0, count).map((entry) => entry.path),\n    app: \"claude\",\n  };\n}\n\nfunction hasBulkScope(options: ResolveCaptureTranscriptsOptions): boolean {\n  return (\n    options.since !== undefined ||\n    options.limit !== undefined ||\n    options.all === true ||\n    options.allApps === true\n  );\n}\n\nfunction normalizeLimit(\n  limit: number | undefined,\n): { ok: true; value?: number } | { ok: false; error: string; fix: string } {\n  if (limit === undefined) return { ok: true };\n  if (Number.isInteger(limit) && limit > 0) {\n    return { ok: true, value: limit };\n  }\n  return {\n    ok: false,\n    error: \"capture --limit must be a positive integer\",\n    fix: \"pass --limit 1 or higher\",\n  };\n}\n\nfunction parseSinceCutoff(\n  since: string | undefined,\n  now: Date,\n): { ok: true; mtime?: number } | { ok: false; error: string; fix: string } {\n  if (since === undefined || since.trim().length === 0) return { ok: true };\n  const trimmed = since.trim();\n  const parsedDate = Date.parse(trimmed);\n  if (!Number.isNaN(parsedDate)) return { ok: true, mtime: parsedDate };\n  try {\n    return {\n      ok: true,\n      mtime: now.getTime() - parseDuration(trimmed) * 1000,\n    };\n  } catch {\n    return {\n      ok: false,\n      error: `invalid --since \"${since}\"`,\n      fix: \"pass a date or a duration like 2w, 30d, 12h, or 45m\",\n    };\n  }\n}\n\nasync function collectTranscripts(\n  projectsDir: string,\n): Promise<TranscriptEntry[]> {\n  const out: TranscriptEntry[] = [];\n  let topLevel: string[];\n  try {\n    topLevel = await readdir(projectsDir);\n  } catch {\n    return out;\n  }\n  for (const name of topLevel) {\n    const projectDir = join(projectsDir, name);\n    let entries: string[];\n    try {\n      entries = await readdir(projectDir);\n    } catch {\n      continue;\n    }\n    for (const entry of entries) {\n      if (!entry.endsWith(\".jsonl\")) continue;\n      const full = join(projectDir, entry);\n      try {\n        const st = await stat(full);\n        if (st.isFile()) out.push({ path: full, mtime: st.mtimeMs });\n      } catch {\n        continue;\n      }\n    }\n  }\n  return out;\n}\n\nasync function filterTranscriptsByCwd(\n  transcripts: TranscriptEntry[],\n  repoRoot: string,\n): Promise<TranscriptEntry[]> {\n  const dirHash = `-${repoRoot.replace(/^\\/+/, \"\").replace(/\\//g, \"-\")}`;\n  const byDirName = transcripts.filter((entry) => {\n    const parent = basename(join(entry.path, \"..\"));\n    return parent === dirHash || parent.endsWith(dirHash);\n  });\n  if (byDirName.length > 0) return byDirName;\n\n  const needle = `\"cwd\":\"${repoRoot}\"`;\n  const hits: TranscriptEntry[] = [];\n  for (const transcript of transcripts) {\n    try {\n      const head = await readHead(transcript.path, 4096);\n      if (head.includes(needle)) hits.push(transcript);\n    } catch {\n      continue;\n    }\n  }\n  return hits;\n}\n\nasync function readHead(path: string, bytes: number): Promise<string> {\n  const content = await readFile(path, \"utf8\");\n  return content.length > bytes ? content.slice(0, bytes) : content;\n}\n","import { runIndexer, type IndexResult } from \"../indexer/index.js\";\nimport { resolveWikiRoot } from \"../indexer/resolve-wiki.js\";\n\nexport interface ReindexOptions {\n  cwd: string;\n  wiki?: string;\n}\n\nexport interface ReindexCommandOutput {\n  result: IndexResult;\n  stdout: string;\n  exitCode: number;\n}\n\n/**\n * `almanac reindex` — force a full rebuild.\n *\n * Unlike the implicit reindex every query command triggers, this one\n * prints a summary line so the user gets feedback for an explicitly\n * requested action. The summary is terse on purpose (one line, three\n * numbers) — verbose progress reporting would fight the design rule that\n * the CLI stays quiet by default.\n */\nexport async function runReindex(\n  options: ReindexOptions,\n): Promise<ReindexCommandOutput> {\n  const repoRoot = await resolveWikiRoot({\n    cwd: options.cwd,\n    wiki: options.wiki,\n  });\n  const result = await runIndexer({ repoRoot });\n  // Summary wording: \"reindexed: N pages (K updated, R removed)\". When\n  // some files were on disk but never made it into the index\n  // (slug collisions, ENOENT races, un-sluggable filenames), tack on a\n  // `; S skipped` suffix so the user notices. The per-file reason was\n  // already written to stderr at indexing time.\n  const skipSuffix =\n    result.filesSkipped > 0 ? `; ${result.filesSkipped} skipped` : \"\";\n  const stdout = `reindexed: ${result.pagesIndexed} page${result.pagesIndexed === 1 ? \"\" : \"s\"} (${result.changed} updated, ${result.removed} removed${skipSuffix})\\n`;\n  return { result, stdout, exitCode: 0 };\n}\n","import { Command } from \"commander\";\n\nimport {\n  runHookInstall,\n  runHookStatus,\n  runHookUninstall,\n} from \"../commands/hook.js\";\nimport {\n  runJobsCancel,\n  runJobsList,\n  runJobsLogs,\n  runJobsShow,\n  streamJobsAttach,\n} from \"../commands/jobs.js\";\nimport {\n  runCaptureCommand,\n  runGardenCommand,\n  runIngestCommand,\n  runInitCommand,\n} from \"../commands/operations.js\";\nimport type { HarnessEvent } from \"../harness/events.js\";\nimport { runReindex } from \"../commands/reindex.js\";\nimport { autoRegisterIfNeeded } from \"../registry/autoregister.js\";\nimport {\n  deprecationWarning,\n  emit,\n  parsePositiveInt,\n  withWarning,\n} from \"./helpers.js\";\n\nexport function registerWikiLifecycleCommands(program: Command): void {\n  program\n    .command(\"init\")\n    .description(\"initialize and build this repo's CodeAlmanac wiki\")\n    .option(\"--using <provider[/model]>\", \"provider and optional model\")\n    .option(\"--background\", \"start as a background job\")\n    .option(\"--json\", \"emit structured JSON for background job start\")\n    .option(\"--force\", \"allow rebuilding an existing wiki\")\n    .option(\"-y, --yes\", \"confirm non-interactively\")\n    .action(\n      async (opts: {\n        using?: string;\n        background?: boolean;\n        json?: boolean;\n        force?: boolean;\n        yes?: boolean;\n      }) => {\n        const result = await runInitCommand({\n          cwd: process.cwd(),\n          using: opts.using,\n          background: opts.background,\n          json: opts.json,\n          force: opts.force,\n          yes: opts.yes,\n          onEvent: opts.background === true ? undefined : writeForegroundEvent,\n        });\n        emit(result);\n      },\n    );\n\n  const capture = program\n    .command(\"capture [sessionFiles...]\")\n    .alias(\"c\")\n    .description(\"absorb coding-session knowledge into the wiki\")\n    .option(\"--app <app>\", \"source app: claude, codex, cursor, or generic\")\n    .option(\"--session <id>\", \"target a specific session by ID\")\n    .option(\"--since <duration-or-date>\", \"capture sessions since a time\")\n    .option(\"--limit <n>\", \"maximum sessions to capture\", parsePositiveInt)\n    .option(\"--all\", \"capture all matching sessions\")\n    .option(\"--all-apps\", \"capture from all supported apps\")\n    .option(\"--using <provider[/model]>\", \"provider and optional model\")\n    .option(\"--foreground\", \"run now instead of starting a background job\")\n    .option(\"--json\", \"emit structured JSON for background job start\")\n    .option(\"-y, --yes\", \"confirm non-interactively\")\n    .action(\n      async (\n        sessionFiles: string[],\n        opts: {\n          app?: string;\n          session?: string;\n          since?: string;\n          limit?: number;\n          all?: boolean;\n          allApps?: boolean;\n          using?: string;\n          foreground?: boolean;\n          json?: boolean;\n          yes?: boolean;\n        },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runCaptureCommand({\n          cwd: process.cwd(),\n          sessionFiles,\n          app: opts.app,\n          session: opts.session,\n          since: opts.since,\n          limit: opts.limit,\n          all: opts.all,\n          allApps: opts.allApps,\n          using: opts.using,\n          foreground: opts.foreground,\n          json: opts.json,\n          yes: opts.yes,\n          onEvent: opts.foreground === true ? writeForegroundEvent : undefined,\n        });\n        emit(result);\n      },\n    );\n\n  program\n    .command(\"ingest <paths...>\")\n    .description(\"absorb knowledge from one or more files or folders\")\n    .option(\"--using <provider[/model]>\", \"provider and optional model\")\n    .option(\"--foreground\", \"run now instead of starting a background job\")\n    .option(\"--json\", \"emit structured JSON for background job start\")\n    .option(\"-y, --yes\", \"confirm non-interactively\")\n    .action(\n      async (\n        paths: string[],\n        opts: {\n          using?: string;\n          foreground?: boolean;\n          json?: boolean;\n          yes?: boolean;\n        },\n      ) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runIngestCommand({\n          cwd: process.cwd(),\n          paths,\n          using: opts.using,\n          foreground: opts.foreground,\n          json: opts.json,\n          yes: opts.yes,\n          onEvent: opts.foreground === true ? writeForegroundEvent : undefined,\n        });\n        emit(result);\n      },\n    );\n\n  program\n    .command(\"garden\")\n    .description(\"clean up, reconcile, and improve the wiki\")\n    .option(\"--using <provider[/model]>\", \"provider and optional model\")\n    .option(\"--foreground\", \"run now instead of starting a background job\")\n    .option(\"--json\", \"emit structured JSON for background job start\")\n    .option(\"-y, --yes\", \"confirm non-interactively\")\n    .action(\n      async (opts: {\n        using?: string;\n        foreground?: boolean;\n        json?: boolean;\n        yes?: boolean;\n      }) => {\n        await autoRegisterIfNeeded(process.cwd());\n        const result = await runGardenCommand({\n          cwd: process.cwd(),\n          using: opts.using,\n          foreground: opts.foreground,\n          json: opts.json,\n          yes: opts.yes,\n          onEvent: opts.foreground === true ? writeForegroundEvent : undefined,\n        });\n        emit(result);\n      },\n    );\n\n  const jobs = program\n    .command(\"jobs\")\n    .description(\"show and manage CodeAlmanac background jobs\");\n\n  jobs\n    .command(\"list\", { isDefault: true })\n    .description(\"list runs for this wiki\")\n    .option(\"--json\", \"emit structured JSON\")\n    .action(async (opts: { json?: boolean }) => {\n      const result = await runJobsList({\n        cwd: process.cwd(),\n        json: opts.json,\n      });\n      emit(result);\n    });\n\n  jobs\n    .command(\"show <run-id>\")\n    .description(\"show one run record\")\n    .option(\"--json\", \"emit structured JSON\")\n    .action(async (runId: string, opts: { json?: boolean }) => {\n      const result = await runJobsShow({\n        cwd: process.cwd(),\n        runId,\n        json: opts.json,\n      });\n      emit(result);\n    });\n\n  jobs\n    .command(\"logs <run-id>\")\n    .description(\"print a run's JSONL event log\")\n    .option(\"--json\", \"emit structured errors as JSON\")\n    .action(async (runId: string, opts: { json?: boolean }) => {\n      const result = await runJobsLogs({\n        cwd: process.cwd(),\n        runId,\n        json: opts.json,\n      });\n      emit(result);\n    });\n\n  jobs\n    .command(\"attach <run-id>\")\n    .description(\"stream a run log until the job exits\")\n    .option(\"--json\", \"emit structured errors as JSON\")\n    .action(async (runId: string, opts: { json?: boolean }) => {\n      const result = await streamJobsAttach({\n        cwd: process.cwd(),\n        runId,\n        json: opts.json,\n      });\n      emit(result);\n    });\n\n  jobs\n    .command(\"cancel <run-id>\")\n    .description(\"cancel a running or queued job\")\n    .option(\"--json\", \"emit structured JSON\")\n    .action(async (runId: string, opts: { json?: boolean }) => {\n      const result = await runJobsCancel({\n        cwd: process.cwd(),\n        runId,\n        json: opts.json,\n      });\n      emit(result);\n    });\n\n  capture\n    .command(\"status\")\n    .description(\"deprecated alias for jobs\")\n    .option(\"--json\", \"emit structured JSON\")\n    .action(async (opts: { json?: boolean }) => {\n      const result = await runJobsList({\n        cwd: process.cwd(),\n        json: opts.json,\n      });\n      emit(withWarning(\n        result,\n        deprecationWarning(\"almanac capture status\", \"almanac jobs\"),\n      ));\n    });\n\n  program\n    .command(\"ps\")\n    .description(\"deprecated alias for jobs\")\n    .option(\"--json\", \"emit structured JSON\")\n    .action(async (opts: { json?: boolean }) => {\n      const result = await runJobsList({\n        cwd: process.cwd(),\n        json: opts.json,\n      });\n      emit(withWarning(\n        result,\n        deprecationWarning(\"almanac ps\", \"almanac jobs\"),\n      ));\n    });\n\n  const hook = program\n    .command(\"hook\")\n    .description(\"manage the SessionEnd auto-capture hook\");\n\n  hook\n    .command(\"install\")\n    .description(\"add a SessionEnd entry that runs 'almanac capture' on session end\")\n    .option(\"--source <source>\", \"claude, codex, cursor, or all\")\n    .action(async (opts: { source?: string }) => {\n      const result = await runHookInstall({\n        source: normalizeHookSource(opts.source),\n      });\n      emit(result);\n    });\n\n  hook\n    .command(\"uninstall\")\n    .description(\"remove codealmanac's SessionEnd entry; leaves foreign entries alone\")\n    .action(async () => {\n      const result = await runHookUninstall();\n      emit(result);\n    });\n\n  hook\n    .command(\"status\")\n    .description(\"report whether the SessionEnd hook is installed\")\n    .action(async () => {\n      const result = await runHookStatus();\n      emit(result);\n    });\n\n  program\n    .command(\"reindex\")\n    .description(\"force a full rebuild of .almanac/index.db\")\n    .option(\"--wiki <name>\", \"target a specific registered wiki\")\n    .action(async (opts: { wiki?: string }) => {\n      await autoRegisterIfNeeded(process.cwd());\n      const result = await runReindex({\n        cwd: process.cwd(),\n        wiki: opts.wiki,\n      });\n      process.stdout.write(result.stdout);\n      if (result.exitCode !== 0) process.exitCode = result.exitCode;\n    });\n}\n\nfunction writeForegroundEvent(event: HarnessEvent): void {\n  const line = formatForegroundEvent(event);\n  if (line !== null) process.stdout.write(`${line}\\n`);\n}\n\nexport function formatForegroundEvent(event: HarnessEvent): string | null {\n  switch (event.type) {\n    case \"text\":\n      return event.content.trim().length > 0 ? event.content.trim() : null;\n    case \"tool_use\":\n      return `[tool] ${event.tool}`;\n    case \"tool_summary\":\n      return `[tool] ${event.summary}`;\n    case \"error\":\n      return null;\n    case \"done\":\n      return event.error !== undefined ? null : \"[done]\";\n    default:\n      return null;\n  }\n}\n\nfunction normalizeHookSource(\n  source: string | undefined,\n): \"claude\" | \"codex\" | \"cursor\" | \"all\" | undefined {\n  if (\n    source === \"claude\" ||\n    source === \"codex\" ||\n    source === \"cursor\" ||\n    source === \"all\"\n  ) {\n    return source;\n  }\n  return undefined;\n}\n","import { Command } from \"commander\";\n\nimport { registerEditCommands } from \"./register-edit-commands.js\";\nimport { registerQueryCommands } from \"./register-query-commands.js\";\nimport { registerSetupCommands } from \"./register-setup-commands.js\";\nimport { registerWikiLifecycleCommands } from \"./register-wiki-lifecycle-commands.js\";\n\nexport function registerCommands(program: Command): void {\n  registerQueryCommands(program);\n  registerEditCommands(program);\n  registerWikiLifecycleCommands(program);\n  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