@unbrained/pm-cli 2026.6.11 → 2026.6.12

package/docs/AGENT_GUIDE.md

@@ -75,6 +75,7 @@ pm append <item-id> --body "Implementation notes..."
 
 ```bash
 pm files <item-id> --add path=src/app.ts,note="entrypoint"
+pm files <item-id> --add src/app.ts --note "entrypoint"
 pm docs <item-id> --add path=docs/COMMANDS.md,note="public docs"
 pm test <item-id> --add command="node scripts/run-tests.mjs test -- tests/unit/app.spec.ts",timeout_seconds=240
 ```
@@ -118,6 +119,7 @@ pm release <item-id>
 | Register custom status | `pm schema add-status <id> --role <active\|terminal\|...> --alias <name> --order <n>` |
 | Remove custom status | `pm schema remove-status <id>` (warns if items use it; built-in statuses refused) |
 | Agent plan create | `pm plan create --title "<scope>" --harness claude-code --scope "<short>" --claim` |
+| Agent plan create with steps | `pm plan create --title "<scope>" --step "<step 1>" --step "<step 2>" --step "<step 3>"` (repeated `--step` seeds ordered steps) |
 | Agent plan step update | `pm plan update-step <plan-id> plan-step-001 --step-status in_progress --step-evidence "<short>"` |
 | Agent plan read | `pm plan show <plan-id> --depth brief` (or `--fields id,title,steps_summary`) |
 | Materialize plan steps | `pm plan materialize <plan-id> --steps plan-step-002 --materialize-type Task` |
@@ -180,7 +182,10 @@ Use these defaults unless the task requires otherwise:
 
 When gating on `pm health` / `pm validate`, read the executable fix command from the output instead of hardcoding a warning-code-to-command mapping:
 
-- `pm health --json` per-check `details.remediation_map` maps each warning-code prefix to a `pm` fix command (for example `{ "history_drift_missing_stream": "pm history-repair <id>" }`). It is present in default/`--full` output and omitted in `--brief`/`--summary`.
+- `pm health --json` per-check `details.remediation_map` maps each warning-code prefix to a `pm` fix command (for example `{ "history_drift_missing_stream": "pm history-repair <id>" }`). It is present in default/`--full` output and omitted in `--brief`/`--summary`. With more than one drifted stream the history_drift commands point at `pm history-repair --all` (one audited bulk pass) instead of the per-item template.
+- `pm health` includes a read-only `locks` check (stale/unreadable/unparseable lock counts using the same classification `pm gc --scope locks` acts on); `locks_stale_count:<n>` remediates via `pm gc --scope locks`, `locks_unreadable:<n>` via `pm gc --scope locks --dry-run`.
 - `pm validate --fix-hints` (read-only) adds `details.fix_hints[]` to each failing check — a uniform list of executable `pm` commands for that check's findings.
+- `pm validate --auto-fix` applies the safe, deterministic subset of those fixes itself (resolution/close_reason backfills derived from the item's own fields) and reports every action in `fixes.planned_fixes[]` / `applied_fixes[]` (item id + field + equivalent `pm` command). Preview with `--dry-run`. Structural lifecycle fixes (reparent an active child off a terminal parent, or clear the parent link) are gated behind an explicit `--fix-scope lifecycle`; they appear in `planned_fixes[]`/`gated_fixes[]` until granted. `--fix-scope` is an exact allowlist (default: `metadata`, `resolution`), so `--fix-scope lifecycle` applies only lifecycle fixes. Auto-fix never closes or deletes items.
+- `pm validate --prune-missing` removes stale linked-file/doc LINKS whose paths classify as `deleted` (no same-basename candidate left in the workspace scan); `moved` paths keep their relink candidate in `details.missing_linked_path_classifications` instead of being pruned. Honors `--dry-run`; never touches real files.
 
 Both draw from the same remediation registry, so an agent can substitute the concrete `<id>` and run the command to auto-repair findings. Extension health checks expose their remediation under `details.triage.remediation` instead. See [Command Reference](COMMANDS.md#self-repair-remediation).

package/docs/COMMANDS.md

@@ -269,12 +269,14 @@ Use comments for progress and evidence, notes for implementation context, and le
 
 ```bash
 pm files <id> --add path=src/cli/main.ts,note="command wiring"
+pm files <id> --add src/cli/main.ts --note "command wiring"
 pm files <id> --add-glob "src/cli/**/*.ts"
 pm docs <id> --add path=docs/COMMANDS.md,note="public command docs"
+pm docs <id> --add docs/COMMANDS.md --note "public command docs"
 pm deps <id> --format tree
 ```
 
-Linked files and docs keep reviews reproducible. `deps` is read-only and projects item relationships.
+Linked files and docs keep reviews reproducible. `deps` is read-only and projects item relationships. The standalone `--note <text>` flag annotates every link added by `--add`/`--add-glob` in the same invocation (a per-entry embedded `note=` wins); `--note` without an add is a usage error.
 
 ## Linked Tests
 
@@ -337,6 +339,9 @@ For `--include events` without explicit `--to`, `--recurrence-lookahead-days`, o
 pm validate --check-resolution --check-history-drift
 pm validate --check-files --scan-mode tracked-all
 pm validate --check-resolution --fix-hints --json
+pm validate --auto-fix --dry-run --json
+pm validate --auto-fix --fix-scope lifecycle
+pm validate --prune-missing --dry-run --json
 pm normalize --dry-run --json
 pm gc --dry-run
 pm gc --scope locks --dry-run
@@ -348,6 +353,12 @@ Use dry-run modes before broad lifecycle or cleanup changes.
 
 `--fix-hints` is a read-only flag: each failing check gains `details.fix_hints`, an array of `pm` command templates derived from the warning codes it raised (for example `pm history-repair <id>` for history drift, or `pm update <id> --reviewer "<name>"` for a missing reviewer). Generic hints may contain `<id>`/`<field>`/`<path>` placeholders the agent substitutes from the check's detail rows; the resolution check aliases concrete per-row commands and marks `fix_hints_truncated` when the list is summarized. It never mutates items. The mapping comes from the shared remediation registry that also backs `pm health --json` (see Self-Repair Remediation below), so agents gating on `pm validate` can auto-repair findings without hardcoding warning-code-to-command lookups.
 
+`pm validate --check-metadata` also groups missing-required-field counts per item type in `details.missing_by_type` (for example `{ "Task": { "close_reason": 3 } }`) — counts only, zero-suppressed, and limited to the active metadata profile's required fields, so remediation can be targeted by type without verbose row dumps.
+
+`--auto-fix` applies the safe, deterministic subset of those remediations automatically and reports the result under a top-level `fixes` object (`planned_fixes[]`, `applied_fixes[]`, `gated_fixes[]`, `failed_fixes[]` — each row lists the item id, check, field, and the equivalent standalone `pm` command). Safe means derivable and non-destructive: a closed item missing `resolution` is backfilled from its own `close_reason` (or the `"completed"` default), and a closed item missing `close_reason` is backfilled from its existing `resolution`. Auto-fix NEVER closes, cancels, or deletes items, and every applied fix runs through the normal audited `pm update` path. Structural lifecycle fixes — an active item whose parent is terminal gets reparented to its active grandparent or has its parent link cleared — are always *planned* but only *applied* when the explicit `--fix-scope lifecycle` grant is passed. `--fix-scope` is an exact allowlist of what `--auto-fix` may mutate (`metadata`, `resolution`, `lifecycle`; comma-separated or repeatable) — `--fix-scope lifecycle` alone applies *only* lifecycle fixes; omitting the flag grants the safe field-backfill scopes (`metadata`, `resolution`) and never lifecycle. `--dry-run` previews the full plan without mutating anything. With `--auto-fix` and no explicit `--check-*` flags, only the fix-capable checks (metadata, resolution, lifecycle) run. The `checks` in the output always describe the pre-fix state; re-run `pm validate` to confirm convergence.
+
+`pm validate --check-files` classifies every stale linked path in `details.missing_linked_path_classifications` as either `moved` (a file with the same basename still exists in the scan — the row carries the top relink candidate, e.g. `old/path.md:moved:new/path.md`) or `deleted` (no candidate anywhere, e.g. `old/path.md:deleted`). `--prune-missing` bulk-removes the stale links classified `deleted` from their items (link removal only — real files are never touched; `moved` links are kept so their relink candidates are not lost) and reports each removal in `fixes.applied_fixes[]` as the equivalent `pm files <id> --remove <path>` / `pm docs <id> --remove <path>` command. It honors `--dry-run` and implies `--check-files`.
+
 ### Telemetry Local Analytics
 
 `pm telemetry` surfaces local queue/runtime telemetry state without running full health checks:
@@ -376,10 +387,16 @@ pm telemetry local-analytics status
 "remediation_map": { "history_drift_missing_stream": "pm history-repair <id>" }
 // vectorization check
 "remediation_map": { "vectorization_stale_items_remaining": "pm health --refresh-vectors" }
+// locks check
+"remediation_map": { "locks_stale_count": "pm gc --scope locks" }
 ```
 
+When more than one history stream is drifted, the `history_drift` remediation commands are rewritten to `pm history-repair --all` so the whole tree is repaired in one audited pass instead of one command per stream.
+
 `remediation_map` appears in default and `--full` output and is omitted in `--brief`/`--summary` to stay token-efficient. Extension checks keep their existing richer `details.triage.remediation` instead.
 
+`pm health` also runs a read-only `locks` check alongside the storage check: it classifies every file in `locks/` with the exact policy `pm gc --scope locks` acts on and reports `active_lock_count`, `stale_lock_count`, `unreadable_lock_count`, and `unparseable_lock_count` (counts appear in all projection modes; nothing is ever removed). It warns with `locks_stale_count:<n>` when stale locks exist (fix: `pm gc --scope locks`) and `locks_unreadable:<n>` when lock files cannot be read (inspect first: `pm gc --scope locks --dry-run`).
+
 ## History and Recovery
 
 ```bash
@@ -394,6 +411,8 @@ pm history-redact <id> --literal "[redacted_path_prefix]/private" --replacement
 pm history-redact <id> --regex "/192\\.168\\.[0-9.]+/g" --dry-run
 pm history-repair <id> --dry-run
 pm history-repair <id> --message "re-anchor legacy drift"
+pm history-repair --all --dry-run
+pm history-repair --all --message "bulk re-anchor drifted streams"
 pm activity --id <id> --limit 50
 pm activity --full --id <id> --limit 50
 pm restore <id> <timestamp-or-version>
@@ -412,6 +431,7 @@ pm stats --storage --json
 `history-redact` rewrites matching history payloads deterministically, recomputes hash chains, and appends an auditable `history_redact` marker entry when changes are applied.
 `history-compact` rewrites long streams into a synthetic checkpoint baseline plus a retained tail (`--before` accepts a 1-based version or ISO timestamp), re-anchors hashes, verifies integrity, and appends an auditable `history_compact` marker when applied.
 `history-repair` re-anchors a drifted history chain when `pm health`/`pm validate --check-history-drift` report stale hashes: it replays the stream, recomputes every before/after hash, repairs legacy patch ops that no longer strictly apply, reconciles the latest hash with the on-disk item, and appends an auditable `history_repair` marker. It never modifies item content and is a safe no-op on a clean stream.
+`history-repair --all` (mutually exclusive with `<id>`) runs the same drift scan `pm health` uses and applies the audited single-stream repair (ownership check, lock, post-repair no-drift verification, `--message` audit marker, per-stream `--force`) to every drifted stream in one pass. One failing stream never aborts the rest: the result lists one compact row per drifted stream (`repaired` / `skipped_clean` / `failed`) plus `totals`, and the command exits non-zero only if any stream failed.
 
 ## Custom Item Types
 
@@ -456,6 +476,7 @@ The option composes with `--defaults`, `--preset`, `--author`, `--agent-guidance
 
 ```bash
 pm plan create --title "Refactor lock retry" --scope "Improve retry semantics" --harness claude-code --parent pm-epic1 --related pm-rel1,pm-rel2 --claim
+pm plan create --title "Fix flaky retry test" --step "Read lock.ts" --step "Write the fix" --step "Run the tests"
 pm plan add-step <plan-id> --step-title "Read lock.ts" --step-body "Inspect retry path" --depends-on pm-task1
 pm plan update-step <plan-id> plan-step-001 --step-status in_progress --step-evidence "started reading lock.ts"
 pm plan complete-step <plan-id> plan-step-001 --step-evidence "lock.ts read; retry path captured"
@@ -497,6 +518,7 @@ Invariants:
 
 - Exactly one step is `in_progress` per Plan; pass `--allow-multiple-active` for explicit parallel branches.
 - Blocking a step requires `--step-blocked-reason` (or an already-recorded reason).
+- `create` accepts repeated `--step <title>` flags to seed ordered steps in argv order (values are never comma-split). When `--step-title` is also given it becomes the first step. Per-step detail flags (`--step-body`, `--step-status`, `--file`, ...) apply to a single initial step only; combining them with multiple `--step` values is a usage error — create the plan first, then refine steps with `add-step`/`update-step`. On step subcommands a single `--step` value still aliases `--step-title`.
 - `materialize` adds `discovered_from` + `parent` to each new item and an `implements` link back on the source step plus a `child` dependency on the Plan.
 - Search keyword corpus includes plan_scope, step titles/bodies, decisions, discoveries, validation, and step linked items.
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@unbrained/pm-cli",
-  "version": "2026.6.11",
+  "version": "2026.6.12",
   "description": "Git-native project management CLI for humans and agents.",
   "type": "module",
   "author": "unbrained",

package/dist/cli-bundle/chunks/chunk-E5DUIJA4.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../../../../../../../cli/commands/linked-artifacts.ts"],
-  "sourcesContent": ["import fs from \"node:fs/promises\";\nimport path from \"node:path\";\nimport fg from \"fast-glob\";\nimport { pathExists } from \"../../core/fs/fs-utils.js\";\nimport { getActiveExtensionRegistrations } from \"../../core/extensions/index.js\";\nimport { createStdinTokenResolver, parseCsvKv } from \"../../core/item/parse.js\";\nimport { resolveItemTypeRegistry } from \"../../core/item/type-registry.js\";\nimport { EXIT_CODE } from \"../../core/shared/constants.js\";\nimport type { GlobalOptions } from \"../../core/shared/command-types.js\";\nimport { PmCliError } from \"../../core/shared/errors.js\";\nimport { listAllFrontMatter, locateItem, mutateItem, readLocatedItem } from \"../../core/store/item-store.js\";\nimport { getSettingsPath, resolvePmRoot } from \"../../core/store/paths.js\";\nimport { readSettings } from \"../../core/store/settings.js\";\nimport { SCOPE_VALUES } from \"../../types/index.js\";\nimport { resolveAuthor } from \"../../core/shared/author.js\";\nimport type { LinkScope } from \"../../types/index.js\";\n\nexport type LinkedArtifact = {\n  path: string;\n  scope: LinkScope;\n  note?: string;\n};\n\nexport interface LinkedArtifactCommandOptions {\n  add?: string[];\n  addGlob?: string[];\n  remove?: string[];\n  migrate?: string[];\n  list?: boolean;\n  appendStable?: boolean;\n  validatePaths?: boolean;\n  audit?: boolean;\n  author?: string;\n  message?: string;\n  force?: boolean;\n}\n\nexport interface PathMigration {\n  from: string;\n  to: string;\n}\n\nexport interface AddGlobEntry {\n  pattern: string;\n  scope: LinkScope;\n  note?: string;\n}\n\nexport interface LinkedPathValidation {\n  checked: number;\n  existing_files: string[];\n  missing_paths: string[];\n  non_file_paths: string[];\n}\n\nexport interface LinkedPathAuditEntry {\n  path: string;\n  linked_by_count: number;\n  linked_item_ids: string[];\n}\n\nexport interface LinkedArtifactResult {\n  id: string;\n  changed: boolean;\n  count: number;\n  migrations_applied?: number;\n  validation?: LinkedPathValidation;\n  audit?: LinkedPathAuditEntry[];\n  artifacts: LinkedArtifact[];\n}\n\n/**\n * Configuration that adapts the shared linked-artifact command core to a\n * specific resource kind (files or docs) while preserving every behavioral\n * detail of the original twin implementations.\n */\nexport interface LinkedArtifactKindConfig {\n  /** Metadata key under which the artifacts are stored (e.g. \"files\" | \"docs\"). */\n  metadataKey: \"files\" | \"docs\";\n  /** Mutation op recorded in history (e.g. \"files_add\" | \"docs_add\"). */\n  op: \"files_add\" | \"docs_add\";\n  /** Noun used in the \"bare <noun> path\" --add usage error (e.g. \"file\" | \"doc\"). */\n  bareNoun: \"file\" | \"doc\";\n  /**\n   * Whether this kind honors the append-stable option. files supports it;\n   * docs always sorts and must never expose append-stable behavior.\n   */\n  supportsAppendStable: boolean;\n}\n\nexport function ensureScope(raw: string | undefined): LinkScope {\n  const value = (raw ?? \"project\") as LinkScope;\n  if (!SCOPE_VALUES.includes(value)) {\n    throw new PmCliError(\n      `Invalid scope \"${raw}\". Valid scopes: ${SCOPE_VALUES.join(\", \")} (default: project).`,\n      EXIT_CODE.USAGE,\n    );\n  }\n  return value;\n}\n\nexport function looksLikeStructuredPathEntry(raw: string): boolean {\n  if (raw.startsWith(\"```\") || raw.includes(\"\\n\")) {\n    return true;\n  }\n  return /^(?:[-*+]\\s+)?(?:path|scope|note)\\s*[:=]/i.test(raw);\n}\n\nexport function parseAddEntries(raw: string[] | undefined, bareNoun: \"file\" | \"doc\"): LinkedArtifact[] {\n  if (!raw) return [];\n  return raw.map((entry) => {\n    const trimmed = entry.trim();\n    const kv = looksLikeStructuredPathEntry(trimmed) ? parseCsvKv(entry, \"--add\") : { path: trimmed };\n    if (!kv.path) {\n      throw new PmCliError(`--add requires path=<value> or a bare ${bareNoun} path`, EXIT_CODE.USAGE);\n    }\n    return {\n      path: kv.path,\n      scope: ensureScope(kv.scope),\n      note: kv.note?.trim() || undefined,\n    };\n  });\n}\n\nexport function parseAddGlobEntries(raw: string[] | undefined): AddGlobEntry[] {\n  if (!raw) return [];\n  return raw.map((entry) => {\n    const trimmed = entry.trim();\n    if (!trimmed) {\n      throw new PmCliError(\"--add-glob requires a glob pattern value\", EXIT_CODE.USAGE);\n    }\n    if (trimmed.includes(\"=\") || /^(?:[-*+]\\s+)?(?:pattern|glob|path)\\s*[:=]/i.test(trimmed) || trimmed.startsWith(\"```\")) {\n      const kv = parseCsvKv(trimmed, \"--add-glob\");\n      const pattern = kv.pattern?.trim() || kv.glob?.trim() || kv.path?.trim();\n      if (!pattern) {\n        throw new PmCliError(\"--add-glob key/value form requires pattern=<glob>\", EXIT_CODE.USAGE);\n      }\n      return {\n        pattern,\n        scope: ensureScope(kv.scope),\n        note: kv.note?.trim() || undefined,\n      };\n    }\n    return {\n      pattern: trimmed,\n      scope: \"project\",\n    };\n  });\n}\n\nexport function parseRemoveEntries(raw: string[] | undefined): string[] {\n  if (!raw) return [];\n  return raw.map((entry) => {\n    const trimmed = entry.trim();\n    if (!trimmed) {\n      throw new PmCliError(\"--remove requires a path value\", EXIT_CODE.USAGE);\n    }\n    if (trimmed.includes(\"=\") || /^(?:[-*+]\\s+)?path\\s*[:=]/i.test(trimmed) || trimmed.startsWith(\"```\")) {\n      const kv = parseCsvKv(trimmed, \"--remove\");\n      if (!kv.path) {\n        throw new PmCliError(\"--remove key/value form requires path=<value>\", EXIT_CODE.USAGE);\n      }\n      return kv.path;\n    }\n    return trimmed;\n  });\n}\n\nexport function parseMigrateEntries(raw: string[] | undefined): PathMigration[] {\n  if (!raw) return [];\n  return raw.map((entry) => {\n    const kv = parseCsvKv(entry, \"--migrate\");\n    const from = kv.from?.trim();\n    const to = kv.to?.trim();\n    if (!from || !to) {\n      throw new PmCliError(\"--migrate requires from=<value> and to=<value>\", EXIT_CODE.USAGE);\n    }\n    return { from, to };\n  });\n}\n\nexport function applyPathMigrations(artifactPath: string, migrations: PathMigration[]): string {\n  let next = artifactPath;\n  for (const migration of migrations) {\n    if (next.startsWith(migration.from)) {\n      next = `${migration.to}${next.slice(migration.from.length)}`;\n    }\n  }\n  return next;\n}\n\nexport function normalizeLinkedPath(value: string): string {\n  return value.split(path.sep).join(\"/\");\n}\n\nexport async function expandAddGlobEntries(entries: AddGlobEntry[]): Promise<LinkedArtifact[]> {\n  const expanded: LinkedArtifact[] = [];\n  for (const entry of entries) {\n    const absolutePattern = path.isAbsolute(entry.pattern);\n    const matches = await fg(entry.pattern, {\n      cwd: process.cwd(),\n      absolute: absolutePattern,\n      onlyFiles: true,\n      dot: true,\n      unique: true,\n      followSymbolicLinks: true,\n    });\n    const sortedMatches = [...new Set(matches.map((match) => normalizeLinkedPath(path.normalize(match))))].sort((left, right) =>\n      left.localeCompare(right),\n    );\n    for (const matchedPath of sortedMatches) {\n      expanded.push({\n        path: matchedPath,\n        scope: entry.scope,\n        note: entry.note,\n      });\n    }\n  }\n  return expanded;\n}\n\nexport function artifactKey(value: Pick<LinkedArtifact, \"path\" | \"scope\">): string {\n  return `${value.path}::${value.scope}`;\n}\n\nexport function sortLinkedArtifacts(artifacts: LinkedArtifact[]): LinkedArtifact[] {\n  return [...artifacts].sort((left, right) => {\n    const byPath = left.path.localeCompare(right.path);\n    if (byPath !== 0) return byPath;\n    return left.scope.localeCompare(right.scope);\n  });\n}\n\nexport function dedupeLinkedArtifacts(artifacts: LinkedArtifact[]): LinkedArtifact[] {\n  return [...new Map(artifacts.map((entry) => [artifactKey(entry), entry])).values()].map((entry) => ({\n    ...entry,\n    note: entry.note?.trim() || undefined,\n  }));\n}\n\nexport async function validateLinkedPaths(paths: string[]): Promise<LinkedPathValidation> {\n  const uniquePaths = [...new Set(paths)].sort((left, right) => left.localeCompare(right));\n  const existingFiles: string[] = [];\n  const missingPaths: string[] = [];\n  const nonFilePaths: string[] = [];\n  for (const relativePath of uniquePaths) {\n    const resolvedPath = path.isAbsolute(relativePath) ? relativePath : path.resolve(process.cwd(), relativePath);\n    try {\n      const stats = await fs.stat(resolvedPath);\n      if (stats.isFile()) {\n        existingFiles.push(relativePath);\n      } else {\n        nonFilePaths.push(relativePath);\n      }\n    } catch (error: unknown) {\n      if (typeof error === \"object\" && error !== null && \"code\" in error && (error as { code?: string }).code === \"ENOENT\") {\n        missingPaths.push(relativePath);\n        continue;\n      }\n      nonFilePaths.push(relativePath);\n    }\n  }\n  return {\n    checked: uniquePaths.length,\n    existing_files: existingFiles,\n    missing_paths: missingPaths,\n    non_file_paths: nonFilePaths,\n  };\n}\n\nexport function buildLinkedPathAudit(\n  paths: string[],\n  allItems: Array<{ id: string; artifacts?: LinkedArtifact[] }>,\n): LinkedPathAuditEntry[] {\n  const index = new Map<string, Set<string>>();\n  for (const item of allItems) {\n    for (const linkedArtifact of item.artifacts ?? []) {\n      const seen = index.get(linkedArtifact.path) ?? new Set<string>();\n      seen.add(item.id);\n      index.set(linkedArtifact.path, seen);\n    }\n  }\n  return [...new Set(paths)]\n    .sort((left, right) => left.localeCompare(right))\n    .map((linkedPath) => {\n      const linkedIds = [...(index.get(linkedPath) ?? new Set<string>())].sort((left, right) => left.localeCompare(right));\n      return {\n        path: linkedPath,\n        linked_by_count: linkedIds.length,\n        linked_item_ids: linkedIds,\n      };\n    });\n}\n\n/**\n * Shared linked-artifact list/mutate command core used by runFiles and runDocs.\n * The kind config selects metadata key, op, bare-path noun, and whether\n * append-stable ordering is honored, preserving each twin's exact semantics.\n */\nexport async function runLinkedArtifacts(\n  id: string,\n  options: LinkedArtifactCommandOptions,\n  global: GlobalOptions,\n  config: LinkedArtifactKindConfig,\n): Promise<LinkedArtifactResult> {\n  const { metadataKey } = config;\n  const stdinResolver = createStdinTokenResolver();\n  const pmRoot = resolvePmRoot(process.cwd(), global.path);\n  if (!(await pathExists(getSettingsPath(pmRoot)))) {\n    throw new PmCliError(`Tracker is not initialized at ${pmRoot}. Run pm init first.`, EXIT_CODE.NOT_FOUND);\n  }\n  const settings = await readSettings(pmRoot);\n  const typeRegistry = resolveItemTypeRegistry(settings, getActiveExtensionRegistrations());\n  const resolvedAdds = await stdinResolver.resolveList(options.add, \"--add\");\n  const resolvedAddGlobs = await stdinResolver.resolveList(options.addGlob, \"--add-glob\");\n  const resolvedRemoves = await stdinResolver.resolveList(options.remove, \"--remove\");\n  const resolvedMigrations = await stdinResolver.resolveList(options.migrate, \"--migrate\");\n  const parsedAdds = parseAddEntries(resolvedAdds, config.bareNoun);\n  const addGlobs = parseAddGlobEntries(resolvedAddGlobs);\n  const expandedGlobAdds = await expandAddGlobEntries(addGlobs);\n  const adds = [...parsedAdds, ...expandedGlobAdds];\n  const removes = parseRemoveEntries(resolvedRemoves);\n  const migrations = parseMigrateEntries(resolvedMigrations);\n  const shouldMutate = adds.length > 0 || removes.length > 0 || migrations.length > 0;\n\n  const collectAuditItems = async (): Promise<Array<{ id: string; artifacts?: LinkedArtifact[] }>> =>\n    (await listAllFrontMatter(pmRoot, settings.item_format, typeRegistry.type_to_folder, undefined, settings.schema)).map((entry) => ({\n      id: entry.id,\n      artifacts: (entry as Record<string, unknown>)[metadataKey] as LinkedArtifact[] | undefined,\n    }));\n\n  if (!shouldMutate) {\n    const located = await locateItem(pmRoot, id, settings.id_prefix, settings.item_format, typeRegistry.type_to_folder);\n    if (!located) {\n      throw new PmCliError(`Item ${id} not found`, EXIT_CODE.NOT_FOUND);\n    }\n    const loaded = await readLocatedItem(located, { schema: settings.schema });\n    const artifacts = ((loaded.document.metadata as Record<string, unknown>)[metadataKey] as LinkedArtifact[] | undefined) ?? [];\n    return {\n      id: located.id,\n      artifacts,\n      changed: false,\n      count: artifacts.length,\n      validation: options.validatePaths ? await validateLinkedPaths(artifacts.map((entry) => entry.path)) : undefined,\n      audit: options.audit ? buildLinkedPathAudit(artifacts.map((entry) => entry.path), await collectAuditItems()) : undefined,\n    };\n  }\n\n  const author = resolveAuthor(options.author, settings.author_default);\n  const result = await mutateItem({\n    pmRoot,\n    settings,\n    id,\n    op: config.op,\n    author,\n    message: options.message,\n    force: options.force,\n    mutate(document) {\n      const metadata = document.metadata as Record<string, unknown>;\n      const next = [...((metadata[metadataKey] as LinkedArtifact[] | undefined) ?? [])];\n      let migrationCount = 0;\n      if (migrations.length > 0) {\n        for (let index = 0; index < next.length; index += 1) {\n          const migratedPath = applyPathMigrations(next[index].path, migrations);\n          if (migratedPath !== next[index].path) {\n            next[index] = { ...next[index], path: migratedPath };\n            migrationCount += 1;\n          }\n        }\n      }\n      const migratedAdds = adds.map((entry) => {\n        const migratedPath = applyPathMigrations(entry.path, migrations);\n        if (migratedPath !== entry.path) {\n          migrationCount += 1;\n        }\n        return {\n          ...entry,\n          path: migratedPath,\n        };\n      });\n      const migratedRemoves = removes.map((entry) => applyPathMigrations(entry, migrations));\n      for (const add of migratedAdds) {\n        const exists = next.some((entry) => entry.path === add.path && entry.scope === add.scope);\n        if (!exists) {\n          next.push(add);\n        }\n      }\n      if (migratedRemoves.length > 0) {\n        for (let i = next.length - 1; i >= 0; i -= 1) {\n          if (migratedRemoves.includes(next[i].path)) {\n            next.splice(i, 1);\n          }\n        }\n      }\n      const deduped = dedupeLinkedArtifacts(next);\n      const normalized = config.supportsAppendStable && options.appendStable ? deduped : sortLinkedArtifacts(deduped);\n      if (normalized.length > 0) {\n        metadata[metadataKey] = normalized;\n      } else {\n        delete metadata[metadataKey];\n      }\n      return { changedFields: [metadataKey], warnings: migrationCount > 0 ? [`path_migrations_applied:${migrationCount}`] : [] };\n    },\n  });\n\n  const artifacts = ((result.item as Record<string, unknown>)[metadataKey] as LinkedArtifact[] | undefined) ?? [];\n  const migrationWarning = result.warnings.find((warning) => warning.startsWith(\"path_migrations_applied:\"));\n  const migrationCount = migrationWarning ? Number(migrationWarning.slice(\"path_migrations_applied:\".length)) : 0;\n  const allItems = options.audit ? await collectAuditItems() : [];\n  return {\n    id: result.item.id,\n    artifacts,\n    changed: true,\n    count: artifacts.length,\n    migrations_applied: migrationCount > 0 ? migrationCount : undefined,\n    validation: options.validatePaths ? await validateLinkedPaths(artifacts.map((entry) => entry.path)) : undefined,\n    audit: options.audit ? buildLinkedPathAudit(artifacts.map((entry) => entry.path), allItems) : undefined,\n  };\n}\n\n/**\n * Re-key the generic `artifacts` field to the resource-specific name (files/docs)\n * while preserving the original key order and presence so kind-specific result\n * shapes (and their deterministic JSON key ordering) stay byte-identical.\n */\nexport function renameArtifactsResultKey(result: LinkedArtifactResult, key: \"files\" | \"docs\"): Record<string, unknown> {\n  const out: Record<string, unknown> = {};\n  for (const [field, value] of Object.entries(result)) {\n    out[field === \"artifacts\" ? key : field] = value;\n  }\n  return out;\n}\n"],
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