@open-agent-toolkit/cli 0.3.16 → 0.3.18

package/assets/skills/oat-wave-execute/SKILL.md

@@ -6,7 +6,7 @@ disable-model-invocation: false
 user-invocable: true
 allowed-tools: Read, Write, Edit, Bash, Grep, Glob, Task
 metadata:
-  version: 1.9.6
+  version: 1.9.7
 ---
 
 # Execute a Wave of External Plans
@@ -25,6 +25,10 @@ Historical `DR-*` and `BL-*` slugs in this skill (including the provenance
 record above) are evidence citations in the source program's repository; they
 are not required artifacts in the consuming repo.
 
+## Hook-safe exact-path commits
+
+Before a parent-branch commit, verify `oat internal commit-paths --help` succeeds. If unavailable, stop and update the OAT CLI; never fall back to a staged-index or pathspec-only commit. Set `COMMIT_IDENTITY` to a unique operation/artifact identity before the first attempt and retain it for every retry; use a new identity for a new operation. Pass only the exact produced file list, including tracked removals and both names of a rename. A blocked/failed result stops the workflow; retain its receipt and follow its diagnostics. Hooks remain enabled. Synced project artifacts continue through `oat project push`.
+
 ## Progress Indicators (User-Facing)
 
 Print this banner once when execution starts:
@@ -256,6 +260,12 @@ terminal state for gate rows (Orc operator-audit S8).
 Persist the gate artifact and its dispositions through the wrapper project's
 scope-aware bookkeeping route:
 
+Before running the gate, initialize `WAVE_GATE_OUTPUT_PATHS=()` and append the
+exact plan, state, implementation, review and receive-receipt files each gate
+producer actually writes. Include tracked removals and both rename sides, omit
+ignored outputs, and retain the list through retries. Do not discover ownership
+from a project-directory or staged-index diff.
+
 ```bash
 PROJECT_PATH=$(oat config get activeProject 2>/dev/null || true)
 if [ -z "$PROJECT_PATH" ]; then
@@ -267,14 +277,9 @@ PROJECT_SCOPE=$(oat project scope "$PROJECT_PATH" --format value) || { echo "oat
 if [ "$PROJECT_SCOPE" = "synced" ]; then
   oat project push "$PROJECT_PATH" --message "chore(oat): record wave plan gate" || { echo "oat: project push failed; run oat project pull, resolve the reported state, and retry" >&2; exit 1; }
 else
-  PROJECT_OUTPUT_PATHS=()
-  while IFS= read -r output_path; do
-    PROJECT_OUTPUT_PATHS+=("$output_path")
-  done < <(git diff --name-only -- "$PROJECT_PATH")
-  [ "${#PROJECT_OUTPUT_PATHS[@]}" -gt 0 ] || exit 1
-  git add -- "${PROJECT_OUTPUT_PATHS[@]}"
-  git diff --cached --quiet -- "${PROJECT_OUTPUT_PATHS[@]}" ||
-    git commit --only -m "chore(oat): record wave plan gate" -- "${PROJECT_OUTPUT_PATHS[@]}"
+  : "${WAVE_GATE_OUTPUT_PATHS:?retain the exact gate producer file list}"
+  OWNED_COMMIT_PATHS=("${WAVE_GATE_OUTPUT_PATHS[@]}")
+  oat internal commit-paths --identity "${COMMIT_IDENTITY:?set once and retain for retries}:oat-wave-execute:1" --message "chore(oat): record wave plan gate" -- "${OWNED_COMMIT_PATHS[@]}" || exit 1
 fi
 ```
 
@@ -392,8 +397,16 @@ archive anything first.
    `summary.md`** (this is the "before any archive step" gate): convention
    verdicts with evidence, adjustments-as-rules for later waves, graduated-entries
    ledger, rolled into `summary.md` `## Workflow Observations`.
-3. **Serialized backlog archival** — `oat backlog archive` with real summaries,
-   one commit.
+3. **Serialized backlog archival** — run `oat backlog archive --json` for
+   each item with its real outcome summary. Union and deduplicate all returned
+   `affectedPaths`, including tracked old item deletions, new destinations,
+   ledger/index and rewritten references; append owned handoff filesystem
+   deletions. Format existing supported text with the repository command,
+   then use `oat internal commit-paths` for one exact-operation commit with
+   enabled hooks and the unique retained `COMMIT_IDENTITY`. Stop if the helper
+   is unavailable or blocked/failed; unrelated staged/unstaged work survives.
+   A settled noop returns only actual repairs; do not infer paths from every
+   archived link or commit only the old missing path.
 4. **Closeout gate run** — after the archival commit, and after ANY later commit
    that touches a gated surface (`.oat/repo/**`, `.agents/**`, `packages/**`,
    `apps/**`), re-run the integration DoD gates with cache bypass. The last

package/assets/skills/oat-wave-execute/assets/wrapper-plan-template.md

@@ -119,8 +119,16 @@ disposition every finding in the phase report. }
 
 **Step { N }: Commit**
 
+Before task edits, initialize `TASK_OWNED_FILES=()` and append the exact files
+at each source-plan producer, including created files, tracked removals and both
+rename sides. Retain the complete list and a stable unique `COMMIT_IDENTITY`
+for this wrapper task through retries; each task uses its own identity/suffix.
+Never infer ownership from the staged index or pass directories. Verify
+`oat internal commit-paths --help` first; if unavailable, stop and update the CLI.
+A nonzero result stops with its receipt and diagnostic; hooks remain enabled.
+
 ```bash
-git commit -m "{type}(p{NN}-t01): { description }"
+oat internal commit-paths --identity "${COMMIT_IDENTITY:?set once and retain for retries}:oat-wave-execute:wrapper-plan-template:p{NN}-t01" --message "{type}(p{NN}-t01): { description }" -- "${TASK_OWNED_FILES[@]}" || exit 1
 ```
 
 ---
@@ -144,7 +152,13 @@ git commit -m "{type}(p{NN}-t01): { description }"
 - [ ] { N }/{ N } phases, { M }/{ M } tasks complete
 - [ ] Every source plan's `## Done criteria` confirmed (recorded in `implementation.md`)
 - [ ] **Serialized backlog bookkeeping** (integration branch, after all merges):
-      `oat backlog archive` with real outcome summaries for { backlog IDs }, one commit
+      `oat backlog archive --json` with real outcome summaries for { backlog IDs }.
+      Union complete returned `affectedPaths` (tracked old deletions, new
+      destinations, ledger/index/references), append owned handoff filesystem
+      deletions, format existing text with the repo command, and create one
+      `oat internal commit-paths` commit with enabled hooks and a retained unique
+      identity. Stop on unavailable/blocked/failed helper; preserve unrelated
+      staged/unstaged work.
 - [ ] Orchestration-log end-of-run synthesis written; roll-up into `summary.md`
       before any archive step
 - [ ] Full DoD gates green on the integration branch

package/assets/skills/oat-worktree-bootstrap-auto/SKILL.md

@@ -6,7 +6,7 @@ disable-model-invocation: false
 user-invocable: false
 allowed-tools: Read, Write, Bash, Glob, Grep
 metadata:
-  version: 1.6.2
+  version: 1.6.3
 ---
 
 # Autonomous Worktree Bootstrap
@@ -17,6 +17,10 @@ This skill is **model-invocable** (`disable-model-invocation: false`): orchestra
 
 > ⚠️ **When not to substitute.** This skill is the **only** supported mechanism for orchestrator-driven worktree creation in OAT skills. Host-native isolation primitives — Claude Code's `Agent({ isolation: "worktree" })`, Cursor's worktree-isolated agent invocations, and equivalents in other hosts — are **not** substitutes. They may use the primary repo's checkout (often `main`) as the base regardless of the caller's current branch, silently producing a worktree at the wrong base. OAT orchestrators dispatching mid-run from a feature branch MUST go through this skill with an explicit `--base` so the resulting worktree contains the orchestrator's prior commits.
 
+## Hook-safe exact-path commits
+
+Before a parent-branch commit, verify `oat internal commit-paths --help` succeeds. If unavailable, stop and update the OAT CLI; never fall back to a staged-index or pathspec-only commit. Set `COMMIT_IDENTITY` to a unique operation/artifact identity before the first attempt and retain it for every retry; use a new identity for a new operation. Pass only the exact produced file list, including tracked removals and both names of a rename. A blocked/failed result stops the workflow; retain its receipt and follow its diagnostics. Hooks remain enabled. Synced project artifacts continue through `oat project push`.
+
 ## Relationship to oat-worktree-bootstrap
 
 This skill is the **autonomous companion** to `oat-worktree-bootstrap`. Key differences:
@@ -358,28 +362,52 @@ Create them if missing, run the `git_clean` baseline check, and then run sync:
 mkdir -p "{target-path}/.claude/skills"
 mkdir -p "{target-path}/.cursor/rules"
 git status --porcelain
-oat sync --scope all
+SYNC_PLAN_JSON=$(oat sync --scope all --dry-run --json) || exit 1
+SYNC_OUTPUT_FILES=()
+# Populate the exact list from the producer evidence described below before apply.
+SYNC_RESULT_JSON=$(oat sync --scope all --json) || exit 1
 ```
 
-After sync completes, commit sync-managed output if any scoped path is dirty:
+Before the apply invocation, populate `SYNC_OUTPUT_FILES` from the supported
+`SYNC_PLAN_JSON.plans[]` entries/removals for `scope: project`:
+
+- `providerPath` is the planned target, and `canonical.isFile` identifies file
+  assets. Include that exact file for a mutating operation; include old tracked
+  paths for removals. Skip `operation: skip` unless the manifest was restamped.
+- A symlink projection owns the single provider symlink path. A copy projection
+  of a directory owns concrete copied members: enumerate the canonical producer
+  files before applying and map each relative member to its provider destination.
+  Capture the exact existing tracked members with literal `git ls-files -z`
+  before a planned removal. Do not discover this list from the staged index.
+- Include `.oat/sync/manifest.json` when the project manifest is written. Omit
+  ignored output files and user-scope paths, which are outside the worktree.
+- `operationResults[]` reports scope/provider/contentKind/asset/action/status,
+  **not file paths**. Match those identities to the planned entries/removals and
+  require successful/current results before committing. Materialization
+  extensions expose their own `operations[].path`; include only verified
+  concrete project files. Collection/directory outcomes require complete
+  producer member evidence. Stop on unknown, failed, incomplete or changed
+  inventories; never pass a directory to the helper.
+
+Append each exact planned output to `SYNC_OUTPUT_FILES` before mutation and
+verify it against the actual result after sync. Include both rename sides and
+retain the list and identity through a retry. The helper never expands a
+provider directory or invents a producer inventory.
+
+After sync completes, commit the retained exact list:
 
 ```bash
-SYNC_PATHS=(.oat/sync/manifest.json .claude .cursor .codex)
-SYNC_STAGE_PATHS=(existing-or-tracked sync paths)
-git status --porcelain -- "${SYNC_STAGE_PATHS[@]}"
-git add -A -- "${SYNC_STAGE_PATHS[@]}"
-STAGED_SYNC_FILES=(staged sync-managed files from git diff --cached)
-git commit -m "chore: run sync" -- "${STAGED_SYNC_FILES[@]}"
+if [ "${#SYNC_OUTPUT_FILES[@]}" -gt 0 ]; then
+  oat internal commit-paths --identity "${COMMIT_IDENTITY:?set once and retain for retries}:oat-worktree-bootstrap-auto:1" --message "chore: run sync" -- "${SYNC_OUTPUT_FILES[@]}" || exit 1
+else
+  echo "sync_commit: skip"
+fi
 ```
 
-Use a staged-diff guard so no empty commit is created. After scoped staging,
-derive the concrete staged sync-managed files from
-`git diff --cached --name-only --no-renames -- "${SYNC_STAGE_PATHS[@]}"` and
-commit only those file paths. Do not pass provider directory pathspecs to
-`git commit`, because empty provider directories can make the commit fail. This
-file-list isolation is what keeps `chore: run sync` limited to sync-managed
-paths even if unrelated files were already staged. If no scoped path is dirty,
-or staging produces no diff, report `sync_commit: skip`.
+A `nothing` result reports `sync_commit: skip`; blocked/failed results
+stop bootstrap and retain the helper's resumable diagnostic. Never use directory
+pathspecs, staged-diff discovery, or an empty broad commit. Smoke mode continues
+to skip sync and this commit entirely.
 
 ### Step 5: Return Structured Status
 

package/assets/templates/pjm-agents.md

@@ -31,15 +31,41 @@ Invariant: `backlog/items/` holds only active work (`status: open` or
 The agent or person shipping the work owns the close-out, in the same
 commit/PR as the work whenever practical.
 
-**Close-out (primary path).** Run `oat backlog archive <id>` — add `--wont-do`
-for abandoned work and `--summary "<text>"` to record the outcome. The command
+**Close-out (primary path).** Run `oat backlog archive <id> --summary "<outcome>" --json`
+for completed work; a nonblank summary is required. Add `--wont-do` for
+abandoned work; that path may omit its summary and ledger entry. The command
 performs the whole close-out atomically: it flips `status` to the terminal
 value and bumps `updated`, appends the canonical `backlog/completed.md` entry
 (always for `closed`; for `wont_do` only when `--summary` is given), moves the
 item file from `backlog/items/` to `backlog/archived/`, rewrites inbound
 `.oat/repo` links and path references to the moved file (reporting each
-rewritten file), and regenerates `backlog/index.md`. Stage the resulting
-changes with the shipping commit/PR.
+rewritten file), and regenerates `backlog/index.md`. Commit the resulting
+changes through the exact-path close-out below with the shipping commit/PR.
+
+Archive never stages files. Capture each successful `--json` result and retain
+its complete `affectedPaths` array, including the old tracked item deletion,
+the archived destination, completed ledger, index and rewritten references.
+On retry use the returned operation paths; do not reconstruct ownership from
+all files that mention the item. If this close-out owns a kickoff handoff,
+remove it with a filesystem operation and append its tracked deletion path.
+Convert returned absolute paths to literal repository-relative files using
+the same repository root (avoiding checkout/scratch-path aliases).
+Deduplicate the exact file list, format only existing supported text files
+with the repository's documented formatter, and commit that list through
+`oat internal commit-paths` with enabled hooks. Verify helper availability
+first; if unavailable, stop and update the CLI. Set a unique `COMMIT_IDENTITY`
+before the first attempt and retain the identity, message and literal paths
+through retries; a blocked/failed helper result stops close-out. Unrelated
+staged and unstaged work must remain intact. An empty settled-noop path list
+needs no commit; omit a missing source path only if Git proves it was never
+tracked, never omit a tracked old path or the new destination.
+
+```bash
+oat internal commit-paths --help || exit 1
+# ARCHIVE_OWNED_FILES is the literal affectedPaths union plus owned handoff deletion.
+# Format the existing text members with the repository's documented write command.
+oat internal commit-paths --identity "${COMMIT_IDENTITY:?set once and retain for retries}:backlog-closeout" --message "chore(pjm): archive completed backlog work" -- "${ARCHIVE_OWNED_FILES[@]}" || exit 1
+```
 
 **Manual fallback.** These are the steps the command automates — follow them, in
 order, only when closing out by hand:
@@ -48,13 +74,16 @@ order, only when closing out by hand:
 2. Append a summary entry to `backlog/completed.md` (newest first; entry format
    is documented at the top of that file). Add the entry for a `wont_do` item
    only when the abandonment itself is worth recording (an explicit summary).
-3. `git mv` the item file from `backlog/items/` to `backlog/archived/`, then
+3. Move the item file with a filesystem rename (`mv`, without staging) from `backlog/items/` to `backlog/archived/`, then
    rewrite inbound `.oat/repo` links to `archived/` (plans, decision records,
    other items, and repository-root paths such as `oat_external_plan_sources`).
-4. Run `oat backlog regenerate-index` and stage the regenerated
-   `backlog/index.md`.
+4. Run `oat backlog regenerate-index`; include the regenerated
+   `backlog/index.md` in the exact owned path list.
 5. If the completion changes the operating picture, refresh
    `current-state.md` and the curated overview section of `backlog/index.md`.
+6. Collect both old/new item names, every written ledger/index/reference and
+   any owned handoff deletion, format existing text, then commit the complete
+   operation through `oat internal commit-paths` as above.
 
 A partial close-out (status flipped or `completed.md` updated, but the file
 left in `items/`) is how drift starts — finish all steps or none. `oat pjm
@@ -97,7 +126,8 @@ convention.
   - repo conventions and verification gates the item file does not restate;
   - a close-out section requiring (a) the **Backlog Lifecycle** above executed
     in the same PR that ships the item and (b) deletion of the handoff file
-    (`git rm`) in that same PR.
+    (filesystem removal, included as an owned tracked deletion in
+    the same exact-path commit) in that same PR.
 - **Staleness:** if a later alignment pass drops an item from the kickoff
   stack, delete its handoff in that pass rather than letting it drift.
 - Every backlog item reference — in review output, alignment docs, and

package/assets/templates/repo-agents.md

@@ -15,3 +15,8 @@ Use this directory as the canonical OAT repo-reference root.
   `oat backlog archive <id>` in the same PR that ships the work.
 - `README.md` is the human-facing orientation for this directory; agent-facing
   rules live in the `AGENTS.md` files alongside each subdirectory.
+
+Backlog archive is staging-neutral. Follow `pjm/AGENTS.md` Backlog Lifecycle:
+consume the complete JSON `affectedPaths`, add any owned handoff deletion,
+format existing text, and commit the exact operation through
+`oat internal commit-paths`, preserving unrelated staged/unstaged work.

package/assets/templates/repo-readme.md

@@ -33,3 +33,8 @@ Agent-facing rules live in the `AGENTS.md` files alongside each directory.
 - **Close-out.** When work ships that satisfies a backlog item's acceptance
   criteria, the item is closed and archived in the same commit/PR — run
   `oat backlog archive <id>`. See the Backlog Lifecycle in `pjm/AGENTS.md`.
+
+Backlog archive is staging-neutral. Follow `pjm/AGENTS.md` Backlog Lifecycle:
+consume the complete JSON `affectedPaths`, add any owned handoff deletion,
+format existing text, and commit the exact operation through
+`oat internal commit-paths`, preserving unrelated staged/unstaged work.

package/dist/commands/backlog/archive.d.ts

@@ -13,6 +13,9 @@ export interface ArchiveBacklogItemResult {
      * repository root.
      */
     rewrittenReferences: string[];
+    /** Normalized absolute paths owned by this operation, including the old
+     * item deletion and retry outputs. Archive never stages any of these paths. */
+    affectedPaths: string[];
     warnings: string[];
 }
 export interface ArchiveBacklogItemOptions {

package/dist/commands/backlog/archive.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"archive.d.ts","sourceRoot":"","sources":["../../../src/commands/backlog/archive.ts"],"names":[],"mappings":"AAUA,OAAO,EAEL,KAAK,iBAAiB,EAGvB,MAAM,sBAAsB,CAAC;AAmB9B,mDAAmD;AACnD,MAAM,WAAW,wBAAwB;IACvC,EAAE,EAAE,MAAM,CAAC;IACX,MAAM,EAAE,UAAU,GAAG,MAAM,CAAC;IAC5B,MAAM,EAAE,iBAAiB,GAAG,IAAI,CAAC;IACjC,cAAc,EAAE,SAAS,GAAG,YAAY,GAAG,SAAS,CAAC;IACrD,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;IACvB,gBAAgB,EAAE,OAAO,CAAC;IAC1B;;;;OAIG;IACH,mBAAmB,EAAE,MAAM,EAAE,CAAC;IAC9B,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,MAAM,WAAW,yBAAyB;IACxC,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,8EAA8E;IAC9E,GAAG,CAAC,EAAE,IAAI,CAAC;CACZ;AAED;;;GAGG;AACH,qBAAa,mBAAoB,SAAQ,KAAK;IAC5C,QAAQ,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,CAAC;IAEzB,YAAY,OAAO,EAAE,MAAM,EAAE,QAAQ,GAAE,CAAC,GAAG,CAAK,EAI/C;CACF;AAkID;;;;;;;GAOG;AACH,wBAAsB,kBAAkB,CACtC,WAAW,EAAE,MAAM,EACnB,EAAE,EAAE,MAAM,EACV,OAAO,GAAE,yBAA8B,GACtC,OAAO,CAAC,wBAAwB,CAAC,CA4InC"}
+{"version":3,"file":"archive.d.ts","sourceRoot":"","sources":["../../../src/commands/backlog/archive.ts"],"names":[],"mappings":"AAUA,OAAO,EAEL,KAAK,iBAAiB,EAGvB,MAAM,sBAAsB,CAAC;AAmB9B,mDAAmD;AACnD,MAAM,WAAW,wBAAwB;IACvC,EAAE,EAAE,MAAM,CAAC;IACX,MAAM,EAAE,UAAU,GAAG,MAAM,CAAC;IAC5B,MAAM,EAAE,iBAAiB,GAAG,IAAI,CAAC;IACjC,cAAc,EAAE,SAAS,GAAG,YAAY,GAAG,SAAS,CAAC;IACrD,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;IACvB,gBAAgB,EAAE,OAAO,CAAC;IAC1B;;;;OAIG;IACH,mBAAmB,EAAE,MAAM,EAAE,CAAC;IAC9B;mFAC+E;IAC/E,aAAa,EAAE,MAAM,EAAE,CAAC;IACxB,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,MAAM,WAAW,yBAAyB;IACxC,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,8EAA8E;IAC9E,GAAG,CAAC,EAAE,IAAI,CAAC;CACZ;AAED;;;GAGG;AACH,qBAAa,mBAAoB,SAAQ,KAAK;IAC5C,QAAQ,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,CAAC;IAEzB,YAAY,OAAO,EAAE,MAAM,EAAE,QAAQ,GAAE,CAAC,GAAG,CAAK,EAI/C;CACF;AAwJD;;;;;;;GAOG;AACH,wBAAsB,kBAAkB,CACtC,WAAW,EAAE,MAAM,EACnB,EAAE,EAAE,MAAM,EACV,OAAO,GAAE,yBAA8B,GACtC,OAAO,CAAC,wBAAwB,CAAC,CA0LnC"}

package/dist/commands/backlog/archive.js

@@ -1,6 +1,6 @@
 import { execFile } from 'node:child_process';
 import { access, readFile, rename, writeFile } from 'node:fs/promises';
-import { join } from 'node:path';
+import { join, relative, resolve } from 'node:path';
 import { promisify } from 'node:util';
 import { getFrontmatterBlock } from '../shared/frontmatter.js';
 import YAML from 'yaml';
@@ -48,15 +48,6 @@ async function pathExists(path) {
         return false;
     }
 }
-async function isInsideGitWorkTree(cwd) {
-    try {
-        await execFileAsync('git', ['rev-parse', '--is-inside-work-tree'], { cwd });
-        return true;
-    }
-    catch {
-        return false;
-    }
-}
 /**
  * Read the item `title` from its frontmatter. Parses the YAML block (rather
  * than a line regex) so a legitimate `#` inside a quoted title — e.g.
@@ -117,19 +108,37 @@ function insertCompletedEntry(completed, entryLine) {
     }
     return { content, scaffolded: false, warning: null };
 }
-async function moveItemFile(backlogRoot, fromPath, toPath, warnings) {
-    if (await isInsideGitWorkTree(backlogRoot)) {
-        try {
-            await execFileAsync('git', ['mv', fromPath, toPath], {
-                cwd: backlogRoot,
-            });
-            return;
-        }
-        catch {
-            warnings.push(`\`git mv\` failed for ${fromPath}; falling back to a plain filesystem rename (the move is no longer staged).`);
-        }
+async function readHeadFile(backlogRoot, path) {
+    try {
+        const { stdout } = await execFileAsync('git', ['show', `HEAD:./${relative(resolve(backlogRoot), resolve(path))}`], { cwd: backlogRoot });
+        return stdout;
+    }
+    catch {
+        // No Git/HEAD or absent path gives no evidence of a prior operation.
+        return null;
     }
-    await rename(fromPath, toPath);
+}
+function hasCompletedEntry(content, id) {
+    return (content !== null &&
+        content
+            .split('\n')
+            .some((line) => line.startsWith('- ') && line.includes(` — ${id} — `)));
+}
+function hasIndexEntry(content, id) {
+    return (content !== null &&
+        content
+            .split('\n')
+            .some((line) => line.startsWith('|') && line.split('|')[1]?.trim() === id));
+}
+function collectAffectedPaths(backlogRoot, id, references, changes) {
+    const paths = [...references];
+    if (changes.item)
+        paths.push(resolve(backlogRoot, 'items', `${id}.md`), resolve(backlogRoot, 'archived', `${id}.md`));
+    if (changes.completed)
+        paths.push(resolve(backlogRoot, 'completed.md'));
+    if (changes.index)
+        paths.push(resolve(backlogRoot, 'index.md'));
+    return [...new Set(paths)].sort();
 }
 /**
  * Atomic backlog close-out. Validates the current status, sets the terminal
@@ -143,6 +152,8 @@ export async function archiveBacklogItem(backlogRoot, id, options = {}) {
     const itemsPath = join(backlogRoot, 'items', `${id}.md`);
     const archivedPath = join(backlogRoot, 'archived', `${id}.md`);
     const warnings = [];
+    const completedPath = join(backlogRoot, 'completed.md');
+    const indexPath = join(backlogRoot, 'index.md');
     // Already archived: no status, completed-log, or move writes; only the
     // idempotent reference rewrite and index regeneration are retried.
     if (await pathExists(archivedPath)) {
@@ -165,7 +176,19 @@ export async function archiveBacklogItem(backlogRoot, id, options = {}) {
         // Retry the idempotent tail of a close-out: a run that failed during the
         // reference rewrite (or an item archived before the rewrite existed)
         // still gets its inbound links repointed and the index regenerated.
-        const references = await rewriteInboundReferences(backlogRoot, itemsPath, archivedPath, { rebaseMovedItem: false });
+        const [headItem, headArchived, headCompleted, headIndex] = await Promise.all([
+            readHeadFile(backlogRoot, itemsPath),
+            readHeadFile(backlogRoot, archivedPath),
+            readHeadFile(backlogRoot, completedPath),
+            readHeadFile(backlogRoot, indexPath),
+        ]);
+        const pendingMove = headItem !== null && headArchived === null;
+        const indexBefore = await readFile(indexPath, 'utf8').catch((error) => {
+            if (error.code === 'ENOENT')
+                return null;
+            throw error;
+        });
+        const references = await rewriteInboundReferences(backlogRoot, itemsPath, archivedPath, { rebaseMovedItem: false, recoverPendingArchive: pendingMove });
         warnings.push(...references.warnings);
         const regeneration = await regenerateBacklogIndex(backlogRoot);
         warnings.push(...regeneration.warnings);
@@ -177,6 +200,20 @@ export async function archiveBacklogItem(backlogRoot, id, options = {}) {
             movedTo: archivedPath,
             indexRegenerated: true,
             rewrittenReferences: references.rewritten,
+            affectedPaths: collectAffectedPaths(backlogRoot, id, references.affectedPaths, {
+                item: pendingMove,
+                completed: pendingMove &&
+                    hasCompletedEntry(await readFile(completedPath, 'utf8').catch((error) => {
+                        if (error.code === 'ENOENT')
+                            return '';
+                        throw error;
+                    }), id) &&
+                    !hasCompletedEntry(headCompleted, id),
+                index: indexBefore !== (await readFile(indexPath, 'utf8')) ||
+                    (pendingMove &&
+                        hasIndexEntry(headIndex, id) &&
+                        !hasIndexEntry(await readFile(indexPath, 'utf8'), id)),
+            }),
             warnings,
         };
     }
@@ -206,7 +243,6 @@ export async function archiveBacklogItem(backlogRoot, id, options = {}) {
     const shouldWriteEntry = targetStatus === 'closed' || summary.length > 0;
     if (shouldWriteEntry) {
         const entryLine = `- ${entryDate} — ${id} — ${title} — ${summary}`;
-        const completedPath = join(backlogRoot, 'completed.md');
         let scaffoldedFile = false;
         let existing;
         if (await pathExists(completedPath)) {
@@ -224,8 +260,8 @@ export async function archiveBacklogItem(backlogRoot, id, options = {}) {
         completedEntry =
             scaffoldedFile || inserted.scaffolded ? 'scaffolded' : 'written';
     }
-    // 6. Move items/<id>.md -> archived/<id>.md (git mv with rename fallback).
-    await moveItemFile(backlogRoot, itemsPath, archivedPath, warnings);
+    // 6. Filesystem-only move: the caller owns staging the complete operation.
+    await rename(itemsPath, archivedPath);
     // 7. Rewrite inbound references so no `.oat/repo` link dangles at items/.
     const references = await rewriteInboundReferences(backlogRoot, itemsPath, archivedPath);
     warnings.push(...references.warnings);
@@ -240,6 +276,7 @@ export async function archiveBacklogItem(backlogRoot, id, options = {}) {
         movedTo: archivedPath,
         indexRegenerated: true,
         rewrittenReferences: references.rewritten,
+        affectedPaths: collectAffectedPaths(backlogRoot, id, references.affectedPaths, { item: true, completed: shouldWriteEntry, index: true }),
         warnings,
     };
 }

package/dist/commands/backlog/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/commands/backlog/index.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,mBAAmB,EAAuB,MAAM,sBAAsB,CAAC;AAChF,OAAO,EAAE,kBAAkB,EAAE,MAAM,wBAAwB,CAAC;AAG5D,OAAO,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAC/C,OAAO,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAC;AAC/C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,OAAO,EAAE,kBAAkB,EAAuB,MAAM,WAAW,CAAC;AACpE,OAAO,EAAE,iBAAiB,EAAE,MAAM,QAAQ,CAAC;AAC3C,OAAO,EAAE,iBAAiB,EAAE,MAAM,OAAO,CAAC;AAC1C,OAAO,EAAE,sBAAsB,EAAE,MAAM,oBAAoB,CAAC;AA8B5D,UAAU,0BAA0B;IAClC,mBAAmB,EAAE,OAAO,mBAAmB,CAAC;IAChD,kBAAkB,EAAE,OAAO,kBAAkB,CAAC;IAC9C,iBAAiB,EAAE,OAAO,iBAAiB,CAAC;IAC5C,kBAAkB,EAAE,OAAO,kBAAkB,CAAC;IAC9C,iBAAiB,EAAE,OAAO,iBAAiB,CAAC;IAC5C,sBAAsB,EAAE,OAAO,sBAAsB,CAAC;IACtD,iBAAiB,EAAE,OAAO,iBAAiB,CAAC;IAC5C,kBAAkB,EAAE,OAAO,kBAAkB,CAAC;IAC9C,UAAU,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,OAAO,CAAC,CAAC;CAChD;AA4ED,wBAAgB,oBAAoB,CAClC,SAAS,GAAE,OAAO,CAAC,0BAA0B,CAAM,GAClD,OAAO,CA6RT"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/commands/backlog/index.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,mBAAmB,EAAuB,MAAM,sBAAsB,CAAC;AAChF,OAAO,EAAE,kBAAkB,EAAE,MAAM,wBAAwB,CAAC;AAG5D,OAAO,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAC/C,OAAO,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAC;AAC/C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,OAAO,EAAE,kBAAkB,EAAuB,MAAM,WAAW,CAAC;AACpE,OAAO,EAAE,iBAAiB,EAAE,MAAM,QAAQ,CAAC;AAC3C,OAAO,EAAE,iBAAiB,EAAE,MAAM,OAAO,CAAC;AAC1C,OAAO,EAAE,sBAAsB,EAAE,MAAM,oBAAoB,CAAC;AA8B5D,UAAU,0BAA0B;IAClC,mBAAmB,EAAE,OAAO,mBAAmB,CAAC;IAChD,kBAAkB,EAAE,OAAO,kBAAkB,CAAC;IAC9C,iBAAiB,EAAE,OAAO,iBAAiB,CAAC;IAC5C,kBAAkB,EAAE,OAAO,kBAAkB,CAAC;IAC9C,iBAAiB,EAAE,OAAO,iBAAiB,CAAC;IAC5C,sBAAsB,EAAE,OAAO,sBAAsB,CAAC;IACtD,iBAAiB,EAAE,OAAO,iBAAiB,CAAC;IAC5C,kBAAkB,EAAE,OAAO,kBAAkB,CAAC;IAC9C,UAAU,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,OAAO,CAAC,CAAC;CAChD;AA4ED,wBAAgB,oBAAoB,CAClC,SAAS,GAAE,OAAO,CAAC,0BAA0B,CAAM,GAClD,OAAO,CAkST"}

package/dist/commands/backlog/index.js

@@ -210,6 +210,9 @@ export function createBacklogCommand(overrides = {}) {
                 for (const path of result.rewrittenReferences) {
                     context.logger.info(`Rewrote references in ${path}`);
                 }
+                for (const path of result.affectedPaths) {
+                    context.logger.info(`Affected path (caller-owned staging): ${path}`);
+                }
             }
             process.exitCode = 0;
         }

package/dist/commands/backlog/rewrite-references.d.ts

@@ -2,6 +2,9 @@
 export interface RewriteInboundReferencesResult {
     /** Files whose content was rewritten, relative to the repository root. */
     rewritten: string[];
+    /** Normalized absolute reference paths associated with this item, including
+     * links already repaired by an interrupted prior archive pass. */
+    affectedPaths: string[];
     /** One warning per reference that names the item but cannot be resolved. */
     warnings: string[];
 }
@@ -13,6 +16,8 @@ export interface RewriteInboundReferencesOptions {
      * because its links were rebased (or written) against `archived/` already.
      */
     rebaseMovedItem?: boolean;
+    /** True only when the archive caller proved an uncommitted old/new move in HEAD. */
+    recoverPendingArchive?: boolean;
 }
 /** A Markdown segment: prose, an inline code span, or a fenced code block. */
 export interface MarkdownSegment {

package/dist/commands/backlog/rewrite-references.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"rewrite-references.d.ts","sourceRoot":"","sources":["../../../src/commands/backlog/rewrite-references.ts"],"names":[],"mappings":"AAsCA,kDAAkD;AAClD,MAAM,WAAW,8BAA8B;IAC7C,0EAA0E;IAC1E,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,4EAA4E;IAC5E,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,oDAAoD;AACpD,MAAM,WAAW,+BAA+B;IAC9C;;;;OAIG;IACH,eAAe,CAAC,EAAE,OAAO,CAAC;CAC3B;AA0RD,8EAA8E;AAC9E,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,OAAO,GAAG,MAAM,GAAG,OAAO,CAAC;IACjC,IAAI,EAAE,MAAM,CAAC;CACd;AAED;;;;;;GAMG;AACH,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,MAAM,GAAG,eAAe,EAAE,CA0EpE;AAmND;;;;;;;;;GASG;AACH,wBAAsB,wBAAwB,CAC5C,WAAW,EAAE,MAAM,EACnB,SAAS,EAAE,MAAM,EACjB,YAAY,EAAE,MAAM,EACpB,OAAO,GAAE,+BAAoC,GAC5C,OAAO,CAAC,8BAA8B,CAAC,CAsCzC"}
+{"version":3,"file":"rewrite-references.d.ts","sourceRoot":"","sources":["../../../src/commands/backlog/rewrite-references.ts"],"names":[],"mappings":"AAsCA,kDAAkD;AAClD,MAAM,WAAW,8BAA8B;IAC7C,0EAA0E;IAC1E,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB;sEACkE;IAClE,aAAa,EAAE,MAAM,EAAE,CAAC;IACxB,4EAA4E;IAC5E,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,oDAAoD;AACpD,MAAM,WAAW,+BAA+B;IAC9C;;;;OAIG;IACH,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B,oFAAoF;IACpF,qBAAqB,CAAC,EAAE,OAAO,CAAC;CACjC;AAqSD,8EAA8E;AAC9E,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,OAAO,GAAG,MAAM,GAAG,OAAO,CAAC;IACjC,IAAI,EAAE,MAAM,CAAC;CACd;AAED;;;;;;GAMG;AACH,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,MAAM,GAAG,eAAe,EAAE,CA0EpE;AAmND;;;;;;;;;GASG;AACH,wBAAsB,wBAAwB,CAC5C,WAAW,EAAE,MAAM,EACnB,SAAS,EAAE,MAAM,EACjB,YAAY,EAAE,MAAM,EACpB,OAAO,GAAE,+BAAoC,GAC5C,OAAO,CAAC,8BAA8B,CAAC,CAsEzC"}

package/dist/commands/backlog/rewrite-references.js

@@ -204,15 +204,25 @@ function rewriteItemToken(token, context) {
     if (isRelativeTarget(token)) {
         const fromFile = resolve(context.baseDirectory, token);
         if (fromFile === itemsPath) {
+            context.affectedReference = true;
             return relativeFrom(context.currentDirectory, archivedPath, token);
         }
+        if (fromFile === archivedPath) {
+            context.affectedReference = true;
+            return null;
+        }
         // A token that already resolves to a different, existing file is a
         // working link: never repoint it through a fallback base.
         if (pathExistsSync(fromFile)) {
             return null;
         }
         for (const base of [layout.repoRoot, layout.scanRoot]) {
+            if (base !== null && resolve(base, token) === archivedPath) {
+                context.affectedReference = true;
+                return null;
+            }
             if (base !== null && resolve(base, token) === itemsPath) {
+                context.affectedReference = true;
                 return toPosix(relative(base, archivedPath));
             }
         }
@@ -487,6 +497,7 @@ export async function rewriteInboundReferences(backlogRoot, itemsPath, archivedP
     const absoluteArchivedPath = resolve(archivedPath);
     const displayRoot = layout.repoRoot ?? layout.scanRoot;
     const rewritten = [];
+    const affectedPaths = [];
     const warnings = [];
     // The moved item goes first, so a failure on a later file never leaves its
     // own links half-rebased: a retry (which skips the rebase) stays correct.
@@ -505,12 +516,39 @@ export async function rewriteInboundReferences(backlogRoot, itemsPath, archivedP
             baseDirectory: moved ? dirname(absoluteItemsPath) : dirname(absoluteFile),
             currentDirectory: dirname(absoluteFile),
             warnings,
+            affectedReference: false,
         };
         const next = rewriteContent(content, context, moved);
         if (next !== content) {
             await replaceAtomically(absoluteFile, next, identity);
             rewritten.push(context.fileName);
         }
+        if (next !== content) {
+            affectedPaths.push(absoluteFile);
+        }
+        else if (options.recoverPendingArchive && context.affectedReference) {
+            // Existing archived links are not ownership evidence. Recover a prior
+            // repaired reference only when HEAD's same grammar still names the old
+            // item and this pending move has not yet been committed.
+            try {
+                const { stdout: headContent } = await execFileAsync('git', [
+                    'show',
+                    `HEAD:./${toPosix(relative(layout.scanRoot, absoluteFile))}`,
+                ], { cwd: layout.scanRoot });
+                const historicalContext = {
+                    ...context,
+                    baseDirectory: dirname(absoluteFile),
+                    warnings: [],
+                    affectedReference: false,
+                };
+                if (rewriteContent(headContent, historicalContext, false) !== headContent) {
+                    affectedPaths.push(absoluteFile);
+                }
+            }
+            catch {
+                // Without historical file bytes there is no proof of prior ownership.
+            }
+        }
     }
-    return { rewritten, warnings };
+    return { rewritten, affectedPaths, warnings };
 }

package/dist/commands/init/index.d.ts.map

@@ -1 +1 @@
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package/dist/commands/init/index.js

@@ -270,6 +270,7 @@ const DOCS_TOOLING_CHOICES = [
     { label: 'Docusaurus', value: 'docusaurus' },
     { label: 'VitePress', value: 'vitepress' },
     { label: 'Nextra', value: 'nextra' },
+    { label: 'Plain Markdown', value: 'markdown' },
 ];
 function trimDocsRoot(pathValue) {
     return pathValue.replace(/\/+$/, '').replace(/^\.\//, '').trim();

package/dist/commands/init/tools/shared/skill-script-references.d.ts.map

@@ -1 +1 @@
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