@mmerterden/multi-agent-pipeline 16.18.0 → 16.19.0

package/pipeline/scripts/triage-memory.mjs

@@ -21,6 +21,7 @@
  * Subcommands:
  *   ingest   --triage <path> --task-id <id> [--task-title "..."] [--stack ios]
  *               [--repo-slug <slug>] [--state <agent-state.json>]
+ *               (--state fills task-id / task-title / stack when the flag is absent)
  *   query    --issue "<text>" [--file-glob "Auth*"] [--top N]
  *               [--repo-slug <slug>] [--json]
  *   show     --id <id> [--repo-slug <slug>]
@@ -214,14 +215,34 @@ function writeRow(slug, row) {
   appendFileSync(p, JSON.stringify(row) + "\n", "utf8");
 }
 
+// --state <agent-state.json> supplies the ingest defaults an explicit flag does
+// not: task id, title and stack, read from the run's own state.
+function stateDefaults() {
+  const p = flags.state;
+  if (!p || p === true) return {};
+  if (!existsSync(p)) die(`state file not found: ${p}`, 1);
+  let state;
+  try {
+    state = JSON.parse(readFileSync(p, "utf8"));
+  } catch (e) {
+    die(`cannot parse state JSON: ${e.message}`, 1);
+  }
+  return {
+    taskId: state.taskId || null,
+    taskTitle: state.taskTitle || state.task?.title || null,
+    stack: state.stack?.primary || state.repos?.[0]?.stack || null,
+  };
+}
+
 function ingest() {
   const triagePath = flags.triage;
   if (!triagePath) die("ingest needs --triage <path>", 1);
   if (!existsSync(triagePath)) die(`triage file not found: ${triagePath}`, 1);
-  const taskId = flags["task-id"];
-  if (!taskId) die("ingest needs --task-id <id>", 1);
-  const taskTitle = flags["task-title"] || null;
-  const stack = flags.stack || null;
+  const fromState = stateDefaults();
+  const taskId = flags["task-id"] || fromState.taskId;
+  if (!taskId) die("ingest needs --task-id <id> (or --state with a taskId)", 1);
+  const taskTitle = flags["task-title"] || fromState.taskTitle || null;
+  const stack = flags.stack || fromState.stack || null;
   const slug = repoSlug();
 
   let triage;

package/pipeline/scripts/uninstall.mjs

@@ -95,11 +95,12 @@ const explicitlyTargeted = flags.some((f) => TOOL_FLAGS.includes(f)) || flags.in
 
 const forClaude = flags.includes("--claude") || flags.includes("--all") || !explicitlyTargeted;
 const forCopilot = flags.includes("--copilot") || flags.includes("--all") || !explicitlyTargeted;
-const forCursor = flags.includes("--cursor") || flags.includes("--all") || !explicitlyTargeted;
-const forCopilotChat =
-  flags.includes("--copilot-chat") || flags.includes("--all") || !explicitlyTargeted;
-const forAntigravity =
-  flags.includes("--antigravity") || flags.includes("--all") || !explicitlyTargeted;
+// The legacy adapters wrote into the PROJECT directory (cwd or --target), not
+// into $HOME, so their cleanup is opt-in: a bare `uninstall` must not walk the
+// current directory's AGENTS.md / .cursorrules / .github on the user's behalf.
+const forCursor = flags.includes("--cursor");
+const forCopilotChat = flags.includes("--copilot-chat");
+const forAntigravity = flags.includes("--antigravity");
 const forCodex = flags.includes("--codex") || flags.includes("--all") || !explicitlyTargeted;
 
 const dryRun = flags.includes("--dry-run");
@@ -566,9 +567,16 @@ function legacyTrailingContent(section) {
  * Strip a marker-wrapped `<!-- multi-agent-pipeline:begin/end -->` block from
  * a user-owned file. Preserves everything outside the markers. Deletes the
  * file entirely if it becomes empty.
+ *
+ * `hostFile` marks the instruction files the installers themselves write
+ * (~/.copilot/copilot-instructions.md, ~/.codex/AGENTS.md). Only there is a
+ * `# Multi-Agent Development Pipeline` heading provably ours, so only there
+ * does the heading-bounded legacy path apply. A project file with that heading
+ * and no marker is user prose and is left alone.
  * @param {string} filePath
+ * @param {{hostFile?: boolean}} [opts]
  */
-function stripManagedBlock(filePath) {
+function stripManagedBlock(filePath, { hostFile = false } = {}) {
   if (!existsSync(filePath)) return false;
   const content = readFileSync(filePath, "utf-8");
   const re = /\s*<!-- multi-agent-pipeline:begin -->[\s\S]*?<!-- multi-agent-pipeline:end -->\s*/m;
@@ -578,7 +586,7 @@ function stripManagedBlock(filePath) {
     // pipeline section; strip only the start..end span so user content BELOW
     // the section survives. Legacy files without the end marker are bounded
     // at the next top-level heading outside code fences, else EOF.
-    if (content.includes("# Multi-Agent Development Pipeline")) {
+    if (hostFile && content.includes("# Multi-Agent Development Pipeline")) {
       const marker = "# Multi-Agent Development Pipeline";
       const idx = content.indexOf(marker);
       if (idx >= 0) {
@@ -823,7 +831,7 @@ export async function main() {
     // Agent definitions are FILES; remove only the pipeline-shipped names so
     // user-authored agents survive.
     rmMatchingFiles(join(COP, "agents"), (name) => PIPELINE_AGENT_FILES.includes(name));
-    stripManagedBlock(join(COP, "copilot-instructions.md"));
+    stripManagedBlock(join(COP, "copilot-instructions.md"), { hostFile: true });
   }
 
   // Full cleanup: pipeline settings, the log root, and the per-repo memory
@@ -851,9 +859,9 @@ export async function main() {
     rmIfExists(join(HOME, ".claude", "knowledge"));
   }
 
-  // Legacy adapter-file cleanup (adapters removed in v10.7.0). These blocks
-  // delete files a pre-v10.7.0 install generated; they never touch user files
-  // outside the multi-agent-* namespace / managed markers.
+  // Legacy adapter-file cleanup (adapters removed in v10.7.0), opt-in per flag.
+  // These blocks delete files a pre-v10.7.0 install generated; they never touch
+  // user files outside the multi-agent-* namespace / begin-end markers.
   if (forCursor) {
     console.log("");
     console.log(`  [Cursor  -  legacy cleanup] Removing from ${adapterTarget}...`);
@@ -913,7 +921,7 @@ export async function main() {
     rmIfExists(join(CODEX, "prompts", "multi-agent.md"));
     removeGeneratedCodexAgents(join(CODEX, "agents"));
 
-    stripManagedBlock(join(CODEX, "AGENTS.md"));
+    stripManagedBlock(join(CODEX, "AGENTS.md"), { hostFile: true });
 
     // The MCP entry was written by `codex mcp add`, so hand it back the same
     // way rather than editing config.toml - Codex also stores marketplace and

package/pipeline/scripts/update-check.sh

@@ -48,8 +48,8 @@ PRINT_REQUIRED=0
 
 while [ $# -gt 0 ]; do
   case "$1" in
-    --local) LOCAL_VERSION="${2:-}"; shift 2 ;;
-    --ttl-hours) TTL_HOURS="${2:-24}"; shift 2 ;;
+    --local) LOCAL_VERSION="${2:-}"; shift; [ $# -gt 0 ] && shift ;;
+    --ttl-hours) TTL_HOURS="${2:-24}"; shift; [ $# -gt 0 ] && shift ;;
     --force) FORCE=1; shift ;;
     --print-required) PRINT_REQUIRED=1; shift ;;
     *) shift ;;

package/pipeline/scripts/update-issue-progress.sh

@@ -134,8 +134,9 @@ G_CC=$(glyph_for "$F_CC")
 G_WIKI=$(glyph_for "$F_WIKI")
 
 # Fetch current body, replace the Progress table, write back.
-TMP_BODY=$(mktemp /tmp/issue-progress-"${TASK_ID}"-XXXXXX.md)
-trap 'rm -f "$TMP_BODY"' EXIT
+TMP_BODY=$(mktemp "/tmp/issue-progress-${TASK_ID}.XXXXXX")
+TMP_NEW=$(mktemp "/tmp/issue-progress-${TASK_ID}.new.XXXXXX")
+trap 'rm -f "$TMP_BODY" "$TMP_NEW"' EXIT
 
 gh issue view "$ISSUE_NUM" --repo "$ORG_REPO" --json body --jq .body > "$TMP_BODY"
 
@@ -144,16 +145,16 @@ NEW_BLOCK=$(build_progress_block "$G_IMPL" "$G_TEST" "$G_CC" "$G_WIKI")
 
 # Replace the table between `### Progress` and the first terminator (legend
 # comment, next heading, or EOF)  -  see rewrite_progress_body above.
-rewrite_progress_body "$NEW_BLOCK" "$TMP_BODY" > "${TMP_BODY}.new"
+rewrite_progress_body "$NEW_BLOCK" "$TMP_BODY" > "$TMP_NEW"
 
 # Check if body actually changed (idempotent no-op).
-if cmp -s "$TMP_BODY" "${TMP_BODY}.new"; then
+if cmp -s "$TMP_BODY" "$TMP_NEW"; then
   echo "update-issue-progress: no change for #$ISSUE_NUM (idempotent no-op)" >&2
   exit 0
 fi
 
 # Apply.
-if ! gh issue edit "$ISSUE_NUM" --repo "$ORG_REPO" --body-file "${TMP_BODY}.new" >/dev/null; then
+if ! gh issue edit "$ISSUE_NUM" --repo "$ORG_REPO" --body-file "$TMP_NEW" >/dev/null; then
   echo "update-issue-progress: gh issue edit failed for #$ISSUE_NUM" >&2
   exit 4
 fi

package/pipeline/scripts/validate-analysis-doc.mjs

@@ -271,7 +271,7 @@ function main() {
       }
     }
 
-    // 2b. JSON does not fit in a table cell (Locked 37).
+    // 2b. JSON does not fit in a table cell (analysis-template.md Section 9.2 / 9.3).
     //
     // One document rendered `Request` as inline JSON with a field note glued to
     // the end, and `Response` as a proper fenced block below the table: two
@@ -284,7 +284,7 @@ function main() {
       if (/[{}]/.test(cell)) {
         errors.push(
           `line ${i + 1}: ${/Request/.test(line) ? "Request" : "Response"} cell holds JSON; ` +
-            "put the payload in a fenced block under the table (Locked 37)",
+            "put the payload in a fenced block under the table (analysis-template.md Section 9.2 / 9.3)",
         );
       }
     }
@@ -335,7 +335,7 @@ function main() {
   // place a Turkish document can quietly go ASCII: one run shipped `Hayir` and
   // `Basarili` in its flow chart while every other line was correct. A warning,
   // not an error - node ids are legitimately ASCII, only labels are checked.
-  if (parsed.fm.language === "tr") {
+  if (parsed?.fm?.language === "tr") {
     const mmLines = text.split("\n");
     let inMermaid = false;
     for (let i = 0; i < mmLines.length; i++) {
@@ -353,12 +353,12 @@ function main() {
       for (const lbl of labels) {
         if (
           /^[\x20-\x7E]+$/.test(lbl) &&
-          /\b(Hayir|Basarili|Basarisiz|Odeme|Iptal|Gecerli|Gecersiz|Secim|Dogrulama|Uyari|Baslangic|Bitis|Onay|Aciklama)\b/.test(
+          /\b(Hayir|Basarili|Basarisiz|Odeme|Iptal|Gecerli|Gecersiz|Secim|Dogrulama|Uyari|Baslangic|Bitis|Aciklama)\b/.test(
             lbl,
           )
         ) {
-          errors.push(
-            `WARN line ${i + 1}: diagram label "${lbl}" looks like Turkish flattened to ASCII (Locked 7)`,
+          warns.push(
+            `line ${i + 1}: diagram label "${lbl}" looks like Turkish flattened to ASCII (Locked 7)`,
           );
         }
       }

package/pipeline/scripts/verify-skills.sh

@@ -31,7 +31,9 @@ ROOT_OVERRIDE=""
 QUIET=0
 while [ $# -gt 0 ]; do
   case "$1" in
-    --root)  ROOT_OVERRIDE="$2"; shift 2 ;;
+    --root)
+      [ $# -ge 2 ] || { echo "verify-skills: --root needs a value" >&2; exit 1; }
+      ROOT_OVERRIDE="$2"; shift 2 ;;
     --quiet) QUIET=1; shift ;;
     *)       shift ;;
   esac

package/pipeline/scripts/worktree-finalize.sh

@@ -34,14 +34,16 @@ WORKTREE=""; PROJECT_ROOT=""; TASK_ID=""; PROJECT=""; BRANCH=""
 LOGS_ROOT="${HOME}/.claude/logs/multi-agent"
 DRY=0; JSON=0
 
+need_value() { [ $# -ge 2 ] || { echo "ERR: $1 needs a value" >&2; exit 1; }; }
+
 while [ $# -gt 0 ]; do
   case "$1" in
-    --worktree) WORKTREE="${2:-}"; shift 2 ;;
-    --project-root) PROJECT_ROOT="${2:-}"; shift 2 ;;
-    --task-id) TASK_ID="${2:-}"; shift 2 ;;
-    --project) PROJECT="${2:-}"; shift 2 ;;
-    --branch) BRANCH="${2:-}"; shift 2 ;;
-    --logs-root) LOGS_ROOT="${2:-}"; shift 2 ;;
+    --worktree) need_value "$@"; WORKTREE="$2"; shift 2 ;;
+    --project-root) need_value "$@"; PROJECT_ROOT="$2"; shift 2 ;;
+    --task-id) need_value "$@"; TASK_ID="$2"; shift 2 ;;
+    --project) need_value "$@"; PROJECT="$2"; shift 2 ;;
+    --branch) need_value "$@"; BRANCH="$2"; shift 2 ;;
+    --logs-root) need_value "$@"; LOGS_ROOT="$2"; shift 2 ;;
     --dry-run) DRY=1; shift ;;
     --json) JSON=1; shift ;;
     *) echo "usage: worktree-finalize.sh --worktree <p> --project-root <p> --task-id <id> [--project <s>] [--branch <b>] [--logs-root <d>] [--dry-run] [--json]" >&2; exit 1 ;;
@@ -129,10 +131,16 @@ esac
 
 # Must be a worktree git actually knows about, so a mistyped path cannot delete an
 # unrelated directory.
-if ! git -C "$rp_pr" worktree list --porcelain 2>/dev/null \
-     | awk '/^worktree /{print substr($0,10)}' \
-     | while IFS= read -r w; do (cd "$w" 2>/dev/null && pwd -P); done \
-     | grep -qxF "$rp_wt"; then
+registered=""
+while IFS= read -r w; do
+  [ -n "$w" ] || continue
+  w_rp="$(cd "$w" 2>/dev/null && pwd -P)" || continue
+  registered="$registered$w_rp
+"
+done <<EOF_WT
+$(git -C "$rp_pr" worktree list --porcelain 2>/dev/null | awk '/^worktree /{print substr($0,10)}')
+EOF_WT
+if ! printf '%s' "$registered" | grep -qxF "$rp_wt"; then
   skip "not a registered worktree of $rp_pr"
 fi
 
@@ -212,6 +220,7 @@ copy_one() {
     return 0
   fi
   mkdir -p "$DEST/$(dirname "$1")" 2>/dev/null
+  [ -d "$DEST/$1" ] && rm -rf "${DEST:?}/$1"
   cp -R "$src" "$DEST/$1" 2>/dev/null && SALVAGED="${SALVAGED:+$SALVAGED,}\"$1\""
 }
 
@@ -223,6 +232,9 @@ copy_one() {
 # actually fired for either file.
 copy_from_logs() {
   src="$LOGS_TASK_DIR/$1"
+  # phase-tracker.sh writes tracker-state.json to <logs-root>/<task-id>/ with
+  # no project segment; the project-scoped dir is agent-state.json's home.
+  [ -e "$src" ] || src="$LOGS_ROOT/$TASK_ID/$1"
   [ -e "$src" ] || return 0
   if [ "$DRY" = "1" ]; then
     SALVAGED="${SALVAGED:+$SALVAGED,}\"$1\""