@bhargavvc/sdd-cc 1.35.0 → 1.42.3

package/sdd/workflows/quick.md

@@ -36,6 +36,8 @@ Parse `$ARGUMENTS` for:
 - `--research` flag → store `$RESEARCH_MODE=true`
 - Remaining text → use as `$DESCRIPTION` if non-empty
 
+After parsing, normalize: if `$DISCUSS_MODE` and `$RESEARCH_MODE` and `$VALIDATE_MODE` are all true, set `$FULL_MODE=true`. This ensures `--discuss --research --validate` is treated identically to `--full`.
+
 If `$DESCRIPTION` is empty after parsing, prompt user interactively:
 
 
@@ -64,15 +66,6 @@ If `$FULL_MODE` (all phases enabled — `--full` or all granular flags):
 ◆ Discussion + research + plan checking + verification enabled
 ```
 
-If `$DISCUSS_MODE` and `$RESEARCH_MODE` and `$VALIDATE_MODE` (no `$FULL_MODE` — composed granularly):
-```
-━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
- SDD ► QUICK TASK (DISCUSS + RESEARCH + VALIDATE)
-━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
-
-◆ Discussion + research + plan checking + verification enabled
-```
-
 If `$DISCUSS_MODE` and `$VALIDATE_MODE` (no research):
 ```
 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
@@ -132,21 +125,52 @@ If `$VALIDATE_MODE` only:
 **Step 2: Initialize**
 
 ```bash
-INIT=$(node "$HOME/.claude/sdd/bin/sdd-tools.cjs" init quick "$DESCRIPTION")
+if ! command -v sdd-sdk &>/dev/null; then
+  echo "⚠ sdd-sdk not found in PATH — /sdd:quick requires it."
+  echo ""
+  echo "Install the query-capable SDD SDK CLI:"
+  echo "  npm install -g @bhargavvc/sdd-cc"
+  echo ""
+  echo "Or update SDD to get the latest packages:"
+  echo "  /sdd:update"
+  exit 1
+fi
+```
+
+```bash
+INIT=$(sdd-sdk query init.quick "$DESCRIPTION")
 if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
-AGENT_SKILLS_PLANNER=$(node "$HOME/.claude/sdd/bin/sdd-tools.cjs" agent-skills sdd-planner 2>/dev/null)
-AGENT_SKILLS_EXECUTOR=$(node "$HOME/.claude/sdd/bin/sdd-tools.cjs" agent-skills sdd-executor 2>/dev/null)
-AGENT_SKILLS_CHECKER=$(node "$HOME/.claude/sdd/bin/sdd-tools.cjs" agent-skills sdd-checker 2>/dev/null)
-AGENT_SKILLS_VERIFIER=$(node "$HOME/.claude/sdd/bin/sdd-tools.cjs" agent-skills sdd-verifier 2>/dev/null)
+AGENT_SKILLS_PLANNER=$(sdd-sdk query agent-skills sdd-planner)
+AGENT_SKILLS_EXECUTOR=$(sdd-sdk query agent-skills sdd-executor)
+AGENT_SKILLS_CHECKER=$(sdd-sdk query agent-skills sdd-plan-checker)
+AGENT_SKILLS_VERIFIER=$(sdd-sdk query agent-skills sdd-verifier)
 ```
 
 Parse JSON for: `planner_model`, `executor_model`, `checker_model`, `verifier_model`, `commit_docs`, `branch_name`, `quick_id`, `slug`, `date`, `timestamp`, `quick_dir`, `task_dir`, `roadmap_exists`, `planning_exists`.
 
 ```bash
-USE_WORKTREES=$(node "$HOME/.claude/sdd/bin/sdd-tools.cjs" config-get workflow.use_worktrees 2>/dev/null || echo "true")
+USE_WORKTREES=$(sdd-sdk query config-get workflow.use_worktrees 2>/dev/null || echo "true")
 ```
 
-**If `roadmap_exists` is false:** Error — Quick mode requires an active project with ROADMAP.md. Run `/sdd-new-project` first.
+If the project uses git submodules, worktree isolation is unsafe **only when the quick task touches a submodule path**. The previous behavior unconditionally disabled worktree isolation whenever `.gitmodules` existed, which penalised every quick task in a submodule project even when the task was nowhere near a submodule. Parse submodule paths from `.gitmodules` so the executor can act on actual submodule paths rather than the mere file's existence:
+
+```bash
+# Parse submodule paths from .gitmodules once (empty if no .gitmodules).
+# SUBMODULE_PATHS is a newline-separated list of repo-relative paths used as
+# a fail-loud commit-time guard inside the quick-task executor — if the
+# executor stages any path that falls inside SUBMODULE_PATHS, it must abort
+# the commit and surface the conflict rather than silently corrupting the
+# submodule state.
+if [ -f .gitmodules ]; then
+  SUBMODULE_PATHS=$(git config --file .gitmodules --get-regexp '^submodule\..*\.path$' 2>/dev/null | awk '{print $2}')
+else
+  SUBMODULE_PATHS=""
+fi
+```
+
+Quick mode does not have a pre-declared `files_modified` list (the task is freeform), so use a fail-loud guard at commit time: when the executor stages files for the quick-task commit, if any staged path falls inside a `SUBMODULE_PATHS` entry, abort with a clear error explaining that worktree-isolated commits cannot safely span submodule boundaries — the user can re-run with `workflow.use_worktrees=false` to fall back to sequential execution on the main tree. If `SUBMODULE_PATHS` is empty (no `.gitmodules` in the repo), worktree isolation proceeds normally.
+
+**If `roadmap_exists` is false:** Error — Quick mode requires an active project with ROADMAP.md. Run `/sdd:new-project` first.
 
 Quick tasks can run mid-phase - validation only checks ROADMAP.md exists, not phase status.
 
@@ -156,10 +180,52 @@ Quick tasks can run mid-phase - validation only checks ROADMAP.md exists, not ph
 
 **If `branch_name` is empty/null:** Skip and continue on the current branch.
 
-**If `branch_name` is set:** Check out the quick-task branch before any planning commits:
+**If `branch_name` is set:** Check out the quick-task branch before any planning commits.
+
+The new branch must fork off the project's default branch (`origin/HEAD`), not
+off whatever HEAD happens to be checked out — otherwise consecutive quick tasks
+compound on top of each other and stay unpushed (#2916). If `$branch_name`
+already exists locally, reuse it as-is so resumed work is not rebased.
 
 ```bash
-git checkout -b "$branch_name" 2>/dev/null || git checkout "$branch_name"
+DEFAULT_BRANCH=$(git symbolic-ref --quiet --short refs/remotes/origin/HEAD 2>/dev/null | sed 's|^origin/||')
+DEFAULT_BRANCH=${DEFAULT_BRANCH:-main}
+
+if git show-ref --verify --quiet "refs/heads/$branch_name"; then
+  git switch "$branch_name" \
+    || { echo "ERROR: Could not switch to existing quick-task branch '$branch_name'." >&2; exit 1; }
+else
+  # Fetch the default branch so origin/$DEFAULT_BRANCH is current. If the fetch
+  # fails (offline, no remote, auth failure) AND we have no local copy of
+  # origin/$DEFAULT_BRANCH to fall back on, abort — creating the branch off
+  # arbitrary HEAD is exactly the bug #2916 fixed.
+  if ! git fetch --quiet origin "$DEFAULT_BRANCH"; then
+    if ! git show-ref --verify --quiet "refs/remotes/origin/$DEFAULT_BRANCH"; then
+      echo "ERROR: Could not fetch origin/$DEFAULT_BRANCH and no local copy exists. Refusing to create '$branch_name' off the current HEAD (#2916). Resolve the remote/network issue and retry." >&2
+      exit 1
+    fi
+    echo "WARNING: git fetch origin $DEFAULT_BRANCH failed; using the local copy of origin/$DEFAULT_BRANCH as base." >&2
+  fi
+
+  if [ -n "$(git status --porcelain)" ]; then
+    echo "WARNING: Uncommitted changes present. Carrying them onto the new quick-task branch — they will be branched off origin/$DEFAULT_BRANCH (not the previous-task HEAD)."
+  else
+    # Best-effort: fast-forward the local default branch so subsequent local
+    # work sees the latest tip. Failure here is non-fatal because we always
+    # create the new branch directly from origin/$DEFAULT_BRANCH below.
+    git switch --quiet "$DEFAULT_BRANCH" 2>/dev/null \
+      && git merge --ff-only --quiet "origin/$DEFAULT_BRANCH" 2>/dev/null \
+      || true
+  fi
+
+  # Pin the new branch to origin/$DEFAULT_BRANCH so the start point is
+  # deterministic regardless of which branch we are currently on (#2916).
+  # On success HEAD is exactly at origin/$DEFAULT_BRANCH, so a post-creation
+  # merge-base / "ahead-of" guard would be unreachable — the explicit base
+  # argument here is the single source of correctness for #2916.
+  git checkout -b "$branch_name" "origin/$DEFAULT_BRANCH" \
+    || { echo "ERROR: Could not create '$branch_name' from origin/$DEFAULT_BRANCH (#2916)." >&2; exit 1; }
+fi
 ```
 
 All quick-task commits for this run stay on that branch. User handles merge/rebase afterward.
@@ -336,7 +402,7 @@ Display banner:
 Spawn a single focused researcher (not 4 parallel researchers like full phases — quick tasks need targeted research, not broad domain surveys):
 
 ```
-Task(
+Agent(
   prompt="
 <research_context>
 
@@ -377,6 +443,8 @@ Return: ## RESEARCH COMPLETE with file path
 )
 ```
 
+> **ORCHESTRATOR RULE — CODEX RUNTIME**: After calling Agent() above, stop working on this task immediately. Do not read more files, edit code, or run tests related to this task while the subagent is active. Wait for the subagent to return its result. This prevents duplicate work, conflicting edits, and wasted context. Only resume when the subagent result is available.
+
 After researcher returns:
 1. Verify research exists at `${QUICK_DIR}/${quick_id}-RESEARCH.md`
 2. Report: "Research complete: ${QUICK_DIR}/${quick_id}-RESEARCH.md"
@@ -392,7 +460,7 @@ If research file not found, warn but continue: "Research agent did not produce o
 **If NOT `$VALIDATE_MODE`:** Use standard `quick` mode.
 
 ```
-Task(
+Agent(
   prompt="
 <planning_context>
 
@@ -433,6 +501,8 @@ Return: ## PLANNING COMPLETE with plan path
 )
 ```
 
+> **ORCHESTRATOR RULE — CODEX RUNTIME**: After calling Agent() above, stop working on this task immediately. Do not read more files, edit code, or run tests related to this task while the subagent is active. Wait for the subagent to return its result. This prevents duplicate work, conflicting edits, and wasted context. Only resume when the subagent result is available.
+
 After planner returns:
 1. Verify plan exists at `${QUICK_DIR}/${quick_id}-PLAN.md`
 2. Extract plan count (typically 1 for quick tasks)
@@ -489,7 +559,7 @@ ${DISCUSS_MODE ? '- Context compliance: Does the plan honor locked decisions fro
 ```
 
 ```
-Task(
+Agent(
   prompt=checker_prompt,
   subagent_type="sdd-plan-checker",
   model="{checker_model}",
@@ -497,6 +567,8 @@ Task(
 )
 ```
 
+> **ORCHESTRATOR RULE — CODEX RUNTIME**: After calling Agent() above, stop working on this task immediately. Do not read more files, edit code, or run tests related to this task while the subagent is active. Wait for the subagent to return its result. This prevents duplicate work, conflicting edits, and wasted context. Only resume when the subagent result is available.
+
 **Handle checker return:**
 
 - **`## VERIFICATION PASSED`:** Display confirmation, proceed to step 6.
@@ -534,7 +606,7 @@ Return what changed.
 ```
 
 ```
-Task(
+Agent(
   prompt=revision_prompt,
   subagent_type="sdd-planner",
   model="{planner_model}",
@@ -542,6 +614,8 @@ Task(
 )
 ```
 
+> **ORCHESTRATOR RULE — CODEX RUNTIME**: After calling Agent() above, stop working on this task immediately. Do not read more files, edit code, or run tests related to this task while the subagent is active. Wait for the subagent to return its result. This prevents duplicate work, conflicting edits, and wasted context. Only resume when the subagent result is available.
+
 After planner returns → spawn checker again, increment iteration_count.
 
 **If iteration_count >= 2:**
@@ -552,28 +626,84 @@ Offer: 1) Force proceed, 2) Abort
 
 ---
 
+**Step 5.6: Pre-dispatch plan commit (worktree mode only)**
+
+When `USE_WORKTREES !== "false"`, commit PLAN.md to the current branch **before** spawning the executor. This ensures the worktree inherits PLAN.md at its branch HEAD so the executor can read it via a worktree-rooted path — avoiding the main-repo path priming that triggers CC #36182 path-resolution drift.
+
+Skip this step entirely if `USE_WORKTREES === "false"` (non-worktree mode: PLAN.md is committed in Step 8 as usual).
+
+```bash
+if [ "${USE_WORKTREES}" != "false" ]; then
+  COMMIT_DOCS=$(sdd-sdk query config-get commit_docs 2>/dev/null || echo "true")
+  if [ "$COMMIT_DOCS" != "false" ]; then
+    git add "${QUICK_DIR}/${quick_id}-PLAN.md"
+    # No-op skip if nothing actually staged (idempotent re-runs).
+    if git diff --cached --quiet -- "${QUICK_DIR}/${quick_id}-PLAN.md"; then
+      echo "ℹ Pre-dispatch PLAN.md commit skipped (no staged changes)"
+    else
+      # Run hooks normally (#2924). If a project opts out via
+      # workflow.worktree_skip_hooks=true, honor that opt-in only.
+      SKIP_HOOKS=$(sdd-sdk query config-get workflow.worktree_skip_hooks 2>/dev/null || echo "false")
+      if [ "$SKIP_HOOKS" = "true" ]; then
+        git commit --no-verify -m "docs(${quick_id}): pre-dispatch plan for ${DESCRIPTION}" -- "${QUICK_DIR}/${quick_id}-PLAN.md" \
+          || { echo "ERROR: pre-dispatch PLAN.md commit failed (--no-verify path). Aborting before executor dispatch." >&2; exit 1; }
+      else
+        git commit -m "docs(${quick_id}): pre-dispatch plan for ${DESCRIPTION}" -- "${QUICK_DIR}/${quick_id}-PLAN.md" \
+          || { echo "ERROR: pre-dispatch PLAN.md commit failed — likely a pre-commit hook failure. Fix the hook output above (or set workflow.worktree_skip_hooks=true to bypass) and re-run." >&2; exit 1; }
+      fi
+    fi
+  fi
+fi
+```
+
+---
+
 **Step 6: Spawn executor**
 
 Capture current HEAD before spawning (used for worktree branch check):
 ```bash
 EXPECTED_BASE=$(git rev-parse HEAD)
+if [ "${USE_WORKTREES:-true}" != "false" ]; then
+  QUICK_WORKTREE_MANIFEST=$(mktemp "${TMPDIR:-/tmp}/sdd-quick-worktree-XXXXXX.json")
+  printf '{"worktrees":[]}\n' > "$QUICK_WORKTREE_MANIFEST"
+  export QUICK_WORKTREE_MANIFEST
+fi
 ```
 
 Spawn sdd-executor with plan reference:
 
 ```
-Task(
+Agent(
   prompt="
 Execute quick task ${quick_id}.
 
 ${USE_WORKTREES !== "false" ? `
 <worktree_branch_check>
-FIRST ACTION before any other work: verify this worktree branch is based on the correct commit.
-Run: git merge-base HEAD ${EXPECTED_BASE}
-If the result differs from ${EXPECTED_BASE}, hard-reset to the correct base (safe — runs before any agent work):
-  git reset --hard ${EXPECTED_BASE}
-Then verify: if [ "$(git rev-parse HEAD)" != "${EXPECTED_BASE}" ]; then echo "ERROR: Could not correct worktree base"; exit 1; fi
-This corrects a known issue where EnterWorktree creates branches from main instead of the feature branch HEAD (affects all platforms).
+FIRST ACTION before any other work: verify this worktree's HEAD is bound to a per-agent
+branch and that the branch is based on the correct commit.
+
+Step 1 — HEAD attachment assertion (MANDATORY, runs before any reset/commit):
+  HEAD_REF=$(git symbolic-ref --quiet HEAD || echo "DETACHED")
+  ACTUAL_BRANCH=$(git rev-parse --abbrev-ref HEAD)
+  if [ "$HEAD_REF" = "DETACHED" ] || echo "$ACTUAL_BRANCH" | grep -Eq '^(main|master|develop|trunk|release/.*)$'; then
+    echo "FATAL: worktree HEAD is on '$ACTUAL_BRANCH' (expected per-agent branch like worktree-agent-*)." >&2
+    echo "Refusing to commit/reset on a protected ref. DO NOT self-recover via 'git update-ref refs/heads/$ACTUAL_BRANCH' — that destroys concurrent work (#2924)." >&2
+    echo "Aborting before any commits. Surface as a blocker for human review." >&2
+    exit 1
+  fi
+  if ! echo "$ACTUAL_BRANCH" | grep -Eq '^worktree-agent-[A-Za-z0-9._/-]+$'; then
+    echo "FATAL: worktree HEAD '$ACTUAL_BRANCH' is not in the worktree-agent-* namespace (Claude Code's per-agent worktree branch namespace)." >&2
+    echo "Refusing to commit; surface as blocker (#2924)." >&2
+    exit 1
+  fi
+
+Step 2 — Base correctness (only after Step 1 passes):
+  Run: git merge-base HEAD ${EXPECTED_BASE}
+  If the result differs from ${EXPECTED_BASE}, hard-reset to the correct base (safe — Step 1 confirmed HEAD is on a per-agent branch and the worktree is fresh):
+    git reset --hard ${EXPECTED_BASE}
+  Then verify: if [ "$(git rev-parse HEAD)" != "${EXPECTED_BASE}" ]; then echo "ERROR: Could not correct worktree base"; exit 1; fi
+
+This corrects a known issue where EnterWorktree creates branches from main instead of the feature branch HEAD (#2015) and prevents the destructive HEAD-on-master self-recovery path (#2924).
 </worktree_branch_check>
 ` : ''}
 
@@ -586,9 +716,44 @@ This corrects a known issue where EnterWorktree creates branches from main inste
 
 ${AGENT_SKILLS_EXECUTOR}
 
+<submodule_commit_guard>
+SUBMODULE_PATHS for this project: ${SUBMODULE_PATHS}
+
+If SUBMODULE_PATHS is non-empty, you MUST run this fail-loud guard immediately
+before EVERY git commit you create during this quick task (after \`git add\`,
+before \`git commit\`). Quick mode does not have a pre-declared files_modified
+list, so the guard runs at commit time:
+
+\`\`\`bash
+SUBMODULE_PATHS=\"${SUBMODULE_PATHS}\"
+if [ -n \"\$SUBMODULE_PATHS\" ]; then
+  STAGED=\$(git diff --cached --name-only)
+  for sm_raw in \$SUBMODULE_PATHS; do
+    sm=\"\${sm_raw#./}\"
+    sm=\"\${sm%/}\"
+    [ -z \"\$sm\" ] && continue
+    for f_raw in \$STAGED; do
+      f=\"\${f_raw#./}\"
+      f=\"\${f%/}\"
+      case \"\$f\" in
+        \"\$sm\"|\"\$sm\"/*)
+          echo \"ABORT: staged path \$f_raw falls inside submodule \$sm — worktree-isolated commits cannot safely span submodule boundaries. Re-run with workflow.use_worktrees=false.\" >&2
+          exit 1 ;;
+      esac
+    done
+  done
+fi
+\`\`\`
+
+If the guard aborts, do NOT attempt the commit, do NOT remove the staged files,
+and do NOT continue subsequent tasks. Surface the abort message in your
+SUMMARY.md and stop — the user must rerun with worktrees disabled.
+</submodule_commit_guard>
+
 <constraints>
 - Execute all tasks in the plan
 - Commit each task atomically (code changes only)
+- Run the <submodule_commit_guard> bash block before every \`git commit\` if SUBMODULE_PATHS is non-empty
 - Create summary at: ${QUICK_DIR}/${quick_id}-SUMMARY.md
 - Do NOT commit docs artifacts (SUMMARY.md, STATE.md, PLAN.md) — the orchestrator handles the docs commit in Step 8
 - Do NOT update ROADMAP.md (quick tasks are separate from planned phases)
@@ -601,28 +766,76 @@ ${AGENT_SKILLS_EXECUTOR}
 )
 ```
 
+> **ORCHESTRATOR RULE — CODEX RUNTIME**: After calling Agent() above, stop working on this task immediately. Do not read more files, edit code, or run tests related to this task while the subagent is active. Wait for the subagent to return its result. This prevents duplicate work, conflicting edits, and wasted context. Only resume when the subagent result is available.
+
+If the executor ran with `isolation="worktree"`, append its returned `{agent_id, worktree_path, branch, expected_base}` metadata to `QUICK_WORKTREE_MANIFEST` before cleanup. If any field is unavailable, stop and ask for recovery; do not discover global worktrees.
+
 After executor returns:
 1. **Worktree cleanup:** If the executor ran with `isolation="worktree"`, merge the worktree branch back and clean up:
    ```bash
-   # Find worktrees created by the executor
-   WORKTREES=$(git worktree list --porcelain | grep "^worktree " | grep -v "$(pwd)$" | sed 's/^worktree //')
-   for WT in $WORKTREES; do
+   QUICK_WORKTREE_MANIFEST=${QUICK_WORKTREE_MANIFEST:-$WAVE_WORKTREE_MANIFEST}
+   [ -n "${QUICK_WORKTREE_MANIFEST:-}" ] && [ -f "$QUICK_WORKTREE_MANIFEST" ] || {
+     echo "BLOCKED: missing QUICK_WORKTREE_MANIFEST; refusing broad worktree cleanup (#3384)." >&2
+     exit 1
+   }
+
+   # Prefer the bounded cleanup helper. It verifies branch identity, expected
+   # base, deletion diffs, merge result, and worktree removal before branch
+   # deletion. If it blocks, resolve the reported manifest entry and rerun.
+   if command -v sdd-sdk >/dev/null 2>&1; then
+     sdd-sdk query worktree.cleanup-wave --manifest "$QUICK_WORKTREE_MANIFEST" || exit 1
+   else
+     echo "WARN: sdd-sdk unavailable; using manifest-scoped shell fallback (#3384)." >&2
+
+   # Find worktrees recorded by the executor manifest only.
+   # Inclusion-based filter (#2774): match ONLY agent-spawned worktrees under
+   # `.claude/worktrees/agent-` (the namespace Claude Code's `isolation="worktree"`
+   # uses). The previous exclusion filter (`grep -v "$(pwd)$"`) destroyed the parent
+   # workspace's `.git` whenever the workspace itself was a worktree (multi-workspace
+   # setups, and the cross-drive Windows case where `git worktree list` reports the
+   # registry path on a different drive than `$(pwd)`).
+   # Read line-by-line so worktree paths containing whitespace are preserved (#2774).
+   WT_PATHS_FILE=$(mktemp "${TMPDIR:-/tmp}/sdd-worktree-paths-XXXXXX")
+   node -e 'const fs=require("fs");const p=process.env.QUICK_WORKTREE_MANIFEST||process.env.WAVE_WORKTREE_MANIFEST;try{if(!p)throw new Error("QUICK_WORKTREE_MANIFEST is unset");if(!fs.existsSync(p))throw new Error("manifest does not exist");const s=fs.readFileSync(p,"utf8");if(!s.trim())throw new Error("manifest is empty");const j=JSON.parse(s);for(const w of j.worktrees||[])if(w.worktree_path)console.log(w.worktree_path)}catch(e){console.error(`ERROR: cannot read worktree manifest ${p||"(unset)"}: ${e.message}`);process.exit(1)}' > "$WT_PATHS_FILE" || { echo "BLOCKED: cannot read QUICK_WORKTREE_MANIFEST; refusing cleanup (#3384)." >&2; exit 1; }
+   while IFS= read -r WT; do
+     [ -z "$WT" ] && continue
+     # Pin CWD to project root before any bare git command (#3521).
+     # An LLM orchestrator may leak CWD into a worktree across tool calls; without
+     # this pin the merge command resolves against the worktree branch itself and
+     # silently no-ops the main-branch merge.
+     PROJECT_ROOT=$(git -C "$WT" rev-parse --git-common-dir 2>/dev/null)
+     # git rev-parse --git-common-dir returns the .git dir, not the working tree root.
+     # Strip the trailing /.git (or bare .git) to get the working tree root.
+     PROJECT_ROOT=$(echo "$PROJECT_ROOT" | sed 's|/\.git$||; s|/\.git/.*||')
+     if [ -z "$PROJECT_ROOT" ] || [ ! -d "$PROJECT_ROOT" ]; then
+       echo "WARN: cannot resolve project root from worktree $WT — skipping cleanup for this entry (#3521)" >&2
+       continue
+     fi
+     cd "$PROJECT_ROOT" || { echo "WARN: cannot cd to project root $PROJECT_ROOT — skipping cleanup for worktree $WT (#3521)" >&2; continue; }
      WT_BRANCH=$(git -C "$WT" rev-parse --abbrev-ref HEAD 2>/dev/null)
      if [ -n "$WT_BRANCH" ] && [ "$WT_BRANCH" != "HEAD" ]; then
        # --- Orchestrator file protection (#1756) ---
        # Backup STATE.md and ROADMAP.md before merge (main always wins)
        STATE_BACKUP=$(mktemp)
        ROADMAP_BACKUP=$(mktemp)
-       git show HEAD:.planning/STATE.md > "$STATE_BACKUP" 2>/dev/null || true
-       git show HEAD:.planning/ROADMAP.md > "$ROADMAP_BACKUP" 2>/dev/null || true
-
-       # Snapshot files on main to detect resurrections
-       PRE_MERGE_FILES=$(git ls-files .planning/)
-
-       git merge "$WT_BRANCH" --no-edit -m "chore: merge quick task worktree ($WT_BRANCH)" 2>&1 || {
-         echo "⚠ Merge conflict — resolve manually"
+       [ -f .planning/STATE.md ] && cp .planning/STATE.md "$STATE_BACKUP" || true
+       [ -f .planning/ROADMAP.md ] && cp .planning/ROADMAP.md "$ROADMAP_BACKUP" || true
+
+       # Pre-merge deletion guard: block merges that delete tracked .planning/ files
+       DELETIONS=$(git diff --diff-filter=D --name-only HEAD..."$WT_BRANCH" 2>/dev/null || true)
+       if [ -n "$DELETIONS" ]; then
+         echo "BLOCKED: Worktree branch $WT_BRANCH contains file deletions: $DELETIONS"
+         echo "Review these deletions before merging. If intentional, remove this guard and re-run."
          rm -f "$STATE_BACKUP" "$ROADMAP_BACKUP"
          continue
+       fi
+
+       git merge "$WT_BRANCH" --no-ff --no-edit -m "chore: merge quick task worktree ($WT_BRANCH)" 2>&1 || {
+         echo "⚠ Merge conflict from worktree $WT_BRANCH — resolve manually"
+         echo "  STATE.md backup:   $STATE_BACKUP"
+         echo "  ROADMAP.md backup: $ROADMAP_BACKUP"
+         echo "  Restore with: cp \$STATE_BACKUP .planning/STATE.md && cp \$ROADMAP_BACKUP .planning/ROADMAP.md"
+         break
        }
 
        # Restore orchestrator-owned files
@@ -630,27 +843,73 @@ After executor returns:
        if [ -s "$ROADMAP_BACKUP" ]; then cp "$ROADMAP_BACKUP" .planning/ROADMAP.md; fi
        rm -f "$STATE_BACKUP" "$ROADMAP_BACKUP"
 
-       # Remove files deleted on main but re-added by worktree
+       # Detect files deleted on main but re-added by worktree merge
+       # (e.g., archived phase directories that were intentionally removed)
+       # A "resurrected" file must have a deletion event in main's ancestry —
+       # brand-new files (e.g. SUMMARY.md just created by the agent) have no
+       # such history and must NOT be removed (#2501, #3195).
        DELETED_FILES=$(git diff --diff-filter=A --name-only HEAD~1 -- .planning/ 2>/dev/null || true)
        for RESURRECTED in $DELETED_FILES; do
-         if ! echo "$PRE_MERGE_FILES" | grep -qxF "$RESURRECTED"; then
+         # Only delete if this file was previously tracked on main and then
+         # deliberately removed (has a deletion event in git history).
+         WAS_DELETED=$(git log --follow --diff-filter=D --name-only --format="" HEAD~1 -- "$RESURRECTED" 2>/dev/null | grep -c . || true)
+         if [ "${WAS_DELETED:-0}" -gt 0 ]; then
            git rm -f "$RESURRECTED" 2>/dev/null || true
          fi
        done
 
        if ! git diff --quiet .planning/STATE.md .planning/ROADMAP.md 2>/dev/null || \
           [ -n "$DELETED_FILES" ]; then
-         COMMIT_DOCS=$(node "$HOME/.claude/sdd/bin/sdd-tools.cjs" config-get commit_docs 2>/dev/null || echo "true")
+         COMMIT_DOCS=$(sdd-sdk query config-get commit_docs 2>/dev/null || echo "true")
          if [ "$COMMIT_DOCS" != "false" ]; then
            git add .planning/STATE.md .planning/ROADMAP.md 2>/dev/null || true
            git commit --amend --no-edit 2>/dev/null || true
          fi
        fi
 
-       git worktree remove "$WT" --force 2>/dev/null || true
-       git branch -D "$WT_BRANCH" 2>/dev/null || true
+       # Safety net: rescue uncommitted SUMMARY.md before worktree removal (#2296, mirrors #2070, #2838).
+       # Filesystem-level (find + cp) bypasses git's --exclude-standard filter, which silently
+       # drops .planning/SUMMARY.md when projects gitignore .planning/ — the rescue's prior
+       # `git ls-files --exclude-standard` form returned empty in that case and the SUMMARY
+       # was lost on `git worktree remove --force`.
+       while IFS= read -r SUMMARY; do
+         [ -z "$SUMMARY" ] && continue
+         REL_PATH="${SUMMARY#$WT/}"
+         if [ ! -f "$REL_PATH" ] || ! cmp -s "$SUMMARY" "$REL_PATH"; then
+           mkdir -p "$(dirname "$REL_PATH")"
+           cp "$SUMMARY" "$REL_PATH"
+           echo "⚠ Rescued $REL_PATH from worktree before removal"
+         fi
+       done < <(find "$WT/.planning" -name "*SUMMARY.md" 2>/dev/null)
+
+       # Remove the worktree before deleting the branch. If removal fails,
+       # leave the branch in place so the worktree remains recoverable (#3384).
+       REMOVE_OK=false
+       if git worktree remove "$WT" --force; then
+         REMOVE_OK=true
+       else
+         WT_NAME=$(basename "$WT")
+         if [ -f ".git/worktrees/${WT_NAME}/locked" ]; then
+           echo "⚠ Worktree $WT is locked — attempting to unlock and retry"
+           git worktree unlock "$WT" 2>/dev/null || true
+           if git worktree remove "$WT" --force; then
+             REMOVE_OK=true
+           else
+             echo "⚠ Residual worktree at $WT — manual cleanup required after session exits:"
+             echo "    git worktree unlock \"$WT\" && git worktree remove \"$WT\" --force && git branch -D \"$WT_BRANCH\""
+           fi
+         else
+           echo "⚠ Residual worktree at $WT (remove failed) — investigate manually"
+         fi
+       fi
+       if [ "$REMOVE_OK" = "true" ]; then
+         git branch -D "$WT_BRANCH" 2>/dev/null || true
+       else
+         echo "⚠ Keeping branch $WT_BRANCH because worktree removal failed (#3384)"
+       fi
      fi
-   done
+   done < "$WT_PATHS_FILE"
+   fi
    ```
    If `workflow.use_worktrees` is `false`, skip this step.
 2. Verify summary exists at `${QUICK_DIR}/${quick_id}-SUMMARY.md`
@@ -671,7 +930,7 @@ Skip this step entirely if `$FULL_MODE` is false.
 
 **Config gate:**
 ```bash
-CODE_REVIEW_ENABLED=$(node "$HOME/.claude/sdd/bin/sdd-tools.cjs" config-get workflow.code_review 2>/dev/null || echo "true")
+CODE_REVIEW_ENABLED=$(sdd-sdk query config-get workflow.code_review 2>/dev/null || echo "true")
 ```
 If `"false"`, skip with message "Code review skipped (workflow.code_review=false)".
 
@@ -700,7 +959,7 @@ If `CHANGED_FILES` is empty, skip with "No source files changed — skipping cod
 
 **Invoke review:**
 ```
-Task(
+Agent(
   prompt="Review these files for bugs, security issues, and code quality.
   Files: ${CHANGED_FILES}
   Output: ${QUICK_DIR}/${quick_id}-REVIEW.md
@@ -710,6 +969,8 @@ Task(
 )
 ```
 
+> **ORCHESTRATOR RULE — CODEX RUNTIME**: After calling Agent() above, stop working on this task immediately. Do not read more files, edit code, or run tests related to this task while the subagent is active. Wait for the subagent to return its result. This prevents duplicate work, conflicting edits, and wasted context. Only resume when the subagent result is available.
+
 If review produces findings, display advisory message. **Error handling:** Failures are non-blocking — catch and proceed.
 
 ---
@@ -728,7 +989,7 @@ Display banner:
 ```
 
 ```
-Task(
+Agent(
   prompt="Verify quick task goal achievement.
 Task directory: ${QUICK_DIR}
 Task goal: ${DESCRIPTION}
@@ -746,6 +1007,8 @@ Check must_haves against actual codebase. Create VERIFICATION.md at ${QUICK_DIR}
 )
 ```
 
+> **ORCHESTRATOR RULE — CODEX RUNTIME**: After calling Agent() above, stop working on this task immediately. Do not read more files, edit code, or run tests related to this task while the subagent is active. Wait for the subagent to return its result. This prevents duplicate work, conflicting edits, and wasted context. Only resume when the subagent result is available.
+
 Read verification status:
 ```bash
 grep "^status:" "${QUICK_DIR}/${quick_id}-VERIFICATION.md" | cut -d: -f2 | tr -d ' '
@@ -818,7 +1081,7 @@ Use Edit tool to make these changes atomically
 
 **Step 8: Final commit and completion**
 
-Stage and commit quick task artifacts. This step MUST always run — even if the executor already committed some files (e.g. when running without worktree isolation). The `sdd-tools commit` command handles already-committed files gracefully.
+Stage and commit quick task artifacts. This step MUST always run — even if the executor already committed some files (e.g. when running without worktree isolation). The `sdd-sdk query commit` command (or legacy `sdd-tools.cjs` commit) handles already-committed files gracefully.
 
 Build file list:
 - `${QUICK_DIR}/${quick_id}-PLAN.md`
@@ -827,19 +1090,20 @@ Build file list:
 - If `$DISCUSS_MODE` and context file exists: `${QUICK_DIR}/${quick_id}-CONTEXT.md`
 - If `$RESEARCH_MODE` and research file exists: `${QUICK_DIR}/${quick_id}-RESEARCH.md`
 - If `$VALIDATE_MODE` and verification file exists: `${QUICK_DIR}/${quick_id}-VERIFICATION.md`
+- If `${QUICK_DIR}/${quick_id}-deferred-items.md` exists: `${QUICK_DIR}/${quick_id}-deferred-items.md`
 
 ```bash
 # Explicitly stage all artifacts before commit — PLAN.md may be untracked
 # if the executor ran without worktree isolation and committed docs early
 # Filter .planning/ files from staging if commit_docs is disabled (#1783)
-COMMIT_DOCS=$(node "$HOME/.claude/sdd/bin/sdd-tools.cjs" config-get commit_docs 2>/dev/null || echo "true")
+COMMIT_DOCS=$(sdd-sdk query config-get commit_docs 2>/dev/null || echo "true")
 if [ "$COMMIT_DOCS" = "false" ]; then
   file_list_filtered=$(echo "${file_list}" | tr ' ' '\n' | grep -v '^\.planning/' | tr '\n' ' ')
   git add ${file_list_filtered} 2>/dev/null
 else
   git add ${file_list} 2>/dev/null
 fi
-node "$HOME/.claude/sdd/bin/sdd-tools.cjs" commit "docs(quick-${quick_id}): ${DESCRIPTION}" --files ${file_list}
+sdd-sdk query commit "docs(quick-${quick_id}): ${DESCRIPTION}" --files ${file_list}
 ```
 
 Get final commit hash:
@@ -864,7 +1128,7 @@ Commit: ${commit_hash}
 
 ---
 
-Ready for next task: /sdd-quick ${SDD_WS}
+Ready for next task: /sdd:quick ${SDD_WS}
 ```
 
 **If NOT `$VALIDATE_MODE`:**
@@ -881,7 +1145,7 @@ Commit: ${commit_hash}
 
 ---
 
-Ready for next task: /sdd-quick ${SDD_WS}
+Ready for next task: /sdd:quick ${SDD_WS}
 ```
 
 </process>