@mmerterden/multi-agent-pipeline 11.5.0 → 12.1.0

package/pipeline/scripts/smoke-prune-logs.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 # smoke-prune-logs.sh  -  prune-logs.sh removes per-task log dirs, honors the
-# project/task/age filters, is dry-run by default, and NEVER deletes the audit
-# trail or metrics corpus.
+# project/task/age filters, is dry-run by default, NEVER deletes the audit
+# trail or metrics corpus (even under adversarial dir names), refuses unsafe
+# log roots, and spares active task dirs.
 #
 # Exit 0 = all pass, 1 = any failure.
 
@@ -40,7 +41,7 @@ seed() {
 
 echo "→ 1. dry-run lists task dirs and deletes nothing"
 seed
-out=$(PRUNE_LOG_ROOT="$LR" bash "$PL" 2>&1)
+out=$(PRUNE_LOG_ROOT="$LR" PRUNE_GRACE_MIN=0 bash "$PL" 2>&1)
 echo "$out" | grep -q "DRY-RUN" && pass "dry-run banner shown" || fail "dry-run banner missing"
 [ -f "$LR/my-ios-app/PROJ-1/agent-state.json" ] && pass "dry-run kept task dirs" || fail "dry-run deleted a task dir"
 echo "$out" | grep -qi "preserved" && pass "dry-run states audit/metrics are preserved" || fail "no preservation note"
@@ -48,7 +49,7 @@ echo "$out" | grep -qi "preserved" && pass "dry-run states audit/metrics are pre
 echo ""
 echo "→ 2. --yes deletes task dirs but preserves audit + metrics + .counter"
 seed
-PRUNE_LOG_ROOT="$LR" bash "$PL" --yes >/dev/null 2>&1
+PRUNE_LOG_ROOT="$LR" PRUNE_GRACE_MIN=0 bash "$PL" --yes >/dev/null 2>&1
 [ -f "$LR/audit.jsonl" ] && pass "audit.jsonl preserved" || fail "audit.jsonl was deleted"
 [ -f "$LR/metrics.jsonl" ] && pass "metrics.jsonl preserved" || fail "metrics.jsonl was deleted"
 [ -f "$LR/my-ios-app/.counter" ] && pass ".counter preserved" || fail ".counter was deleted"
@@ -58,21 +59,21 @@ PRUNE_LOG_ROOT="$LR" bash "$PL" --yes >/dev/null 2>&1
 echo ""
 echo "→ 3. --project scopes deletion to one project"
 seed
-PRUNE_LOG_ROOT="$LR" bash "$PL" --project=my-ios-app --yes >/dev/null 2>&1
+PRUNE_LOG_ROOT="$LR" PRUNE_GRACE_MIN=0 bash "$PL" --project=my-ios-app --yes >/dev/null 2>&1
 [ ! -e "$LR/my-ios-app/PROJ-1" ] && pass "my-ios-app task removed" || fail "my-ios-app task survived"
 [ -f "$LR/other/PROJ-9/agent-log.md" ] && pass "other project untouched" || fail "other project was deleted"
 
 echo ""
 echo "→ 4. --task scopes deletion to one task dir"
 seed
-PRUNE_LOG_ROOT="$LR" bash "$PL" --task=PROJ-1 --yes >/dev/null 2>&1
+PRUNE_LOG_ROOT="$LR" PRUNE_GRACE_MIN=0 bash "$PL" --task=PROJ-1 --yes >/dev/null 2>&1
 [ ! -e "$LR/my-ios-app/PROJ-1" ] && pass "PROJ-1 removed" || fail "PROJ-1 survived"
 [ -f "$LR/my-ios-app/PROJ-2/tracker-state.json" ] && pass "PROJ-2 untouched" || fail "PROJ-2 was deleted"
 
 echo ""
 echo "→ 5. --older-than excludes fresh task dirs"
 seed
-out=$(PRUNE_LOG_ROOT="$LR" bash "$PL" --older-than=1 2>&1)
+out=$(PRUNE_LOG_ROOT="$LR" PRUNE_GRACE_MIN=0 bash "$PL" --older-than=1 2>&1)
 echo "$out" | grep -q "nothing" && pass "freshly-created dirs excluded by --older-than=1" || fail "--older-than did not exclude fresh dirs"
 
 echo ""
@@ -82,6 +83,55 @@ PRUNE_LOG_ROOT="$LR" bash "$PL" --bogus >/dev/null 2>&1
 PRUNE_LOG_ROOT="/nonexistent-$$-dir" bash "$PL" >/dev/null 2>&1
 [ "$?" = "0" ] && pass "missing log root exits 0 (no-op)" || fail "missing log root did not exit 0"
 
+echo ""
+echo "→ 7. adversarial dirs named like preserved files survive --yes"
+rm -rf "${LR:?}"/*
+mkdir -p "$LR/audit.jsonl" "$LR/proj/metrics.jsonl" "$LR/proj/metrics-summary.md" "$LR/proj/.counter" "$LR/proj/PROJ-5"
+echo '{}' >"$LR/audit.jsonl/agent-state.json"
+echo '{}' >"$LR/proj/metrics.jsonl/agent-log.md"
+echo '{}' >"$LR/proj/metrics-summary.md/tracker-state.json"
+echo '{}' >"$LR/proj/.counter/agent-state.json"
+echo '{}' >"$LR/proj/PROJ-5/agent-state.json"
+PRUNE_LOG_ROOT="$LR" PRUNE_GRACE_MIN=0 bash "$PL" --yes >/dev/null 2>&1
+[ -d "$LR/audit.jsonl" ] && pass "dir named audit.jsonl spared" || fail "dir named audit.jsonl deleted"
+[ -d "$LR/proj/metrics.jsonl" ] && pass "dir named metrics.jsonl spared" || fail "dir named metrics.jsonl deleted"
+[ -d "$LR/proj/metrics-summary.md" ] && pass "dir named metrics-summary.md spared" || fail "dir named metrics-summary.md deleted"
+[ -d "$LR/proj/.counter" ] && pass "dir named .counter spared" || fail "dir named .counter deleted"
+[ ! -e "$LR/proj/PROJ-5" ] && pass "normal task dir beside them still removed" || fail "normal task dir survived"
+
+echo ""
+echo "→ 8. unsafe log roots are refused (exit 2, dry-run only)"
+PRUNE_LOG_ROOT="$HOME" bash "$PL" >/dev/null 2>&1
+[ "$?" = "2" ] && pass "\$HOME as log root refused" || fail "\$HOME as log root not refused"
+GITROOT="$(mktemp -d)"
+mkdir -p "$GITROOT/.git"
+PRUNE_LOG_ROOT="$GITROOT" bash "$PL" --yes >/dev/null 2>&1
+rc=$?
+rm -rf "$GITROOT"
+[ "$rc" = "2" ] && pass "git work tree as log root refused" || fail "git work tree as log root not refused"
+
+echo ""
+echo "→ 9. default grace spares freshly-touched (active) task dirs"
+seed
+out=$(PRUNE_LOG_ROOT="$LR" bash "$PL" --yes 2>&1)
+rc=$?
+[ "$rc" = "0" ] && pass "grace run exits 0" || fail "grace run exited $rc"
+[ -f "$LR/my-ios-app/PROJ-1/agent-state.json" ] && pass "active task dir spared by default grace" || fail "default grace deleted an active task dir"
+echo "$out" | grep -qi "spared" && pass "output mentions spared active dirs" || fail "no spared-active note in output"
+PRUNE_LOG_ROOT="$LR" bash "$PL" --task=PROJ-1 --yes >/dev/null 2>&1
+[ ! -e "$LR/my-ios-app/PROJ-1" ] && pass "explicit --task bypasses the grace" || fail "--task did not bypass the grace"
+
+echo ""
+echo "→ 10. traversal-shaped --task/--project values are rejected"
+PRUNE_LOG_ROOT="$LR" bash "$PL" "--task=../evil" >/dev/null 2>&1
+[ "$?" = "2" ] && pass "--task=../evil exits 2" || fail "--task=../evil accepted"
+PRUNE_LOG_ROOT="$LR" bash "$PL" "--task=.counter" >/dev/null 2>&1
+[ "$?" = "2" ] && pass "--task=.counter (leading dot) exits 2" || fail "--task=.counter accepted"
+PRUNE_LOG_ROOT="$LR" bash "$PL" "--project=a/b" >/dev/null 2>&1
+[ "$?" = "2" ] && pass "--project=a/b exits 2" || fail "--project=a/b accepted"
+PRUNE_LOG_ROOT="$LR" bash "$PL" "--task=" >/dev/null 2>&1
+[ "$?" = "2" ] && pass "empty --task exits 2" || fail "empty --task accepted"
+
 echo ""
 echo "══ prune-logs smoke: $PASS passed, $FAIL failed ══"
 [ "$FAIL" -eq 0 ]

package/pipeline/scripts/smoke-purge.sh

@@ -0,0 +1,138 @@
+#!/usr/bin/env bash
+# smoke-purge.sh  -  purge.sh wipes .worktrees/ worktrees (registered and
+# orphaned), their local branches, and the project task counter; is dry-run
+# by default; preserves the main worktree, protected branches, and the
+# audit/metrics corpus; and never follows symlinks out of .worktrees/.
+#
+# Exit 0 = all pass, 1 = any failure.
+
+set -uo pipefail
+
+ROOT="$(cd "$(dirname "$0")/../.." && pwd)"
+PG="$ROOT/pipeline/scripts/purge.sh"
+PASS=0
+FAIL=0
+pass() {
+  PASS=$((PASS + 1))
+  echo "  ✓ $1"
+}
+fail() {
+  FAIL=$((FAIL + 1))
+  echo "  ✗ $1"
+}
+[ -f "$PG" ] || {
+  echo "FAIL: purge.sh missing" >&2
+  exit 1
+}
+
+SB="$(cd "$(mktemp -d)" && pwd -P)"
+trap 'rm -rf "$SB"' EXIT
+
+REPO="$SB/repo"
+LR="$SB/logs"
+VICTIM="$SB/victim"
+
+seed() {
+  rm -rf "$REPO" "$LR" "$VICTIM"
+  mkdir -p "$REPO" "$LR/repo" "$VICTIM"
+  echo keep >"$VICTIM/keep.txt"
+  git -C "$REPO" init -q -b main
+  git -C "$REPO" -c user.email=t@t.t -c user.name=t commit -q --allow-empty -m init
+  git -C "$REPO" worktree add -q -b feature/PROJ-1-x "$REPO/.worktrees/PROJ-1" >/dev/null 2>&1
+  git -C "$REPO" worktree add -q -b bugfix/PROJ-2-y "$REPO/.worktrees/PROJ-2" >/dev/null 2>&1
+  mkdir -p "$REPO/.worktrees/PROJ-9" # orphan: dir git no longer registers
+  echo '{}' >"$REPO/.worktrees/PROJ-9/agent-state.json"
+  ln -s "$VICTIM" "$REPO/.worktrees/evil-link" # symlink escape attempt
+  echo '7' >"$LR/repo/.counter"
+  echo audit >"$LR/audit.jsonl"
+  echo metric >"$LR/metrics.jsonl"
+}
+
+has_branch() {
+  git -C "$REPO" show-ref --verify -q "refs/heads/$1"
+}
+
+echo "→ 1. dry-run lists everything and deletes nothing"
+seed
+out=$(PURGE_LOG_ROOT="$LR" bash "$PG" --repo "$REPO" 2>&1)
+rc=$?
+[ "$rc" = "0" ] && pass "dry-run exits 0" || fail "dry-run exited $rc"
+echo "$out" | grep -q "DRY-RUN" && pass "dry-run banner shown" || fail "dry-run banner missing"
+echo "$out" | grep -q "PROJ-1" && pass "worktree PROJ-1 listed" || fail "worktree PROJ-1 not listed"
+echo "$out" | grep -q "feature/PROJ-1-x" && pass "branch listed" || fail "branch not listed"
+echo "$out" | grep -q ".counter" && pass "counter listed" || fail "counter not listed"
+[ -d "$REPO/.worktrees/PROJ-1" ] && pass "dry-run kept worktrees" || fail "dry-run deleted a worktree"
+[ -f "$LR/repo/.counter" ] && pass "dry-run kept the counter" || fail "dry-run deleted the counter"
+has_branch feature/PROJ-1-x && pass "dry-run kept branches" || fail "dry-run deleted a branch"
+
+echo ""
+echo "→ 2. --yes wipes worktrees + branches + counter, preserves the rest"
+seed
+PURGE_LOG_ROOT="$LR" bash "$PG" --repo "$REPO" --yes >/dev/null 2>&1
+rc=$?
+[ "$rc" = "0" ] && pass "--yes exits 0" || fail "--yes exited $rc"
+[ ! -e "$REPO/.worktrees/PROJ-1" ] && pass "registered worktree PROJ-1 removed" || fail "PROJ-1 survived"
+[ ! -e "$REPO/.worktrees/PROJ-2" ] && pass "registered worktree PROJ-2 removed" || fail "PROJ-2 survived"
+[ ! -e "$REPO/.worktrees/PROJ-9" ] && pass "orphan worktree dir removed" || fail "orphan PROJ-9 survived"
+! has_branch feature/PROJ-1-x && pass "branch feature/PROJ-1-x deleted" || fail "feature/PROJ-1-x survived"
+! has_branch bugfix/PROJ-2-y && pass "branch bugfix/PROJ-2-y deleted" || fail "bugfix/PROJ-2-y survived"
+has_branch main && pass "main branch preserved" || fail "main branch was deleted"
+git -C "$REPO" rev-parse --is-inside-work-tree >/dev/null 2>&1 && pass "main worktree still a git repo" || fail "main worktree destroyed"
+wt_count=$(git -C "$REPO" worktree list 2>/dev/null | wc -l | tr -d ' ')
+[ "$wt_count" = "1" ] && pass "only the main worktree remains registered" || fail "expected 1 registered worktree, got $wt_count"
+[ ! -e "$LR/repo/.counter" ] && pass "task counter removed" || fail "task counter survived"
+[ -f "$LR/audit.jsonl" ] && pass "audit.jsonl preserved" || fail "audit.jsonl was deleted"
+[ -f "$LR/metrics.jsonl" ] && pass "metrics.jsonl preserved" || fail "metrics.jsonl was deleted"
+[ -f "$VICTIM/keep.txt" ] && pass "symlink target outside repo untouched" || fail "symlink target was deleted"
+
+echo ""
+echo "→ 3. protected branch carried by a worktree survives, worktree still removed"
+seed
+git -C "$REPO" worktree add -q -b develop "$REPO/.worktrees/DEV-1" >/dev/null 2>&1
+PURGE_LOG_ROOT="$LR" bash "$PG" --repo "$REPO" --yes >/dev/null 2>&1
+[ ! -e "$REPO/.worktrees/DEV-1" ] && pass "develop worktree removed" || fail "develop worktree survived"
+has_branch develop && pass "develop branch preserved" || fail "develop branch was deleted"
+
+echo ""
+echo "→ 4. clean repo and non-repo are no-ops (exit 0)"
+CLEAN="$SB/clean"
+mkdir -p "$CLEAN"
+git -C "$CLEAN" init -q -b main
+out=$(PURGE_LOG_ROOT="$LR" bash "$PG" --repo "$CLEAN" 2>&1)
+rc=$?
+{ [ "$rc" = "0" ] && echo "$out" | grep -q "nothing to do"; } && pass "clean repo is a no-op" || fail "clean repo not a clean no-op (rc=$rc)"
+PLAIN="$SB/plain"
+mkdir -p "$PLAIN"
+out=$(bash "$PG" --repo "$PLAIN" 2>&1)
+rc=$?
+{ [ "$rc" = "0" ] && echo "$out" | grep -q "not a git work tree"; } && pass "non-repo dir is a no-op" || fail "non-repo dir not a clean no-op (rc=$rc)"
+
+echo ""
+echo "→ 5. usage errors exit 2"
+bash "$PG" --bogus >/dev/null 2>&1
+[ "$?" = "2" ] && pass "unknown argument exits 2" || fail "unknown argument did not exit 2"
+bash "$PG" --repo >/dev/null 2>&1
+[ "$?" = "2" ] && pass "--repo without a path exits 2" || fail "--repo without a path did not exit 2"
+
+echo ""
+echo "→ 6. --delete-remote without a remote warns but does not fail"
+seed
+out=$(PURGE_LOG_ROOT="$LR" bash "$PG" --repo "$REPO" --delete-remote 2>&1)
+echo "$out" | grep -q "remote branch origin/feature/PROJ-1-x" && pass "dry-run lists remote branch deletion" || fail "dry-run missing remote branch line"
+out=$(PURGE_LOG_ROOT="$LR" bash "$PG" --repo "$REPO" --delete-remote --yes 2>&1)
+rc=$?
+[ "$rc" = "0" ] && pass "--delete-remote --yes exits 0 without a remote" || fail "--delete-remote --yes exited $rc"
+echo "$out" | grep -qi "warning" && pass "missing remote surfaces a warning" || fail "no warning for missing remote"
+
+echo ""
+echo "→ 7. purge from inside a linked worktree still anchors on the main repo"
+seed
+out=$(PURGE_LOG_ROOT="$LR" bash "$PG" --repo "$REPO/.worktrees/PROJ-1" --yes 2>&1)
+rc=$?
+[ "$rc" = "0" ] && pass "run from linked worktree exits 0" || fail "run from linked worktree exited $rc"
+[ ! -e "$REPO/.worktrees/PROJ-1" ] && pass "worktrees removed when invoked from inside one" || fail "worktrees survived"
+git -C "$REPO" rev-parse --is-inside-work-tree >/dev/null 2>&1 && pass "main repo intact" || fail "main repo destroyed"
+
+echo ""
+echo "══ purge smoke: $PASS passed, $FAIL failed ══"
+[ "$FAIL" -eq 0 ]

package/pipeline/scripts/smoke-source-parity.sh

@@ -0,0 +1,85 @@
+#!/usr/bin/env bash
+# smoke-source-parity.sh  -  guard the two divergent SOURCE trees of the same
+# feature set from drifting out of alignment.
+#
+# The pipeline ships each sub-command twice, in parallel trees:
+#   1. pipeline/commands/multi-agent/<name>/        (Claude slash commands)
+#   2. pipeline/skills/shared/core/multi-agent-<name>/  (Copilot skills)
+# Both are meant to cover the SAME feature SET. A feature present in one tree
+# but absent from the other is the single biggest maintainability liability
+# here: users on one CLI silently lose a capability the other CLI advertises.
+#
+# This is a STRUCTURAL set-parity check only. It auto-discovers feature names
+# from the directory listings (nothing is hardcoded), strips the
+# 'multi-agent-' prefix from the skills tree, and FAILS if the symmetric
+# difference of the two name sets is non-empty. It deliberately does NOT diff
+# prose / behavior content between a matched command and its skill  -  content
+# drift is a separate concern (see smoke-sync-parity.sh / sync-parity-check).
+
+set -uo pipefail
+
+REPO_ROOT="$(cd "$(dirname "$0")/../.." && pwd)"
+CMDS_DIR="$REPO_ROOT/pipeline/commands/multi-agent"
+SKILLS_DIR="$REPO_ROOT/pipeline/skills/shared/core"
+
+PASS=0
+FAIL=0
+pass() { PASS=$((PASS+1)); echo "  ✓ $1"; }
+fail() { FAIL=$((FAIL+1)); echo "  ✗ $1"; }
+
+if [ ! -d "$CMDS_DIR" ]; then
+  echo "FAIL: commands tree missing at $CMDS_DIR" >&2
+  exit 1
+fi
+if [ ! -d "$SKILLS_DIR" ]; then
+  echo "FAIL: skills tree missing at $SKILLS_DIR" >&2
+  exit 1
+fi
+
+echo "→ 1. discover feature names in each source tree"
+
+# Claude slash commands: every immediate sub-directory is a feature.
+CMD_FEATURES=$(find "$CMDS_DIR" -mindepth 1 -maxdepth 1 -type d \
+  -exec basename {} \; | sort -u)
+
+# Copilot skills: multi-agent-<name> sub-directories; strip the prefix.
+# Non-prefixed skill dirs (e.g. apple-archive-compliance) are standalone
+# skills without a slash-command twin, so they are intentionally excluded.
+SKILL_FEATURES=$(find "$SKILLS_DIR" -mindepth 1 -maxdepth 1 -type d \
+  -name 'multi-agent-*' -exec basename {} \; \
+  | sed 's/^multi-agent-//' | sort -u)
+
+CMD_COUNT=$(printf '%s\n' "$CMD_FEATURES" | grep -c . || true)
+SKILL_COUNT=$(printf '%s\n' "$SKILL_FEATURES" | grep -c . || true)
+pass "commands tree: $CMD_COUNT features"
+pass "skills tree:   $SKILL_COUNT features"
+
+echo ""
+echo "→ 2. set symmetric difference must be empty"
+
+# In commands tree but missing from skills tree.
+ONLY_CMD=$(comm -23 \
+  <(printf '%s\n' "$CMD_FEATURES") \
+  <(printf '%s\n' "$SKILL_FEATURES"))
+# In skills tree but missing from commands tree.
+ONLY_SKILL=$(comm -13 \
+  <(printf '%s\n' "$CMD_FEATURES") \
+  <(printf '%s\n' "$SKILL_FEATURES"))
+
+if [ -z "$ONLY_CMD" ]; then
+  pass "no command-only features (all present as skills)"
+else
+  fail "features in commands/ but NOT in skills tree:"
+  printf '      - %s\n' $ONLY_CMD
+fi
+
+if [ -z "$ONLY_SKILL" ]; then
+  pass "no skill-only features (all present as commands)"
+else
+  fail "features in skills tree but NOT in commands/:"
+  printf '      - %s\n' $ONLY_SKILL
+fi
+
+echo ""
+echo "══ source-parity smoke: $PASS passed, $FAIL failed ══"
+[ "$FAIL" -eq 0 ]

package/pipeline/scripts/smoke-update-check.sh

@@ -67,6 +67,19 @@ else
   record_fail "local-ahead should be silent (got '$out', rc=$rc)"
 fi
 
+# 3b2. No --local, no repo clone -> falls back to the install-time version
+# marker (npx-only installs have no clone to read a version from)
+marker_home="$tmpdir/marker-home"
+mkdir -p "$marker_home/.claude"
+printf '10.0.0\n' > "$marker_home/.claude/.pipeline-version"
+printf '%s|99.0.0\n' "$now" > "$CACHE"
+out=$(HOME="$marker_home" UPDATE_CHECK_CACHE="$CACHE" bash "$SCRIPT" 2>/dev/null); rc=$?
+if [ "$rc" -eq 0 ] && [ "$out" = "10.0.0|99.0.0" ]; then
+  record_pass "no clone -> .pipeline-version marker fallback works"
+else
+  record_fail "marker fallback should print '10.0.0|99.0.0' (got '$out', rc=$rc)"
+fi
+
 # 3c. Offline + stale cache -> silent exit 0 (advisory: never blocks)
 printf '0|10.0.0\n' > "$CACHE"
 out=$(UPDATE_CHECK_CACHE="$CACHE" http_proxy="http://127.0.0.1:1" https_proxy="http://127.0.0.1:1" \

package/pipeline/scripts/uninstall.mjs

@@ -12,21 +12,26 @@
  *   node uninstall.mjs                  # interactive, removes from all installed targets
  *   node uninstall.mjs --yes            # skip prompts, remove from all
  *   node uninstall.mjs --claude         # only Claude Code
+ *   node uninstall.mjs --all-data       # ALSO remove pipeline settings + logs/state/metrics
  *   node uninstall.mjs --cursor --target=/path/to/repo   # legacy adapter-file cleanup
  *   node uninstall.mjs --dry-run        # report what would be removed, change nothing
  *
  * Targeted by:
- *   - `/multi-agent:delete` slash command (Claude Code)
- *   - `multi-agent-delete` skill (Copilot CLI)
+ *   - `/multi-agent:uninstall` slash command (Claude Code)
+ *   - `multi-agent-uninstall` skill (Copilot CLI)
  *   - `npx @mmerterden/multi-agent-pipeline uninstall` (direct CLI)
  *
- * Always preserved:
- *   - $HOME/.claude/CLAUDE.md (user customizations)
- *   - $HOME/.claude/multi-agent-preferences.json
+ * Always preserved (both modes):
  *   - Personal access tokens in the OS credential store
+ *   - $HOME/.claude/CLAUDE.md (user customizations)
+ *   - $HOME/.claude/rules/ (user-owned; installed write-if-missing)
  *   - User content outside the `<!-- multi-agent-pipeline:begin/end -->` markers
  *     in shared rules files (copilot-instructions.md)
  *
+ * Preserved by default, removed with --all-data:
+ *   - $HOME/.claude/multi-agent-preferences.json (pipeline settings)
+ *   - $HOME/.claude/logs/multi-agent/ (task logs, state, metrics, audit trail)
+ *
  * @module pipeline/scripts/runtime/uninstall
  */
 
@@ -86,6 +91,9 @@ const forCodex = flags.includes("--codex") || flags.includes("--all") || !explic
 
 const dryRun = flags.includes("--dry-run");
 const skipPrompt = flags.includes("--yes") || flags.includes("-y");
+// Full cleanup: also remove pipeline settings + the multi-agent log root
+// (task logs, state, metrics, audit). Tokens, CLAUDE.md and rules/ stay.
+const allData = flags.includes("--all-data");
 
 const adapterTarget = (() => {
   const raw = flags.find((f) => f.startsWith("--target="));
@@ -312,11 +320,17 @@ async function main() {
   if (forAntigravity) console.log(`    - Antigravity (${adapterTarget}/.agent/rules + .agent/workflows + AGENTS.md block + .agent/mcp_config.json)`);
   if (forCodex) console.log("    - OpenAI Codex CLI (~/.codex/prompts/multi-agent.md + AGENTS.md block + config.toml mcp block)");
   console.log("");
+  if (allData) {
+    console.log("  FULL CLEANUP (--all-data) also removes:");
+    console.log("    - ~/.claude/multi-agent-preferences.json (pipeline settings)");
+    console.log("    - ~/.claude/logs/multi-agent/ (task logs, state, metrics, audit trail)");
+    console.log("");
+  }
   console.log("  PRESERVED (never touched):");
   console.log("    - Personal access tokens in OS credential store (Keychain / Credential Manager / libsecret)");
   console.log("    - ~/.claude/CLAUDE.md (your customizations)");
   console.log("    - ~/.claude/rules/ (user-owned; installed write-if-missing, never overwritten)");
-  console.log("    - ~/.claude/multi-agent-preferences.json (your settings)");
+  if (!allData) console.log("    - ~/.claude/multi-agent-preferences.json (your settings)");
   console.log("    - Your own content in copilot-instructions.md above the pipeline section");
   console.log("");
 
@@ -335,6 +349,7 @@ async function main() {
     rmIfExists(join(CLAUDE, "multi-agent-refs"));
     rmIfExists(join(CLAUDE, "schemas"));
     rmIfExists(join(CLAUDE, "lib"));
+    rmIfExists(join(CLAUDE, ".pipeline-version"));
     // NOTE: ~/.claude/rules/ is USER-OWNED. install lays baseline rules down
     // write-if-missing and NEVER overwrites them (install/claude.mjs
     // installRules, skipExisting) so users can evolve their global rules
@@ -363,6 +378,7 @@ async function main() {
     // Pipeline-managed trees the installer lays down alongside scripts/.
     rmIfExists(join(COP, "schemas"));
     rmIfExists(join(COP, "lib"));
+    rmIfExists(join(COP, ".pipeline-version"));
     const skills = join(COP, "skills");
     let n = rmMatchingDirs(skills, (name) => name === "multi-agent" || name.startsWith("multi-agent-"));
     n += rmMatchingDirs(skills, (name) => name === "figma-ios" || name === "figma-android" || name === "figma-common" || name === "figma-to-component");
@@ -377,6 +393,16 @@ async function main() {
     stripManagedBlock(join(COP, "copilot-instructions.md"));
   }
 
+  // Full cleanup: pipeline settings + the multi-agent log root. Both are
+  // pipeline-generated data (not user-authored like CLAUDE.md / rules), so
+  // --all-data removes them; the default run leaves them in place.
+  if (allData && HOME) {
+    console.log("");
+    console.log("  [Full cleanup] Removing pipeline settings + logs...");
+    rmIfExists(join(HOME, ".claude", "multi-agent-preferences.json"));
+    rmIfExists(join(HOME, ".claude", "logs", "multi-agent"));
+  }
+
   // 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.
@@ -423,6 +449,15 @@ async function main() {
 
   console.log("");
   console.log("  ✓ Pipeline removed.");
+  if (!allData) {
+    console.log("");
+    console.log("  Kept your pipeline settings + logs. To remove those too, re-run with --all-data.");
+  } else {
+    console.log("");
+    console.log("  Full cleanup done. Still on disk (user-owned, remove by hand if you want a bare system):");
+    console.log("    - ~/.claude/CLAUDE.md");
+    console.log("    - ~/.claude/rules/");
+  }
   console.log("");
   console.log("  Personal access tokens were NOT touched. Inspect with:");
   console.log("    macOS:   security find-generic-password -s \"<service>\" -w");

package/pipeline/scripts/update-check.sh

@@ -46,6 +46,15 @@ if [ -z "$LOCAL_VERSION" ]; then
     fi
   done
 fi
+# npx-only installs have no repo clone; the installer stamps the version here.
+if [ -z "$LOCAL_VERSION" ]; then
+  for marker in "$HOME/.claude/.pipeline-version" "$HOME/.copilot/.pipeline-version"; do
+    if [ -f "$marker" ]; then
+      LOCAL_VERSION=$(head -1 "$marker" 2>/dev/null | tr -d '[:space:]')
+      [ -n "$LOCAL_VERSION" ] && break
+    fi
+  done
+fi
 [ -z "$LOCAL_VERSION" ] && exit 0  # cannot determine local version -> silent no-op
 
 now=$(date +%s)

package/pipeline/skills/.skill-manifest.json

@@ -1,6 +1,6 @@
 {
   "schemaVersion": "1.0.0",
-  "generatedAt": "2026-07-10T13:33:19Z",
+  "generatedAt": "2026-07-20T07:34:26Z",
   "skillCount": 189,
   "entries": [
     {
@@ -35,10 +35,6 @@
       "path": "shared/core/multi-agent-create-jira/SKILL.md",
       "sha256": "40caf0489ad8322cd00d792a244e772d4ddb6ccfd7c3807729d6b17590e7f81c"
     },
-    {
-      "path": "shared/core/multi-agent-delete/SKILL.md",
-      "sha256": "aa48d1e0fe111b9dc1b681025f16880410d47266f12f522df1835857e6cb9551"
-    },
     {
       "path": "shared/core/multi-agent-dev-autopilot/SKILL.md",
       "sha256": "82b1cf4a4bbd84fcfef54fcdbcdefa27f2747df6d4fac5c86b42e861013c6d58"
@@ -153,19 +149,23 @@
     },
     {
       "path": "shared/core/multi-agent-sync/SKILL.md",
-      "sha256": "28a057b30ec642f5cc1f22c9c50834aae280e6abaf58194b36d85bde717cfb14"
+      "sha256": "de38486056c99a599d93ae5166a2071875331a7d77f1e34f66d8b72657a73c2f"
     },
     {
       "path": "shared/core/multi-agent-test/SKILL.md",
       "sha256": "f90c34f71ea6cd5cccbfa128597eaaa221a0ca5f62924eb9cfb6b1ed2d07de04"
     },
+    {
+      "path": "shared/core/multi-agent-uninstall/SKILL.md",
+      "sha256": "775bcaf9248659986c3c5ef1c4f07d3d85784bd10c73cb33c47648bdfc8d834c"
+    },
     {
       "path": "shared/core/multi-agent-update/SKILL.md",
       "sha256": "4f31addb21ab5ec31a1288dc4ee56f102d0936473a964f8a6f4075a9c44889cd"
     },
     {
       "path": "shared/core/multi-agent/SKILL.md",
-      "sha256": "758646b660047bb4595528a57153afda0e1b331c70ad8c04bbd18066fc4bb336"
+      "sha256": "fe03eb27cae0489178cc327b3ca370e998638b6de08d4caa8c755dd53f45a30e"
     },
     {
       "path": "shared/external/accessibility-compliance-accessibility-audit/SKILL.md",

package/pipeline/skills/.skills-index.json

@@ -794,15 +794,6 @@
       "triggerPaths": [],
       "relativePath": "shared/core/multi-agent-create-jira/SKILL.md"
     },
-    {
-      "name": "multi-agent-delete",
-      "description": "Uninstall the pipeline from Claude Code + Copilot CLI. Keychain access tokens are left untouched. Asks for double confirmation.",
-      "platform": null,
-      "group": "core",
-      "triggerKeywords": [],
-      "triggerPaths": [],
-      "relativePath": "shared/core/multi-agent-delete/SKILL.md"
-    },
     {
       "name": "multi-agent-dev",
       "description": "Fast development mode: Init → Dev (Opus) → Test → Commit → Report. Analysis, planning, and review phases are skipped.",
@@ -1073,6 +1064,15 @@
       "triggerPaths": [],
       "relativePath": "shared/core/multi-agent-test/SKILL.md"
     },
+    {
+      "name": "multi-agent-uninstall",
+      "description": "Uninstall the pipeline from Claude Code + Copilot CLI. Keychain access tokens are always left untouched; --all-data also clears pipeline settings and logs. Asks for double confirmation.",
+      "platform": null,
+      "group": "core",
+      "triggerKeywords": [],
+      "triggerPaths": [],
+      "relativePath": "shared/core/multi-agent-uninstall/SKILL.md"
+    },
     {
       "name": "multi-agent-update",
       "description": "Update the pipeline to the latest version: git pull, install, migrate.",