@sparkleideas/claude-flow-patch 3.1.0-alpha.44.patch.10 → 3.1.0-alpha.44.patch.11

package/CLAUDE.md

@@ -6,7 +6,7 @@ Runtime patches for `@claude-flow/cli` **v3.1.0-alpha.41**, `ruvector`, and `ruv
 
 | Term | Meaning | Example |
 |------|---------|---------|
-| **Defect** | A tracked problem (bug or missing feature). Each defect has its own directory under `patch/` with a README.md and fix.py. | "Defect HW-001", "29 defects across 13 categories" |
+| **Defect** | A tracked problem (bug or missing feature). Each defect has its own directory under `patch/` with a README.md and fix.py. | "Defect HW-001", "60 defects across 15 categories" |
 | **Patch** | The code change that addresses a defect. Implemented as `fix.py` (or `fix.sh`) using `patch()`/`patch_all()` calls. We patch because we can't fix upstream. | "fix.py contains 3 patch ops" |
 | **GitHub issue** | The upstream issue on github.com/ruvnet/claude-flow. Always say "GitHub issue", never just "issue". | "GitHub issue #1111" |
 | **Defect ID** | The unique identifier for a defect: `{PREFIX}-{NNN}`. | HW-001, NS-003, RS-001 |
@@ -145,8 +145,8 @@ Save the returned GitHub issue number for the defect README.md.
 <!-- GENERATED:defect-tables:begin -->
 | Prefix | Category | Count |
 |--------|----------|-------|
-| CF | Config & Doctor | 2 |
-| DM | Daemon & Workers | 6 |
+| CF | Config & Doctor | 6 |
+| DM | Daemon & Workers | 5 |
 | EM | Embeddings & HNSW | 2 |
 | GV | Ghost Vectors | 1 |
 | HK | Hooks | 5 |
@@ -156,10 +156,12 @@ Save the returned GitHub issue number for the defect README.md.
 | NS | Memory Namespace | 3 |
 | RS | ruv-swarm | 1 |
 | RV | RuVector Intelligence | 3 |
-| SG | Settings Generator | 4 |
+| SG | Settings Generator | 10 |
 | UI | Display & Cosmetic | 2 |
+| WM | Wiring / Memory Integration | 9 |
+| DOC | Documentation | 1 |
 
-## All 35 Defects
+## All 54 Defects
 
 | ID | GitHub Issue | Severity |
 |----|-------------|----------|
@@ -168,8 +170,7 @@ Save the returned GitHub issue number for the defect README.md.
 | DM-001 | [#1116 daemon.log always 0 bytes](https://github.com/ruvnet/claude-flow/issues/1116) | Medium |
 | DM-002 | [#1138 maxCpuLoad=2.0 blocks all workers on multi-core](https://github.com/ruvnet/claude-flow/issues/1138) | Critical |
 | DM-003 | [#1077 macOS freemem() always ~0% — workers blocked](https://github.com/ruvnet/claude-flow/issues/1077) | Critical |
-| DM-004 | [#1139 Preload worker stub + missing from defaults](https://github.com/ruvnet/claude-flow/issues/1139) | Enhancement |
-| DM-005 | [#1140 Consolidation worker stub (no decay/rebuild)](https://github.com/ruvnet/claude-flow/issues/1140) | Enhancement |
+| DM-004 | [#1139 Worker stubs — preload + consolidation](https://github.com/ruvnet/claude-flow/issues/1139) | Enhancement |
 | EM-001 | [#1143 Embedding system ignores project config (model + HNSW dims)](https://github.com/ruvnet/claude-flow/issues/1143) | High |
 | EM-002 | [#1144 @xenova/transformers cache EACCES](https://github.com/ruvnet/claude-flow/issues/1144) | Medium |
 | GV-001 | [#1122 HNSW ghost vectors persist after memory delete](https://github.com/ruvnet/claude-flow/issues/1122) | Medium |
@@ -198,6 +199,26 @@ Save the returned GitHub issue number for the defect README.md.
 | HW-004 | [#1117 runWithTimeout rejects but does not kill child process](https://github.com/ruvnet/claude-flow/issues/1117) | Medium |
 | SG-004 | [#1181 init wizard lacks parity with init](https://github.com/ruvnet/claude-flow/issues/1181) | High |
 | SG-005 | [#1177 add 'start all' subcommand to start everything at once](https://github.com/ruvnet/claude-flow/issues/1177) | Enhancement |
+| SG-006 | [#1184 Wizard captures permissionRequest hook but never assigns it + topology hardcoded](https://github.com/ruvnet/claude-flow/issues/1184) | Medium |
+| WM-001 | [#829 Wire @claude-flow/memory HybridBackend into CLI](https://github.com/ruvnet/claude-flow/issues/829) | Critical |
+| WM-002 | [#1185 Neural config gating (neural.enabled not consumed at runtime)](https://github.com/ruvnet/claude-flow/issues/1185) | Medium |
+| WM-003 | [#1102 Activate AutoMemoryBridge in auto-memory-hook.mjs](https://github.com/ruvnet/claude-flow/issues/1102) | High |
+| CF-003 | [#1186 Doctor --install native dependency resolution](https://github.com/ruvnet/claude-flow/issues/1186) | Medium |
+| SG-007 | [#1188 --skip-claude / --only-claude mutate shared init options via shallow copy](https://github.com/ruvnet/claude-flow/issues/1188) | Medium |
+| WM-004 | [#1190 Source hook silently falls back to JsonFileBackend](https://github.com/ruvnet/claude-flow/issues/1190) | High |
+| CF-004 | [#1193 config get/export uses hand-rolled YAML parser instead of config.json](https://github.com/ruvnet/claude-flow/issues/1193) | Medium |
+| SG-008 | [#1195 init should generate .claude-flow/config.json (not config.yaml)](https://github.com/ruvnet/claude-flow/issues/1195) | Enhancement |
+| CF-006 | [#1197 config.yaml -> config.json migration in start.js, status.js, init.js](https://github.com/ruvnet/claude-flow/issues/1197) | Medium |
+| DOC-001 | [#1201 Update upstream README.md to match patched CLI behavior](https://github.com/ruvnet/claude-flow/issues/1201) | Enhancement |
+| SG-009 | [#1202 Remove --v3-mode from swarm init, make v3 the default](https://github.com/ruvnet/claude-flow/issues/1202) | High |
+| CF-009 | [#1203 Upgrade MINIMAL init preset to v3 runtime defaults](https://github.com/ruvnet/claude-flow/issues/1203) | High |
+| WM-007 | [#1204 Wire dead config.json keys into runtime consumers](https://github.com/ruvnet/claude-flow/issues/1204) | High |
+| SG-010 | [#1205 Add CLI options to init for all config.json settings](https://github.com/ruvnet/claude-flow/issues/1205) | Enhancement |
+| SG-011 | [#1206 Fix stale --topology hierarchical references](https://github.com/ruvnet/claude-flow/issues/1206) | Medium |
+| WM-008 | [#1207 Upgrade AgentDB v2 to v3 (RVF backend, self-learning, witness chain)](https://github.com/ruvnet/claude-flow/issues/1207) | High |
+| WM-009 | [#1209 Wire AgentDB learning loop (recordFeedback)](https://github.com/ruvnet/claude-flow/issues/1209) | High |
+| WM-010 | [#1208 Wire witness chain verification at session start](https://github.com/ruvnet/claude-flow/issues/1208) | High |
+| WM-011 | [#1210 Instantiate ReasoningBank controller](https://github.com/ruvnet/claude-flow/issues/1210) | High |
 <!-- GENERATED:defect-tables:end -->
 
 ---
@@ -464,15 +485,30 @@ Execution order is controlled by the 3-digit numeric prefix on each directory na
 `patch-all.sh` globs `patch/*/fix.py` which sorts lexicographically, so numeric prefixes
 execute in the correct order automatically.
 
-Two dependency chains exist:
+Three dependency chains exist:
 
 | Chain | Directories | Reason |
 |-------|-------------|--------|
 | IN-001 -> SG-003 | `170-IN-001-*` before `270-SG-003-*` | SG-003's `old_string` contains code introduced by IN-001 |
 | NS-001 -> NS-002 -> NS-003 | `190-NS-001-*` before `200-NS-002-*` before `210-NS-003-*` | Sequential namespace fixes |
+| WM-003 -> WM-004 | `370-WM-003-*` before `390-WM-004-*` | WM-004's `old_string` matches code written by WM-003 (doImport/doSync HybridBackend stubs) |
 
 All other patches are independent.
 
+### Absorbed Patches
+
+Three patches have been absorbed into their parent patches to eliminate dead YAML
+regex code that was immediately replaced by later config.json readers:
+
+| Absorbed | Into | Reason |
+|----------|------|--------|
+| WM-005 | WM-001 | WM-001a now writes config.json reader directly |
+| WM-006 | WM-002 | WM-002c now writes config.json reader directly; WM-002d deleted (regex fix for removed code) |
+| CF-005 | CF-003 | CF-003a now writes config.json reader and updated error messages directly |
+
+These patches retain their directories and README files for GitHub issue tracking
+but their `fix.py` files are empty (no ops) and sentinels are set to `none`.
+
 ## Preflight & Pre-Commit Hook
 
 A git pre-commit hook at `hooks/pre-commit` runs automatically on every commit. It calls `npm run preflight:check` (read-only) and `npm test`. If anything is stale or tests fail, the commit is blocked.
@@ -498,6 +534,49 @@ Then `git add -u` to stage the regenerated files.
 
 Manual edits to generated sections (`<!-- GENERATED:*:begin/end -->`) will be overwritten.
 
+## Auto-Reapply on Update (Sentinel Watch)
+
+When `npx` fetches a new version of `@claude-flow/cli`, `ruvector`, or `ruv-swarm`, it replaces cached files and wipes all patches. Projects using these patches need a sentinel to detect and auto-reapply.
+
+### Claude Code Hook (recommended for AI agents)
+
+Add to the project's `.claude/settings.json`:
+
+```jsonc
+{
+  "hooks": {
+    "session_start": [
+      {
+        "command": "bash /absolute/path/to/claude-flow-patch/check-patches.sh --global",
+        "timeout": 30000
+      }
+    ]
+  }
+}
+```
+
+For projects with a local install, use `--global --target .` instead.
+
+### Cron (headless environments)
+
+```bash
+*/5 * * * * bash /path/to/claude-flow-patch/check-patches.sh --global >> /tmp/patch-sentinel.log 2>&1
+```
+
+### npm postinstall (project dependency)
+
+```jsonc
+{
+  "scripts": {
+    "postinstall": "npx --yes @sparkleideas/claude-flow-patch --target ."
+  }
+}
+```
+
+### How it works
+
+`check-patches.sh` reads each `patch/*/sentinel` file and verifies the patched strings exist in the target files. If any sentinel fails, it auto-runs `patch-all.sh` and restarts the daemon. The check is idempotent and takes ~2s when patches are intact.
+
 ## Key Design Decisions
 
 - **Idempotent**: `patch()` checks if `new` string is already present before replacing.

package/README.md

@@ -10,8 +10,10 @@
   - [Dependency Order](#dependency-order)
   - [Key Design Decisions](#key-design-decisions)
   - [Repository Structure](#repository-structure)
+- [Memory System](#memory-system)
 - [Defect Index](#defect-index)
 - [Init-Script Patches](#init-script-patches)
+- [Auto-Reapply on Update](#auto-reapply-on-update)
 - [Compatibility](#compatibility)
 - [Links](#links)
 
@@ -19,7 +21,7 @@
 
 Community patches for [`@claude-flow/cli`](https://www.npmjs.com/package/@claude-flow/cli) **v3.1.0-alpha.41**, [`ruvector`](https://www.npmjs.com/package/ruvector), and [`ruv-swarm`](https://www.npmjs.com/package/ruv-swarm) **v1.0.20**.
 
-These patches fix 29 defects across 13 categories. They are applied at runtime via idempotent Python scripts that perform targeted string replacements on the npx-cached source files.
+These patches fix 60 defects across 15 categories. They are applied at runtime via idempotent Python scripts that perform targeted string replacements on the npx-cached source files.
 
 <a id="quick-start"></a>
 
@@ -168,12 +170,50 @@ claude-flow-patch/
     (29 defect directories total)
 ```
 
+<a id="memory-system"></a>
+
+## Memory System
+
+The patched CLI runs a dual-write memory backend (SQLite + AgentDB v3) with three learning subsystems:
+
+| Layer | What It Does | Key Patch |
+|-------|-------------|-----------|
+| **HybridBackend** | Dual-writes entries to SQLite (structured) + AgentDB RVF (vector search) | [WM-001](patch/350-WM-001-memory-wiring/) |
+| **AutoMemoryBridge** | Syncs `~/.claude/memory/*.json` into the backend at session start/end | [WM-003](patch/370-WM-003-auto-memory-bridge/) |
+| **Intelligence.cjs** | PageRank graph + trigram matching + confidence decay/boost | [IN-001](patch/170-IN-001-intelligence-stub/) |
+| **AgentDB self-learning** | Records search feedback to improve future vector search relevance | [WM-009](patch/570-WM-009-agentdb-learning-loop/) |
+| **Witness chain** | SHAKE-256 tamper detection on the memory database at session start | [WM-010](patch/580-WM-010-witness-chain-verify/) |
+| **ReasoningBank** | Stores and retrieves successful reasoning patterns across sessions | [WM-011](patch/590-WM-011-reasoning-bank-controller/) |
+
+Database files live in `.swarm/`:
+
+```
+.swarm/
+  hybrid-memory.db         # SQLite (structured queries, WAL mode)
+  agentdb-memory.rvf       # AgentDB v3 (HNSW vectors, learning state, witness chain)
+```
+
+All memory config is in `.claude-flow/config.json` under `memory.*`. Key settings:
+
+```json
+{
+  "memory": {
+    "backend": "hybrid",
+    "agentdb": { "enableLearning": true, "vectorBackend": "rvf" },
+    "learningBridge": { "enabled": true, "sonaMode": "balanced" },
+    "memoryGraph": { "enabled": true, "pageRankDamping": 0.85 }
+  }
+}
+```
+
+Full documentation: **[docs/memory-system.md](docs/memory-system.md)**
+
 <a id="defect-index"></a>
 
 ## Defect Index
 
 <!-- GENERATED:defect-index:begin -->
-35 defects across 13 categories.
+54 defects across 15 categories.
 
 ### CF -- Config & Doctor
 
@@ -181,6 +221,10 @@ claude-flow-patch/
 |----|-------------|----------|--------------|
 | [CF&#8209;001](patch/010-CF-001-doctor-yaml/) | Doctor ignores YAML config files | Low | [#1141](https://github.com/ruvnet/claude-flow/issues/1141) |
 | [CF&#8209;002](patch/020-CF-002-config-export-yaml/) | Config export shows hardcoded defaults | Medium | [#1142](https://github.com/ruvnet/claude-flow/issues/1142) |
+| [CF&#8209;003](patch/380-CF-003-doctor-native-deps/) | Doctor --install native dependency resolution | Medium | [#1186](https://github.com/ruvnet/claude-flow/issues/1186) |
+| [CF&#8209;004](patch/420-CF-004-config-export-json/) | config get/export uses hand-rolled YAML parser instead of config.json | Medium | [#1193](https://github.com/ruvnet/claude-flow/issues/1193) |
+| [CF&#8209;006](patch/450-CF-006-config-yaml-to-json/) | config.yaml -> config.json migration in start.js, status.js, init.js | Medium | [#1197](https://github.com/ruvnet/claude-flow/issues/1197) |
+| [CF&#8209;009](patch/500-CF-009-minimal-v3-defaults/) | Upgrade MINIMAL init preset to v3 runtime defaults | High | [#1203](https://github.com/ruvnet/claude-flow/issues/1203) |
 
 ### DM -- Daemon & Workers
 
@@ -189,8 +233,7 @@ claude-flow-patch/
 | [DM&#8209;001](patch/030-DM-001-daemon-log-zero/) | daemon.log always 0 bytes | Medium | [#1116](https://github.com/ruvnet/claude-flow/issues/1116) |
 | [DM&#8209;002](patch/040-DM-002-cpu-load-threshold/) | maxCpuLoad=2.0 blocks all workers on multi-core | Critical | [#1138](https://github.com/ruvnet/claude-flow/issues/1138) |
 | [DM&#8209;003](patch/050-DM-003-macos-freemem/) | macOS freemem() always ~0% — workers blocked | Critical | [#1077](https://github.com/ruvnet/claude-flow/issues/1077) |
-| [DM&#8209;004](patch/060-DM-004-preload-worker-stub/) | Preload worker stub + missing from defaults | Enhancement | [#1139](https://github.com/ruvnet/claude-flow/issues/1139) |
-| [DM&#8209;005](patch/070-DM-005-consolidation-worker-stub/) | Consolidation worker stub (no decay/rebuild) | Enhancement | [#1140](https://github.com/ruvnet/claude-flow/issues/1140) |
+| [DM&#8209;004](patch/060-DM-004-worker-stubs/) | Worker stubs — preload + consolidation | Enhancement | [#1139](https://github.com/ruvnet/claude-flow/issues/1139) |
 | [DM&#8209;006](patch/300-DM-006-log-rotation/) | No log rotation — logs grow unbounded | Medium | [#1114](https://github.com/ruvnet/claude-flow/issues/1114) |
 
 ### EM -- Embeddings & HNSW
@@ -267,6 +310,12 @@ claude-flow-patch/
 | [SG&#8209;003](patch/270-SG-003-init-helpers-all-paths/) | Init missing helpers for --dual, --minimal, hooks, and upgrade paths | Critical | [#1169](https://github.com/ruvnet/claude-flow/issues/1169) |
 | [SG&#8209;004](patch/320-SG-004-wizard-parity/) | init wizard lacks parity with init | High | [#1181](https://github.com/ruvnet/claude-flow/issues/1181) |
 | [SG&#8209;005](patch/330-SG-005-start-all-subcommand/) | add 'start all' subcommand to start everything at once | Enhancement | [#1177](https://github.com/ruvnet/claude-flow/issues/1177) |
+| [SG&#8209;006](patch/340-SG-006-wizard-capture/) | Wizard captures permissionRequest hook but never assigns it + topology hardcoded | Medium | [#1184](https://github.com/ruvnet/claude-flow/issues/1184) |
+| [SG&#8209;007](patch/385-SG-007-init-shallow-copy/) | --skip-claude / --only-claude mutate shared init options via shallow copy | Medium | [#1188](https://github.com/ruvnet/claude-flow/issues/1188) |
+| [SG&#8209;008](patch/440-SG-008-init-config-json/) | init should generate .claude-flow/config.json (not config.yaml) | Enhancement | [#1195](https://github.com/ruvnet/claude-flow/issues/1195) |
+| [SG&#8209;009](patch/490-SG-009-remove-v3-mode/) | Remove --v3-mode from swarm init, make v3 the default | High | [#1202](https://github.com/ruvnet/claude-flow/issues/1202) |
+| [SG&#8209;010](patch/540-SG-010-init-cli-options/) | Add CLI options to init for all config.json settings | Enhancement | [#1205](https://github.com/ruvnet/claude-flow/issues/1205) |
+| [SG&#8209;011](patch/550-SG-011-topology-hierarchical-refs/) | Fix stale --topology hierarchical references | Medium | [#1206](https://github.com/ruvnet/claude-flow/issues/1206) |
 
 ### UI -- Display & Cosmetic
 
@@ -274,6 +323,26 @@ claude-flow-patch/
 |----|-------------|----------|--------------|
 | [UI&#8209;001](patch/280-UI-001-intelligence-stats-crash/) | intelligence stats crashes on .toFixed() | Critical | [#1145](https://github.com/ruvnet/claude-flow/issues/1145) |
 | [UI&#8209;002](patch/290-UI-002-neural-status-not-loaded/) | neural status shows "Not loaded" | Low | [#1146](https://github.com/ruvnet/claude-flow/issues/1146) |
+
+### WM -- Wiring / Memory Integration
+
+| ID | Description <img width="500" height="1" /> | Severity | GitHub&nbsp;Issue |
+|----|-------------|----------|--------------|
+| [WM&#8209;001](patch/350-WM-001-memory-wiring/) | Wire @claude-flow/memory HybridBackend into CLI | Critical | [#829](https://github.com/ruvnet/claude-flow/issues/829) |
+| [WM&#8209;002](patch/360-WM-002-config-respect/) | Neural config gating (neural.enabled not consumed at runtime) | Medium | [#1185](https://github.com/ruvnet/claude-flow/issues/1185) |
+| [WM&#8209;003](patch/370-WM-003-auto-memory-bridge/) | Activate AutoMemoryBridge in auto-memory-hook.mjs | High | [#1102](https://github.com/ruvnet/claude-flow/issues/1102) |
+| [WM&#8209;004](patch/390-WM-004-source-hook-fail-loud/) | Source hook silently falls back to JsonFileBackend | High | [#1190](https://github.com/ruvnet/claude-flow/issues/1190) |
+| [WM&#8209;007](patch/530-WM-007-wire-dead-config-keys/) | Wire dead config.json keys into runtime consumers | High | [#1204](https://github.com/ruvnet/claude-flow/issues/1204) |
+| [WM&#8209;008](patch/560-WM-008-agentdb-v3-upgrade/) | Upgrade AgentDB v2 to v3 (RVF backend, self-learning, witness chain) | High | [#1207](https://github.com/ruvnet/claude-flow/issues/1207) |
+| [WM&#8209;009](patch/570-WM-009-agentdb-learning-loop/) | Wire AgentDB learning loop (recordFeedback) | High | [#1209](https://github.com/ruvnet/claude-flow/issues/1209) |
+| [WM&#8209;010](patch/580-WM-010-witness-chain-verify/) | Wire witness chain verification at session start | High | [#1208](https://github.com/ruvnet/claude-flow/issues/1208) |
+| [WM&#8209;011](patch/590-WM-011-reasoning-bank-controller/) | Instantiate ReasoningBank controller | High | [#1210](https://github.com/ruvnet/claude-flow/issues/1210) |
+
+### DOC -- Documentation
+
+| ID | Description <img width="500" height="1" /> | Severity | GitHub&nbsp;Issue |
+|----|-------------|----------|--------------|
+| [DOC&#8209;001](patch/480-DOC-001-readme-docs/) | Update upstream README.md to match patched CLI behavior | Enhancement | [#1201](https://github.com/ruvnet/claude-flow/issues/1201) |
 <!-- GENERATED:defect-index:end -->
 
 <a id="init-script-patches"></a>
@@ -329,6 +398,89 @@ These patches fix the **generator functions** inside the npm package (e.g., `gen
 
 Additionally, `init upgrade` only force-overwrites 3 "critical" helpers (`auto-memory-hook.mjs`, `hook-handler.cjs`, `intelligence.cjs`). The other 30+ helper files (shell scripts for daemon management, health monitoring, security scanning, swarm hooks, etc.) are only copied on fresh `init`, not on upgrade. If these are missing, use Option A above.
 
+<a id="auto-reapply-on-update"></a>
+
+## Auto-Reapply on Update
+
+When `npx` fetches a new version of `@claude-flow/cli`, `ruvector`, or `ruv-swarm`, it replaces the cached files and wipes all patches. Use one of these approaches to detect this and auto-reapply.
+
+### Option A: Claude Code Hook (Recommended for AI Agents)
+
+Add a `session_start` hook to your project's `.claude/settings.json`. This runs `check-patches.sh` every time Claude starts a session — it detects missing patches and reapplies automatically:
+
+```jsonc
+// .claude/settings.json
+{
+  "hooks": {
+    "session_start": [
+      {
+        "command": "bash /path/to/claude-flow-patch/check-patches.sh --global",
+        "timeout": 30000
+      }
+    ]
+  }
+}
+```
+
+Replace `/path/to/claude-flow-patch` with the absolute path to your clone. If your project also has a local install, use `--global --target .` instead.
+
+`check-patches.sh` is fast and idempotent — if patches are intact it prints `OK` and exits. If any sentinel fails, it runs `patch-all.sh`, restarts the daemon, and reports what happened.
+
+### Option B: Cron / systemd Timer
+
+Poll every 5 minutes with cron:
+
+```bash
+# crontab -e
+*/5 * * * * bash /path/to/claude-flow-patch/check-patches.sh --global >> /tmp/patch-sentinel.log 2>&1
+```
+
+Or with a systemd user timer:
+
+```ini
+# ~/.config/systemd/user/patch-sentinel.timer
+[Timer]
+OnBootSec=60
+OnUnitActiveSec=300
+
+[Install]
+WantedBy=timers.target
+```
+
+```ini
+# ~/.config/systemd/user/patch-sentinel.service
+[Service]
+Type=oneshot
+ExecStart=/bin/bash /path/to/claude-flow-patch/check-patches.sh --global
+```
+
+```bash
+systemctl --user enable --now patch-sentinel.timer
+```
+
+### Option C: npm postinstall Hook
+
+If you install `@claude-flow/cli` as a project dependency, add a postinstall script that reapplies patches whenever `npm install` refreshes it:
+
+```jsonc
+// package.json
+{
+  "scripts": {
+    "postinstall": "npx --yes @sparkleideas/claude-flow-patch --target ."
+  }
+}
+```
+
+### How the Sentinel Works
+
+`check-patches.sh` reads the `sentinel` file in each `patch/*/` directory and checks whether the patched strings are present in the target files. If any check fails:
+
+1. Prints a warning identifying the likely cause (npx cache update)
+2. Runs `patch-all.sh` to reapply all patches
+3. Stops and restarts the claude-flow daemon so it picks up the patched code
+
+The entire check takes under 2 seconds when patches are intact. Reapplication takes 5-10 seconds.
+
 <a id="compatibility"></a>
 
 ## Compatibility

package/check-patches.sh

@@ -59,6 +59,13 @@ resolve_path() {
   case "$pkg" in
     ruvector)  echo "$rv_base/$relpath" ;;
     ruv-swarm) echo "$rs_base/$relpath" ;;
+    @claude-flow/*)
+      # base is <nm>/@claude-flow/cli/dist/src → derive <nm>/@claude-flow/<pkg>
+      local cf_scope
+      cf_scope="$(cd "$base/../../../.." 2>/dev/null && pwd)"
+      local subpkg="${pkg#@claude-flow/}"
+      echo "$cf_scope/@claude-flow/$subpkg/$relpath"
+      ;;
     *)         echo "$base/$relpath" ;;
   esac
 }
@@ -93,27 +100,39 @@ check_sentinels_for_install() {
       continue
     fi
 
-    # Read package line (default: claude-flow)
+    # Default package context (can be switched by "package:" directives in the file)
     local pkg="claude-flow"
-    local pkg_line
-    pkg_line=$(grep -m1 '^package:' "$sentinel_file" 2>/dev/null || true)
-    if [ -n "$pkg_line" ]; then
-      pkg="${pkg_line#package:}"
-      pkg="${pkg#"${pkg%%[![:space:]]*}"}"  # trim leading whitespace
-      pkg="${pkg%%[[:space:]]*}"            # trim trailing whitespace
-    fi
 
-    # Skip if required package not installed
-    case "$pkg" in
-      ruvector)  [ -z "$rv_cli" ] && continue ;;
-      ruv-swarm) [ -z "$rs_root" ] && continue ;;
-    esac
+    # Check if first package: line is for an optional package we don't have
+    local first_pkg_line
+    first_pkg_line=$(grep -m1 '^package:' "$sentinel_file" 2>/dev/null || true)
+    if [ -n "$first_pkg_line" ]; then
+      local first_pkg="${first_pkg_line#package:}"
+      first_pkg="${first_pkg#"${first_pkg%%[![:space:]]*}"}"
+      first_pkg="${first_pkg%%[[:space:]]*}"
+      # Only skip the whole file if ALL lines are for a single unavailable package
+      local has_non_pkg_default=false
+      grep -v '^package:' "$sentinel_file" | grep -v '^$' | grep -v '^none$' | head -1 | grep -q '.' && has_non_pkg_default=true
+      if ! $has_non_pkg_default; then
+        case "$first_pkg" in
+          ruvector)  [ -z "$rv_cli" ] && continue ;;
+          ruv-swarm) [ -z "$rs_root" ] && continue ;;
+        esac
+      fi
+    fi
 
-    # Process each line
+    # Process each line — "package:" switches the current package context
     while IFS= read -r line; do
       line="${line#"${line%%[![:space:]]*}"}"  # trim leading whitespace
       [[ -z "$line" ]] && continue
-      [[ "$line" == package:* ]] && continue
+
+      # package: directive switches context for subsequent grep/absent lines
+      if [[ "$line" == package:* ]]; then
+        pkg="${line#package:}"
+        pkg="${pkg#"${pkg%%[![:space:]]*}"}"  # trim leading whitespace
+        pkg="${pkg%%[[:space:]]*}"            # trim trailing whitespace
+        continue
+      fi
 
       if [[ "$line" == "none" ]]; then
         continue
@@ -130,7 +149,8 @@ check_sentinels_for_install() {
         local pattern="${BASH_REMATCH[1]}"
         local filepath
         filepath=$(resolve_path "$base" "$rv_base" "$rs_root" "$pkg" "${BASH_REMATCH[2]}")
-        if ! grep -q "$pattern" "$filepath" 2>/dev/null; then
+        # Skip if target file doesn't exist (e.g. umbrella layout missing .claude/helpers/)
+        if [ -f "$filepath" ] && ! grep -q "$pattern" "$filepath" 2>/dev/null; then
           all_ok=false
         fi
       fi
@@ -158,6 +178,60 @@ for entry in "${INSTALLS[@]}"; do
   fi
 done
 
+# ── Syntax validation: node --check on ALL patched JS files ──
+# Runs independently of sentinel checks so SyntaxErrors are always caught.
+
+syntax_failed=false
+for entry in "${INSTALLS[@]}"; do
+  IFS=$'\t' read -r dist_src version rv_cli rs_root writable <<< "$entry"
+
+  # Derive @claude-flow scope from dist/src path
+  cf_scope="$(cd "$dist_src/../../../.." 2>/dev/null && pwd)"
+
+  SYNTAX_FILES=(
+    # @claude-flow/cli
+    "$dist_src/commands/config.js"
+    "$dist_src/commands/start.js"
+    "$dist_src/commands/init.js"
+    "$dist_src/commands/doctor.js"
+    "$dist_src/commands/status.js"
+    "$dist_src/commands/swarm.js"
+    "$dist_src/commands/daemon.js"
+    "$dist_src/commands/hooks.js"
+    "$dist_src/commands/memory.js"
+    "$dist_src/commands/neural.js"
+    "$dist_src/memory/memory-initializer.js"
+    "$dist_src/memory/intelligence.js"
+    "$dist_src/init/executor.js"
+    "$dist_src/init/helpers-generator.js"
+    "$dist_src/init/settings-generator.js"
+    "$dist_src/init/types.js"
+    "$dist_src/init/claudemd-generator.js"
+    "$dist_src/mcp-tools/hooks-tools.js"
+    "$dist_src/mcp-tools/memory-tools.js"
+    "$dist_src/mcp-tools/embeddings-tools.js"
+    "$dist_src/services/worker-daemon.js"
+    "$dist_src/services/headless-worker-executor.js"
+    "$dist_src/index.js"
+    # @claude-flow/memory (WM-008)
+    "$cf_scope/@claude-flow/memory/dist/agentdb-backend.js"
+    # @claude-flow/neural (WM-008)
+    "$cf_scope/@claude-flow/neural/dist/reasoning-bank.js"
+    # @claude-flow/shared (WM-008)
+    "$cf_scope/@claude-flow/shared/dist/core/config/defaults.js"
+  )
+  for js_file in "${SYNTAX_FILES[@]}"; do
+    [ -f "$js_file" ] || continue
+    if ! node --check "$js_file" 2>/tmp/syntax-check-err.$$; then
+      echo "[PATCHES] SYNTAX ERROR: $js_file"
+      cat /tmp/syntax-check-err.$$
+      syntax_failed=true
+      any_failed=true
+    fi
+    rm -f /tmp/syntax-check-err.$$
+  done
+done
+
 VERSION="${first_version:-unknown}"
 
 if ! $any_failed; then

package/lib/categories.json

@@ -11,5 +11,7 @@
   "MM": "Memory Management",
   "HK": "Hooks",
   "RV": "RuVector Intelligence",
-  "RS": "ruv-swarm"
+  "RS": "ruv-swarm",
+  "WM": "Wiring / Memory Integration",
+  "DOC": "Documentation"
 }

package/lib/common.py

@@ -67,6 +67,7 @@ WD = services + "/worker-daemon.js" if services else ""
 DJ = commands + "/daemon.js" if commands else ""
 DOC = commands + "/doctor.js" if commands else ""
 MI = memory + "/memory-initializer.js" if memory else ""
+INTEL = memory + "/intelligence.js" if memory else ""
 
 MCP_MEMORY = base + "/mcp-tools/memory-tools.js" if base else ""
 MCP_HOOKS = base + "/mcp-tools/hooks-tools.js" if base else ""
@@ -82,13 +83,27 @@ SETTINGS_GEN = init + "/settings-generator.js" if init else ""
 HELPERS_GEN = init + "/helpers-generator.js" if init else ""
 EXECUTOR = init + "/executor.js" if init else ""
 TYPES = init + "/types.js" if init else ""
+SWARM_CMD = commands + "/swarm.js" if commands else ""
+CLI_INDEX = base + "/index.js" if base else ""
+CLAUDEMD_GEN = init + "/claudemd-generator.js" if init else ""
 INIT_CMD = commands + "/init.js" if commands else ""
 START_CMD = commands + "/start.js" if commands else ""
+STATUS_CMD = commands + "/status.js" if commands else ""
 CMDS_INDEX = commands + "/index.js" if commands else ""
 
 # Source helpers (shipped with package, copied by writeHelpers when source dir found)
 _pkg_root = os.path.dirname(os.path.dirname(base)) if base else ""
+_cf_scope = os.path.dirname(_pkg_root) if _pkg_root else ""
+AGENTDB_BACKEND = os.path.join(_cf_scope, "memory", "dist", "agentdb-backend.js") if _cf_scope else ""
+MEMORY_PKG_JSON = os.path.join(_cf_scope, "memory", "package.json") if _cf_scope else ""
 SRC_HOOK_HANDLER = os.path.join(_pkg_root, ".claude", "helpers", "hook-handler.cjs") if _pkg_root else ""
+SRC_AUTO_MEMORY_HOOK = os.path.join(_pkg_root, ".claude", "helpers", "auto-memory-hook.mjs") if _pkg_root else ""
+README_MD = os.path.join(_pkg_root, "README.md") if _pkg_root else ""
+
+# Cross-package targets (sibling packages under node_modules/)
+_nm_root = os.path.dirname(_cf_scope) if _cf_scope else ""
+NEURAL_REASONING_BANK = os.path.join(_cf_scope, "neural", "dist", "reasoning-bank.js") if _cf_scope else ""
+SHARED_DEFAULTS = os.path.join(_cf_scope, "shared", "dist", "core", "config", "defaults.js") if _cf_scope else ""
 
 # RuVector (separate package, path set by patch-all.sh)
 ruvector_cli = os.environ.get("RUVECTOR_CLI", "")

package/package.json

@@ -1,12 +1,12 @@
 {
   "name": "@sparkleideas/claude-flow-patch",
-  "version": "3.1.0-alpha.44.patch.10",
+  "version": "3.1.0-alpha.44.patch.11",
   "description": "Patch toolkit for @claude-flow/cli init/runtime defects with verify and post-init repair commands",
   "scripts": {
     "preflight": "node scripts/preflight.mjs",
     "preflight:check": "node scripts/preflight.mjs --check",
     "prepublishOnly": "npm run preflight && npm test",
-    "test": "node --test tests/*.test.mjs",
+    "test": "node --test --test-concurrency=1 tests/*.test.mjs",
     "package": "bash npm/package.sh",
     "package:dry": "bash npm/package.sh --dry-run",
     "publish:npm": "bash npm/publish.sh",
@@ -82,5 +82,8 @@
     "ruv-swarm",
     "automation"
   ],
-  "packageManager": "npm@10"
+  "packageManager": "npm@10",
+  "dependencies": {
+    "@sparkleideas/claude-flow-guidance": "file:../../claude-flow-guidance-implementation"
+  }
 }

package/patch/010-CF-001-doctor-yaml/sentinel

@@ -1 +1 @@
-grep "config.yaml" commands/doctor.js
+grep "configPath.endsWith('.json')" commands/doctor.js

package/patch/020-CF-002-config-export-yaml/README.md

@@ -8,4 +8,4 @@ Add `readYamlConfig()` helper function. Merge YAML config values over defaults i
 ## Files Patched
 - commands/config.js
 ## Ops
-3 ops in fix.py
+2 ops in fix.py (16a removed — bundler already provides readYamlConfig)

package/patch/020-CF-002-config-export-yaml/fix.py

@@ -3,49 +3,9 @@
 # NOTE: This patch was originally applied via sed, not via patch().
 # The patch() calls below replicate the same changes.
 
-# Add fs/path imports after existing imports
-patch("16a: config.js add readYamlConfig",
-    CONF,
-    "const getCommand = {",
-    """import { readFileSync, existsSync } from 'fs';
-import { join } from 'path';
-
-// Helper to read config.yaml if it exists
-function readYamlConfig() {
-    const configPath = join(process.cwd(), '.claude-flow', 'config.yaml');
-    if (!existsSync(configPath)) { return {}; }
-    try {
-        const content = readFileSync(configPath, 'utf8');
-        const config = {};
-        const lines = content.split('\\n');
-        let currentSection = null;
-        for (const line of lines) {
-            const trimmed = line.trim();
-            if (!trimmed || trimmed.startsWith('#')) continue;
-            if (!trimmed.includes(':')) continue;
-            const indent = line.match(/^\\s*/)[0].length;
-            if (indent === 0) {
-                const [key, ...rest] = trimmed.split(':');
-                const value = rest.join(':').trim();
-                if (value && value !== '') {
-                    config[key.trim()] = value.replace(/^["']|["']$/g, '');
-                } else {
-                    currentSection = key.trim();
-                    config[currentSection] = {};
-                }
-            } else if (currentSection && indent > 0) {
-                const [key, ...rest] = trimmed.split(':');
-                const value = rest.join(':').trim();
-                if (value && value !== '') {
-                    config[currentSection][key.trim()] = value.replace(/^["']|["']$/g, '');
-                }
-            }
-        }
-        return config;
-    } catch (error) { return {}; }
-}
-
-const getCommand = {""")
+# Op 16a removed: the upstream bundler already emits readYamlConfig() twice.
+# CF-004 (order 420) upgrades the first copy to read config.json and removes the second.
+# Inserting a third copy here caused a re-application conflict on every run.
 
 # Update getCommand to merge YAML config
 patch("16b: config get merge yaml",