@sparkleideas/claude-flow-patch 3.1.0-alpha.44.patch.6 → 3.1.0-alpha.44.patch.8

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Files changed (13) hide show
  1. package/CLAUDE.md +21 -3
  2. package/README.md +306 -83
  3. package/lib/common.py +1 -0
  4. package/package.json +1 -1
  5. package/patch/137-HK-005-daemon-pid-guard/README.md +11 -0
  6. package/patch/137-HK-005-daemon-pid-guard/fix.py +53 -0
  7. package/patch/137-HK-005-daemon-pid-guard/sentinel +2 -0
  8. package/patch/320-SG-004-wizard-parity/README.md +32 -0
  9. package/patch/320-SG-004-wizard-parity/fix.py +133 -0
  10. package/patch/320-SG-004-wizard-parity/sentinel +1 -0
  11. package/patch/330-SG-005-start-all-subcommand/README.md +32 -0
  12. package/patch/330-SG-005-start-all-subcommand/fix.py +58 -0
  13. package/patch/330-SG-005-start-all-subcommand/sentinel +1 -0
package/CLAUDE.md CHANGED
@@ -91,7 +91,13 @@ gh issue comment <NUMBER> --repo ruvnet/claude-flow --body "$(cat <<'EOF'
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91
 
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  Defect **{PREFIX}-{NNN}** in [claude-flow-patch](https://github.com/sparkling/claude-flow-patch).
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+ **Root cause:** <1-2 sentences explaining why the bug occurs at the code level>
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+
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  <What the patch does. Be specific. Include a table if multiple ops.>
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+
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+ **Affected versions:** `@claude-flow/cli` 3.1.0-alpha.44 through current
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+
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+ **Related issues:** #NNN, #NNN
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  EOF
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  )"
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  ```
@@ -115,6 +121,12 @@ gh issue create --repo ruvnet/claude-flow \
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  ## Files Affected
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  - <dist/src/path/to/file.js>
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+
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+ ## Affected Versions
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+ `@claude-flow/cli` 3.1.0-alpha.44 through current
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+
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+ ## Related Issues
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+ - #NNN — <short description of relationship>
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  EOF
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  )"
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  ```
@@ -124,6 +136,7 @@ Save the returned GitHub issue number for the defect README.md.
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  ### Comment hygiene:
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137
 
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  - One comment per defect, describing the patch. No meta-commentary.
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+ - Every comment/body MUST include affected versions and related issues (use "None" if truly standalone).
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  - If you need to replace a comment, delete the old one first (`gh api -X DELETE`).
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141
  - Do not reference defect history, deletion/restoration, or internal decisions.
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@@ -136,17 +149,17 @@ Save the returned GitHub issue number for the defect README.md.
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  | DM | Daemon & Workers | 6 |
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  | EM | Embeddings & HNSW | 2 |
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  | GV | Ghost Vectors | 1 |
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- | HK | Hooks | 4 |
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+ | HK | Hooks | 5 |
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  | HW | Headless Worker | 4 |
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  | IN | Intelligence | 1 |
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  | MM | Memory Management | 1 |
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  | NS | Memory Namespace | 3 |
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  | RS | ruv-swarm | 1 |
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  | RV | RuVector Intelligence | 3 |
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- | SG | Settings Generator | 2 |
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+ | SG | Settings Generator | 4 |
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  | UI | Display & Cosmetic | 2 |
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- ## All 32 Defects
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+ ## All 35 Defects
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  | ID | GitHub Issue | Severity |
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  |----|-------------|----------|
@@ -164,6 +177,7 @@ Save the returned GitHub issue number for the defect README.md.
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  | HK-002 | [#1058 MCP hook handlers are stubs that don't persist data](https://github.com/ruvnet/claude-flow/issues/1058) | High |
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  | HK-003 | [#1158 hooks_metrics MCP handler returns hardcoded fake data](https://github.com/ruvnet/claude-flow/issues/1158) | High |
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  | HK-004 | [#1175 hooks_session-start ignores daemon.autoStart from settings.json](https://github.com/ruvnet/claude-flow/issues/1175) | High |
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+ | HK-005 | [#1171 Multiple MCP servers start independent in-process daemons](https://github.com/ruvnet/claude-flow/issues/1171) | Critical |
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  | HW-001 | [#1111 Headless workers hang — stdin pipe never closed](https://github.com/ruvnet/claude-flow/issues/1111) | Critical |
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  | HW-002 | [#1112 Headless failures silently swallowed as success](https://github.com/ruvnet/claude-flow/issues/1112) | High |
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  | HW-003 | [#1113 Worker scheduling intervals too aggressive + settings ignored](https://github.com/ruvnet/claude-flow/issues/1113) | High |
@@ -182,6 +196,8 @@ Save the returned GitHub issue number for the defect README.md.
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  | UI-002 | [#1146 neural status shows "Not loaded"](https://github.com/ruvnet/claude-flow/issues/1146) | Low |
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  | DM-006 | [#1114 No log rotation — logs grow unbounded](https://github.com/ruvnet/claude-flow/issues/1114) | Medium |
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  | HW-004 | [#1117 runWithTimeout rejects but does not kill child process](https://github.com/ruvnet/claude-flow/issues/1117) | Medium |
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+ | SG-004 | [#1181 init wizard lacks parity with init](https://github.com/ruvnet/claude-flow/issues/1181) | High |
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+ | SG-005 | [#1177 add 'start all' subcommand to start everything at once](https://github.com/ruvnet/claude-flow/issues/1177) | Enhancement |
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  <!-- GENERATED:defect-tables:end -->
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  ---
@@ -307,6 +323,8 @@ Both are idempotent: skip if `new` already present, warn if `old` not found.
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  | `SETTINGS_GEN` | `init/settings-generator.js` | @claude-flow/cli |
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  | `HELPERS_GEN` | `init/helpers-generator.js` | @claude-flow/cli |
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  | `EXECUTOR` | `init/executor.js` | @claude-flow/cli |
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+ | `INIT_CMD` | `commands/init.js` | @claude-flow/cli |
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+ | `START_CMD` | `commands/start.js` | @claude-flow/cli |
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  | `ruvector_cli` | `bin/cli.js` | ruvector |
311
329
 
312
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  To target a new file, add a variable to `lib/common.py` following the existing pattern.
package/README.md CHANGED
@@ -1,71 +1,42 @@
1
1
  # @sparkleideas/claude-flow-patch
2
2
 
3
- Patch toolkit for `@claude-flow/cli` runtime and init-script defects.
4
-
5
- This package applies verified, idempotent patches to your local CLI source in the npm cache or local `node_modules`, then verifies sentinels and can repair projects initialized before patching.
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-
7
- ## What This Solves
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-
9
- `claude-flow init` can generate incomplete or broken project helpers when upstream defects are present. This toolkit addresses known defects in:
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-
11
- - `@claude-flow/cli`
12
- - `ruvector`
13
- - `ruv-swarm`
14
-
15
- <!-- GENERATED:npm-defects:begin -->
16
- 32 tracked defects across 13 categories.
17
-
18
- | Defect | Description | GitHub Issue |
19
- |--------|-------------|-------------|
20
- | [CF-001](https://github.com/sparkling/claude-flow-patch/tree/master/patch/010-CF-001-doctor-yaml) | Doctor ignores YAML config files | [#1141](https://github.com/ruvnet/claude-flow/issues/1141) |
21
- | [CF-002](https://github.com/sparkling/claude-flow-patch/tree/master/patch/020-CF-002-config-export-yaml) | Config export shows hardcoded defaults | [#1142](https://github.com/ruvnet/claude-flow/issues/1142) |
22
- | [DM-001](https://github.com/sparkling/claude-flow-patch/tree/master/patch/030-DM-001-daemon-log-zero) | daemon.log always 0 bytes | [#1116](https://github.com/ruvnet/claude-flow/issues/1116) |
23
- | [DM-002](https://github.com/sparkling/claude-flow-patch/tree/master/patch/040-DM-002-cpu-load-threshold) | maxCpuLoad=2.0 blocks all workers on multi-core | [#1138](https://github.com/ruvnet/claude-flow/issues/1138) |
24
- | [DM-003](https://github.com/sparkling/claude-flow-patch/tree/master/patch/050-DM-003-macos-freemem) | macOS freemem() always ~0% — workers blocked | [#1077](https://github.com/ruvnet/claude-flow/issues/1077) |
25
- | [DM-004](https://github.com/sparkling/claude-flow-patch/tree/master/patch/060-DM-004-preload-worker-stub) | Preload worker stub + missing from defaults | [#1139](https://github.com/ruvnet/claude-flow/issues/1139) |
26
- | [DM-005](https://github.com/sparkling/claude-flow-patch/tree/master/patch/070-DM-005-consolidation-worker-stub) | Consolidation worker stub (no decay/rebuild) | [#1140](https://github.com/ruvnet/claude-flow/issues/1140) |
27
- | [DM-006](https://github.com/sparkling/claude-flow-patch/tree/master/patch/300-DM-006-log-rotation) | No log rotation — logs grow unbounded | [#1114](https://github.com/ruvnet/claude-flow/issues/1114) |
28
- | [EM-001](https://github.com/sparkling/claude-flow-patch/tree/master/patch/080-EM-001-embedding-ignores-config) | Embedding system ignores project config (model + HNSW dims) | [#1143](https://github.com/ruvnet/claude-flow/issues/1143) |
29
- | [EM-002](https://github.com/sparkling/claude-flow-patch/tree/master/patch/090-EM-002-transformers-cache-eacces) | @xenova/transformers cache EACCES | [#1144](https://github.com/ruvnet/claude-flow/issues/1144) |
30
- | [GV-001](https://github.com/sparkling/claude-flow-patch/tree/master/patch/100-GV-001-hnsw-ghost-vectors) | HNSW ghost vectors persist after memory delete | [#1122](https://github.com/ruvnet/claude-flow/issues/1122) |
31
- | [HK-001](https://github.com/sparkling/claude-flow-patch/tree/master/patch/110-HK-001-post-edit-file-path) | post-edit hook records file_path as "unknown" | [#1155](https://github.com/ruvnet/claude-flow/issues/1155) |
32
- | [HK-002](https://github.com/sparkling/claude-flow-patch/tree/master/patch/120-HK-002-hooks-tools-stub) | MCP hook handlers are stubs that don't persist data | [#1058](https://github.com/ruvnet/claude-flow/issues/1058) |
33
- | [HK-003](https://github.com/sparkling/claude-flow-patch/tree/master/patch/130-HK-003-metrics-hardcoded) | hooks_metrics MCP handler returns hardcoded fake data | [#1158](https://github.com/ruvnet/claude-flow/issues/1158) |
34
- | [HK-004](https://github.com/sparkling/claude-flow-patch/tree/master/patch/135-HK-004-respect-daemon-autostart) | hooks_session-start ignores daemon.autoStart from settings.json | [#1175](https://github.com/ruvnet/claude-flow/issues/1175) |
35
- | [HW-001](https://github.com/sparkling/claude-flow-patch/tree/master/patch/140-HW-001-stdin-hang) | Headless workers hang — stdin pipe never closed | [#1111](https://github.com/ruvnet/claude-flow/issues/1111) |
36
- | [HW-002](https://github.com/sparkling/claude-flow-patch/tree/master/patch/150-HW-002-failures-swallowed) | Headless failures silently swallowed as success | [#1112](https://github.com/ruvnet/claude-flow/issues/1112) |
37
- | [HW-003](https://github.com/sparkling/claude-flow-patch/tree/master/patch/160-HW-003-aggressive-intervals) | Worker scheduling intervals too aggressive + settings ignored | [#1113](https://github.com/ruvnet/claude-flow/issues/1113) |
38
- | [HW-004](https://github.com/sparkling/claude-flow-patch/tree/master/patch/310-HW-004-runwithtimeout-orphan) | runWithTimeout rejects but does not kill child process | [#1117](https://github.com/ruvnet/claude-flow/issues/1117) |
39
- | [IN-001](https://github.com/sparkling/claude-flow-patch/tree/master/patch/170-IN-001-intelligence-stub) | intelligence.cjs is a stub that doesn't actually learn | [#1154](https://github.com/ruvnet/claude-flow/issues/1154) |
40
- | [MM-001](https://github.com/sparkling/claude-flow-patch/tree/master/patch/180-MM-001-memory-persist-path) | Remove dead persistPath config option | [#1152](https://github.com/ruvnet/claude-flow/issues/1152) |
41
- | [NS-001](https://github.com/sparkling/claude-flow-patch/tree/master/patch/190-NS-001-discovery-default-namespace) | Discovery ops default to wrong namespace | [#1123](https://github.com/ruvnet/claude-flow/issues/1123) |
42
- | [NS-002](https://github.com/sparkling/claude-flow-patch/tree/master/patch/200-NS-002-targeted-require-namespace) | Store/delete/retrieve fall back to 'default' + accept 'all' | [#581](https://github.com/ruvnet/claude-flow/issues/581) |
43
- | [NS-003](https://github.com/sparkling/claude-flow-patch/tree/master/patch/210-NS-003-namespace-typo-pattern) | Namespace typo 'pattern' vs 'patterns' | [#1136](https://github.com/ruvnet/claude-flow/issues/1136) |
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- | [RS-001](https://github.com/sparkling/claude-flow-patch/tree/master/patch/220-RS-001-better-sqlite3-node24) | ruv-swarm MCP fails on Node 24 — better-sqlite3 missing native bindings | [ruv-FANN#185](https://github.com/ruvnet/ruv-FANN/issues/185) |
45
- | [RV-001](https://github.com/sparkling/claude-flow-patch/tree/master/patch/230-RV-001-force-learn-tick) | force-learn command calls intel.tick() which doesn't exist | [#1156](https://github.com/ruvnet/claude-flow/issues/1156) |
46
- | [RV-002](https://github.com/sparkling/claude-flow-patch/tree/master/patch/240-RV-002-trajectory-load) | activeTrajectories not loaded from saved file | [#1157](https://github.com/ruvnet/claude-flow/issues/1157) |
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- | [RV-003](https://github.com/sparkling/claude-flow-patch/tree/master/patch/250-RV-003-trajectory-stats-sync) | trajectory-end does not update stats counters | [ruv-FANN#186](https://github.com/ruvnet/ruv-FANN/issues/186) |
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- | [SG-001](https://github.com/sparkling/claude-flow-patch/tree/master/patch/260-SG-001-init-settings) | Init generates invalid settings | [#1150](https://github.com/ruvnet/claude-flow/issues/1150) |
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- | [SG-003](https://github.com/sparkling/claude-flow-patch/tree/master/patch/270-SG-003-init-helpers-all-paths) | Init missing helpers for --dual, --minimal, hooks, and upgrade paths | [#1169](https://github.com/ruvnet/claude-flow/issues/1169) |
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- | [UI-001](https://github.com/sparkling/claude-flow-patch/tree/master/patch/280-UI-001-intelligence-stats-crash) | intelligence stats crashes on .toFixed() | [#1145](https://github.com/ruvnet/claude-flow/issues/1145) |
51
- | [UI-002](https://github.com/sparkling/claude-flow-patch/tree/master/patch/290-UI-002-neural-status-not-loaded) | neural status shows "Not loaded" | [#1146](https://github.com/ruvnet/claude-flow/issues/1146) |
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- <!-- GENERATED:npm-defects:end -->
3
+ ## Contents
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+
5
+ - [Quick Start](#quick-start)
6
+ - [CLI Commands](#cli-commands)
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+ - [How It Works](#how-it-works)
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+ - [Sentinel Files](#sentinel-files)
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+ - [Target Packages](#target-packages)
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+ - [Dependency Order](#dependency-order)
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+ - [Key Design Decisions](#key-design-decisions)
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+ - [Repository Structure](#repository-structure)
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+ - [Defect Index](#defect-index)
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+ - [Init-Script Patches](#init-script-patches)
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+ - [Compatibility](#compatibility)
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+ - [Links](#links)
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+
18
+ ---
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+
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+ 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**.
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+
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+ 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.
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+
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+ <a id="quick-start"></a>
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54
26
  ## Quick Start
55
27
 
56
- Patch first, then initialize projects.
28
+ **Patch before init.** Several patches fix the init/generator scripts. If you run `claude-flow init` before patching, the generated `.claude/helpers/` files will be stubs with no learning, no PageRank, and no-op feedback. Always patch first:
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29
 
58
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  ```bash
59
- # 1) apply patches (global npx cache)
31
+ # 1. Patch first -- fixes the init generators
60
32
  npx --yes @sparkleideas/claude-flow-patch --global
61
33
 
62
- # 2) verify sentinels
63
- npx --yes @sparkleideas/claude-flow-patch check
34
+ # 2. Then init (or re-init if already initialized)
35
+ npx @claude-flow/cli@latest init # fresh project
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+ npx @claude-flow/cli@latest init upgrade # existing project
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37
 
65
- # 3) now initialize or upgrade project
66
- npx @claude-flow/cli@latest init
67
- # or
68
- npx @claude-flow/cli@latest init upgrade
38
+ # 3. Verify
39
+ npx --yes @sparkleideas/claude-flow-patch check
69
40
  ```
70
41
 
71
42
  If you already initialized before patching:
@@ -74,6 +45,19 @@ If you already initialized before patching:
74
45
  npx --yes @sparkleideas/claude-flow-patch repair --target /path/to/project
75
46
  ```
76
47
 
48
+ ### Target Options
49
+
50
+ ```bash
51
+ npx --yes @sparkleideas/claude-flow-patch # global npx cache (default)
52
+ npx --yes @sparkleideas/claude-flow-patch --global # explicit global
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+ npx --yes @sparkleideas/claude-flow-patch --target ~/my-project # project's node_modules
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+ npx --yes @sparkleideas/claude-flow-patch --global --target ~/my-project # both
55
+ ```
56
+
57
+ `npx @claude-flow/cli` uses local `node_modules` if present, otherwise the global npx cache. Use `--target` to patch a project's local install.
58
+
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+ <a id="cli-commands"></a>
60
+
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61
  ## CLI Commands
78
62
 
79
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  | Command | Purpose |
@@ -83,46 +67,285 @@ npx --yes @sparkleideas/claude-flow-patch repair --target /path/to/project
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67
  | `claude-flow-patch check` | Verify patch sentinels and auto-detect drift |
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68
  | `claude-flow-patch repair --target <dir> [--source auto\|local\|global] [--dry-run]` | Rehydrate `.claude/helpers` in projects initialized before patching |
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69
 
86
- ## Target Behavior
70
+ <a id="how-it-works"></a>
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88
- | Flag | Patched location |
89
- |---|---|
90
- | (none) | Global npx cache (default) |
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- | `--global` | `~/.npm/_npx/*/node_modules/...` |
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- | `--target <dir>` | `<dir>/node_modules/...` |
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- | `--global --target <dir>` | Both locations |
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+ ## How It Works
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+
74
+ 1. `patch-all.sh` locates the `@claude-flow/cli` dist files in the npm/npx cache
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+ 2. Globs `patch/*/fix.py` (numeric prefixes on directories ensure correct execution order)
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+ 3. Concatenates `lib/common.py` with each `fix.py` and runs as a single Python process
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+ 4. Each patch is idempotent: skips if already applied, warns if source changed
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+
79
+ The `check-patches.sh` sentinel runs on session start to detect npx cache wipes and auto-reapply. It reads `sentinel` files from each patch directory — no hardcoded patch list.
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+
81
+ <a id="sentinel-files"></a>
82
+
83
+ ### Sentinel Files
84
+
85
+ Each patch directory contains a `sentinel` file that declares how to verify the patch is applied:
86
+
87
+ ```
88
+ grep "pattern to find" relative/path/to/file.js
89
+ absent "pattern that should NOT exist" relative/path.js
90
+ none
91
+ package: ruvector
92
+ ```
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+
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+ | Directive | Meaning |
95
+ |-----------|---------|
96
+ | `grep "..." file` | Pass if pattern is found in file (standard check) |
97
+ | `absent "..." file` | Pass if pattern is **not** found (removal check) |
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+ | `none` | No sentinel — skip verification |
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+ | `package: X` | Target package (default: `@claude-flow/cli`). Skipped if package not installed |
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+
101
+ `check-patches.sh` and `lib/discover.mjs` both read these files dynamically. Adding a new patch requires no edits to any script — just create the `sentinel` file in the new patch directory.
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+
103
+ <a id="target-packages"></a>
104
+
105
+ ### Target Packages
106
+
107
+ | Package | Version | Location | Env var |
108
+ |---------|---------|----------|---------|
109
+ | `@claude-flow/cli` | `3.1.0-alpha.41` | `~/.npm/_npx/*/node_modules/@claude-flow/cli/dist/src/` | `BASE` |
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+ | `ruvector` | (bundled) | `~/.npm/_npx/*/node_modules/ruvector/bin/cli.js` | `RUVECTOR_CLI` |
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+ | `ruv-swarm` | `1.0.20` | `~/.npm/_npx/*/node_modules/ruv-swarm/` | (found via glob) |
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+
113
+ `BASE` is set by `patch-all.sh`. All path variables in `lib/common.py` derive from it.
114
+ `RUVECTOR_CLI` is set by `patch-all.sh` to the ruvector CLI entry point.
115
+ RS-001 locates its own target via `find`.
116
+
117
+ <a id="dependency-order"></a>
118
+
119
+ ### Dependency Order
120
+
121
+ Execution order is controlled by 3-digit numeric prefixes on directory names (e.g. `010-CF-001-*`,
122
+ `170-IN-001-*`). `patch-all.sh` globs `patch/*/fix.py`, which sorts lexicographically — numeric
123
+ prefixes guarantee correct order.
124
+
125
+ Two dependency chains exist:
126
+
127
+ | Chain | Directories | Reason |
128
+ |-------|-------------|--------|
129
+ | IN-001 -> SG-003 | `170-IN-001-*` before `270-SG-003-*` | SG-003's patch targets code introduced by IN-001 |
130
+ | NS-001 -> NS-002 -> NS-003 | `190-NS-001-*` before `200-NS-002-*` before `210-NS-003-*` | Sequential namespace fixes |
131
+
132
+ All other patches are independent.
133
+
134
+ <a id="key-design-decisions"></a>
135
+
136
+ ### Key Design Decisions
137
+
138
+ - **Zero-maintenance discovery**: `patch-all.sh`, `check-patches.sh`, and doc generation all discover patches dynamically — no hardcoded lists.
139
+ - **Idempotent**: `patch()` checks if `new` string is already present before replacing.
140
+ - **Non-destructive**: patches only modify the npx cache, never the npm registry package.
141
+ - **Platform-aware**: DM-003 is macOS-only (auto-skipped on Linux).
142
+ - **Sentinel-guarded**: `check-patches.sh` reads `sentinel` files from each patch directory to detect cache wipes and auto-reapply.
143
+
144
+ <a id="repository-structure"></a>
145
+
146
+ ### Repository Structure
147
+
148
+ ```
149
+ claude-flow-patch/
150
+ README.md # This file
151
+ CLAUDE.md # Claude Code instructions (defect workflow, policies)
152
+ AGENTS.md # Codex agent configuration
153
+ patch-all.sh # Apply all patches (globs patch/*/fix.py dynamically)
154
+ check-patches.sh # Sentinel: reads patch/*/sentinel files dynamically
155
+ repair-post-init.sh # Post-init helper repair
156
+ lib/
157
+ common.py # Shared patch()/patch_all() helpers + path variables
158
+ discover.mjs # Dynamic patch discovery — single source of truth
159
+ categories.json # Prefix-to-label mapping (e.g. HW → Headless Worker)
160
+ scripts/
161
+ preflight.mjs # Pre-commit sync: doc tables, versions, config
162
+ patch/
163
+ {NNN}-{PREFIX}-{NNN}-{slug}/ # NNN = 3-digit execution order
164
+ README.md # Defect report: title, severity, root cause, fix
165
+ fix.py # Idempotent patch script
166
+ fix.sh # Shell-based patch script (EM-002 only)
167
+ sentinel # Verification directives for check-patches.sh
168
+ (29 defect directories total)
169
+ ```
170
+
171
+ <a id="defect-index"></a>
172
+
173
+ ## Defect Index
174
+
175
+ <!-- GENERATED:defect-index:begin -->
176
+ 35 defects across 13 categories.
177
+
178
+ ### CF -- Config & Doctor
179
+
180
+ | ID | Description <img width="500" height="1" /> | Severity | GitHub&nbsp;Issue |
181
+ |----|-------------|----------|--------------|
182
+ | [CF&#8209;001](patch/010-CF-001-doctor-yaml/) | Doctor ignores YAML config files | Low | [#1141](https://github.com/ruvnet/claude-flow/issues/1141) |
183
+ | [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) |
94
184
 
95
- Use `--target` when your project has a local `@claude-flow/cli` install.
185
+ ### DM -- Daemon & Workers
96
186
 
97
- ## Why `repair` Exists
187
+ | ID | Description <img width="500" height="1" /> | Severity | GitHub&nbsp;Issue |
188
+ |----|-------------|----------|--------------|
189
+ | [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) |
190
+ | [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) |
191
+ | [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) |
192
+ | [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) |
193
+ | [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) |
194
+ | [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) |
98
195
 
99
- Some fixes patch generator code (`init/executor.js`, `init/settings-generator.js`, `init/helpers-generator.js`). Those fixes affect future generated files only.
196
+ ### EM -- Embeddings & HNSW
100
197
 
101
- If your repo was initialized before patching, existing `.claude/helpers/*` can remain stale. `repair` copies patched helper files into the target repo and creates .js/.cjs compatibility copies where needed.
198
+ | ID | Description <img width="500" height="1" /> | Severity | GitHub&nbsp;Issue |
199
+ |----|-------------|----------|--------------|
200
+ | [EM&#8209;001](patch/080-EM-001-embedding-ignores-config/) | Embedding system ignores project config (model + HNSW dims) | High | [#1143](https://github.com/ruvnet/claude-flow/issues/1143) |
201
+ | [EM&#8209;002](patch/090-EM-002-transformers-cache-eacces/) | @xenova/transformers cache EACCES | Medium | [#1144](https://github.com/ruvnet/claude-flow/issues/1144) |
102
202
 
103
- ## How Patching Works
203
+ ### GV -- Ghost Vectors
104
204
 
105
- 1. Locate CLI/package targets.
106
- 2. Concatenate shared helpers (`lib/common.py`) with each defect `fix.py`.
107
- 3. Apply string-based replacements with idempotency guards.
108
- 4. Validate with sentinel checks.
205
+ | ID | Description <img width="500" height="1" /> | Severity | GitHub&nbsp;Issue |
206
+ |----|-------------|----------|--------------|
207
+ | [GV&#8209;001](patch/100-GV-001-hnsw-ghost-vectors/) | HNSW ghost vectors persist after memory delete | Medium | [#1122](https://github.com/ruvnet/claude-flow/issues/1122) |
109
208
 
110
- Design guarantees:
209
+ ### HK -- Hooks
111
210
 
112
- - **Idempotent**: safe to re-run
113
- - **Non-destructive**: modifies local cache/install only
114
- - **Ordered**: dependent patches applied in sequence (e.g. NS-001 -> NS-002 -> NS-003)
115
- - **Platform-aware**: macOS-specific patches auto-skip on Linux
211
+ | ID | Description <img width="500" height="1" /> | Severity | GitHub&nbsp;Issue |
212
+ |----|-------------|----------|--------------|
213
+ | [HK&#8209;001](patch/110-HK-001-post-edit-file-path/) | post-edit hook records file_path as "unknown" | Medium | [#1155](https://github.com/ruvnet/claude-flow/issues/1155) |
214
+ | [HK&#8209;002](patch/120-HK-002-hooks-tools-stub/) | MCP hook handlers are stubs that don't persist data | High | [#1058](https://github.com/ruvnet/claude-flow/issues/1058) |
215
+ | [HK&#8209;003](patch/130-HK-003-metrics-hardcoded/) | hooks_metrics MCP handler returns hardcoded fake data | High | [#1158](https://github.com/ruvnet/claude-flow/issues/1158) |
216
+ | [HK&#8209;004](patch/135-HK-004-respect-daemon-autostart/) | hooks_session-start ignores daemon.autoStart from settings.json | High | [#1175](https://github.com/ruvnet/claude-flow/issues/1175) |
217
+ | [HK&#8209;005](patch/137-HK-005-daemon-pid-guard/) | Multiple MCP servers start independent in-process daemons | Critical | [#1171](https://github.com/ruvnet/claude-flow/issues/1171) |
218
+
219
+ ### HW -- Headless Worker
220
+
221
+ | ID | Description <img width="500" height="1" /> | Severity | GitHub&nbsp;Issue |
222
+ |----|-------------|----------|--------------|
223
+ | [HW&#8209;001](patch/140-HW-001-stdin-hang/) | Headless workers hang — stdin pipe never closed | Critical | [#1111](https://github.com/ruvnet/claude-flow/issues/1111) |
224
+ | [HW&#8209;002](patch/150-HW-002-failures-swallowed/) | Headless failures silently swallowed as success | High | [#1112](https://github.com/ruvnet/claude-flow/issues/1112) |
225
+ | [HW&#8209;003](patch/160-HW-003-aggressive-intervals/) | Worker scheduling intervals too aggressive + settings ignored | High | [#1113](https://github.com/ruvnet/claude-flow/issues/1113) |
226
+ | [HW&#8209;004](patch/310-HW-004-runwithtimeout-orphan/) | runWithTimeout rejects but does not kill child process | Medium | [#1117](https://github.com/ruvnet/claude-flow/issues/1117) |
227
+
228
+ ### IN -- Intelligence
229
+
230
+ | ID | Description <img width="500" height="1" /> | Severity | GitHub&nbsp;Issue |
231
+ |----|-------------|----------|--------------|
232
+ | [IN&#8209;001](patch/170-IN-001-intelligence-stub/) | intelligence.cjs is a stub that doesn't actually learn | Critical | [#1154](https://github.com/ruvnet/claude-flow/issues/1154) |
233
+
234
+ ### MM -- Memory Management
235
+
236
+ | ID | Description <img width="500" height="1" /> | Severity | GitHub&nbsp;Issue |
237
+ |----|-------------|----------|--------------|
238
+ | [MM&#8209;001](patch/180-MM-001-memory-persist-path/) | Remove dead persistPath config option | Low | [#1152](https://github.com/ruvnet/claude-flow/issues/1152) |
239
+
240
+ ### NS -- Memory Namespace
241
+
242
+ | ID | Description <img width="500" height="1" /> | Severity | GitHub&nbsp;Issue |
243
+ |----|-------------|----------|--------------|
244
+ | [NS&#8209;001](patch/190-NS-001-discovery-default-namespace/) | Discovery ops default to wrong namespace | Critical | [#1123](https://github.com/ruvnet/claude-flow/issues/1123) |
245
+ | [NS&#8209;002](patch/200-NS-002-targeted-require-namespace/) | Store/delete/retrieve fall back to 'default' + accept 'all' | Critical | [#581](https://github.com/ruvnet/claude-flow/issues/581) |
246
+ | [NS&#8209;003](patch/210-NS-003-namespace-typo-pattern/) | Namespace typo 'pattern' vs 'patterns' | Medium | [#1136](https://github.com/ruvnet/claude-flow/issues/1136) |
247
+
248
+ ### RS -- ruv-swarm
249
+
250
+ | ID | Description <img width="500" height="1" /> | Severity | GitHub&nbsp;Issue |
251
+ |----|-------------|----------|--------------|
252
+ | [RS&#8209;001](patch/220-RS-001-better-sqlite3-node24/) | ruv-swarm MCP fails on Node 24 — better-sqlite3 missing native bindings | Critical | [ruv-FANN#185](https://github.com/ruvnet/ruv-FANN/issues/185) |
253
+
254
+ ### RV -- RuVector Intelligence
255
+
256
+ | ID | Description <img width="500" height="1" /> | Severity | GitHub&nbsp;Issue |
257
+ |----|-------------|----------|--------------|
258
+ | [RV&#8209;001](patch/230-RV-001-force-learn-tick/) | force-learn command calls intel.tick() which doesn't exist | Medium | [#1156](https://github.com/ruvnet/claude-flow/issues/1156) |
259
+ | [RV&#8209;002](patch/240-RV-002-trajectory-load/) | activeTrajectories not loaded from saved file | High | [#1157](https://github.com/ruvnet/claude-flow/issues/1157) |
260
+ | [RV&#8209;003](patch/250-RV-003-trajectory-stats-sync/) | trajectory-end does not update stats counters | Medium | [ruv-FANN#186](https://github.com/ruvnet/ruv-FANN/issues/186) |
261
+
262
+ ### SG -- Settings Generator
263
+
264
+ | ID | Description <img width="500" height="1" /> | Severity | GitHub&nbsp;Issue |
265
+ |----|-------------|----------|--------------|
266
+ | [SG&#8209;001](patch/260-SG-001-init-settings/) | Init generates invalid settings | High | [#1150](https://github.com/ruvnet/claude-flow/issues/1150) |
267
+ | [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) |
268
+ | [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) |
269
+ | [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) |
270
+
271
+ ### UI -- Display & Cosmetic
272
+
273
+ | ID | Description <img width="500" height="1" /> | Severity | GitHub&nbsp;Issue |
274
+ |----|-------------|----------|--------------|
275
+ | [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) |
276
+ | [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) |
277
+ <!-- GENERATED:defect-index:end -->
278
+
279
+ <a id="init-script-patches"></a>
280
+
281
+ ## Init-Script Patches (Local Project Action Required)
282
+
283
+ Five patches target the **init/generator scripts** (`executor.js`, `settings-generator.js`, `helpers-generator.js`). These fix the code that *generates* your `.claude/` project files -- but applying patches does **not** update files already generated in your project. You must take one additional step.
284
+
285
+ ### Affected Defects
286
+
287
+ | ID | Generator patched | Local file affected | Problem if not refreshed |
288
+ |----|-------------------|---------------------|--------------------------|
289
+ | IN-001 | `init/executor.js` | `.claude/helpers/intelligence.cjs` | 197-line stub: no PageRank, no graph, `feedback()` is a no-op, no learning |
290
+ | HK-001 | `init/helpers-generator.js` | `.claude/helpers/hook-handler.cjs` | Reads env vars instead of stdin JSON; post-edit logs `file: "unknown"` |
291
+ | SG-001 | `init/settings-generator.js` | `.claude/settings.json` | May contain invalid hook events, broad permissions, relative paths |
292
+ | SG-002 | `init/executor.js` | `.claude/helpers/*.js` / `*.cjs` | Missing .js/.cjs compat copies; `hook-handler.cjs` require() calls fail silently |
293
+ | MM-001 | `init/executor.js` | `.claude-flow/config.yaml` | Misleading `persistPath` setting that nothing reads |
294
+
295
+ ### How to Fix
296
+
297
+ **Option A: Run `repair`** (recommended)
298
+
299
+ ```bash
300
+ npx --yes @sparkleideas/claude-flow-patch --global
301
+ npx --yes @sparkleideas/claude-flow-patch repair --target .
302
+ npx --yes @sparkleideas/claude-flow-patch apply SG-002 # apply a single patch
303
+ ```
304
+
305
+ This copies patched helper files into your project and creates any missing .js/.cjs compat copies.
306
+
307
+ **Option B: Copy full helpers from the package manually**
308
+
309
+ ```bash
310
+ npx --yes @sparkleideas/claude-flow-patch --global
311
+ SRC=$(find ~/.npm/_npx -path '*/@claude-flow/cli/.claude/helpers' -type d 2>/dev/null | head -1)
312
+ for f in intelligence.cjs hook-handler.cjs session.js learning-service.mjs metrics-db.mjs statusline.cjs; do
313
+ [ -f "$SRC/$f" ] && cp "$SRC/$f" .claude/helpers/ && echo "Copied: $f"
314
+ done
315
+ ```
316
+
317
+ **Option C: Re-run init upgrade** (regenerates from patched scripts)
318
+
319
+ ```bash
320
+ npx --yes @sparkleideas/claude-flow-patch --global
321
+ npx @claude-flow/cli@latest init upgrade --force
322
+ ```
323
+
324
+ Caution: Option C may overwrite other customizations in `.claude/`.
325
+
326
+ ### Why This Happens
327
+
328
+ These patches fix the **generator functions** inside the npm package (e.g., `generateIntelligenceStub()` in `executor.js`). When the generator runs via `claude-flow init`, it produces the project files in `.claude/helpers/`. If your project was initialized *before* patches were applied, the stubs are already on disk. Patches only modify the npm package source -- they do not touch files already generated in your project.
329
+
330
+ 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.
331
+
332
+ <a id="compatibility"></a>
116
333
 
117
334
  ## Compatibility
118
335
 
119
- - Tested with `@claude-flow/cli@3.1.0-alpha.41`
120
- - Tested with `ruv-swarm@1.0.20`
121
- - Requires Bash + Python 3.6+
122
- - Linux and macOS supported
336
+ - Tested against `@claude-flow/cli@3.1.0-alpha.41` and `ruv-swarm@1.0.20`
337
+ - Requires Python 3.6+ and Bash
338
+ - Works on Linux and macOS (DM-003 is macOS-only, auto-skipped on Linux)
339
+
340
+ <a id="links"></a>
123
341
 
124
342
  ## Links
125
343
 
126
344
  - Homepage: https://sparklingideas.co.uk/claude-flow/patch
345
+ - Package: https://www.npmjs.com/package/@sparkleideas/claude-flow-patch
127
346
  - GitHub: https://github.com/sparkling/claude-flow-patch
128
347
  - Issues: https://github.com/sparkling/claude-flow-patch/issues
348
+
349
+ ## License
350
+
351
+ MIT
package/lib/common.py CHANGED
@@ -83,6 +83,7 @@ HELPERS_GEN = init + "/helpers-generator.js" if init else ""
83
83
  EXECUTOR = init + "/executor.js" if init else ""
84
84
  TYPES = init + "/types.js" if init else ""
85
85
  INIT_CMD = commands + "/init.js" if commands else ""
86
+ START_CMD = commands + "/start.js" if commands else ""
86
87
 
87
88
  # Source helpers (shipped with package, copied by writeHelpers when source dir found)
88
89
  _pkg_root = os.path.dirname(os.path.dirname(base)) if base else ""
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@sparkleideas/claude-flow-patch",
3
- "version": "3.1.0-alpha.44.patch.6",
3
+ "version": "3.1.0-alpha.44.patch.8",
4
4
  "description": "Patch toolkit for @claude-flow/cli init/runtime defects with verify and post-init repair commands",
5
5
  "scripts": {
6
6
  "preflight": "node scripts/preflight.mjs",
package/patch/137-HK-005-daemon-pid-guard/README.md ADDED
@@ -0,0 +1,11 @@
1
+ # HK-005: Multiple MCP servers start independent in-process daemons
2
+ **Severity**: Critical
3
+ **GitHub**: [#1171](https://github.com/ruvnet/claude-flow/issues/1171)
4
+ ## Root Cause
5
+ `hooks_session-start` calls `startDaemon()` (worker-daemon.js) which creates an in-process `WorkerDaemon` singleton per Node.js process. Each MCP server is a separate process with its own singleton — no cross-process coordination. The CLI background daemon path (`daemon.js`) has PID-file coordination but the MCP hook path bypasses it entirely. Result: N MCP servers per project = N daemon instances = N × 6 workers.
6
+ ## Fix
7
+ Add PID-file guard to the MCP hook path using `.claude-flow/daemon.pid` (same file the CLI path uses). Before calling `startDaemon()`, check PID file: if a different process owns it and is alive, skip (reuse). If the PID is our own process or stale, proceed and overwrite. No cleanup on session-end — stale PIDs self-heal via `kill(pid, 0)` on next start. The PID file becomes a universal one-daemon-per-project lock across both MCP and CLI paths.
8
+ ## Files Patched
9
+ - mcp-tools/hooks-tools.js
10
+ ## Ops
11
+ 2 ops in fix.py
package/patch/137-HK-005-daemon-pid-guard/fix.py ADDED
@@ -0,0 +1,53 @@
1
+ # HK-005: Multiple MCP servers start independent in-process daemons
2
+ # No cross-process coordination on the hooks_session-start path.
3
+ # GitHub: #1171
4
+
5
+ # Op 1: Add PID-file guard before startDaemon()
6
+ patch("HK-005a: cross-process daemon PID guard",
7
+ MCP_HOOKS,
8
+ """ // Auto-start daemon if enabled
9
+ let daemonStatus = { started: false };
10
+ if (shouldStartDaemon) {
11
+ try {
12
+ // Dynamic import to avoid circular dependencies
13
+ const { startDaemon } = await import('../services/worker-daemon.js');
14
+ const daemon = await startDaemon(process.cwd());""",
15
+ """ // Auto-start daemon if enabled
16
+ let daemonStatus = { started: false };
17
+ if (shouldStartDaemon) {
18
+ try {
19
+ // HK-005: PID-file guard — one daemon per project across processes
20
+ const _pidDir = join(process.cwd(), '.claude-flow');
21
+ const _pidPath = join(_pidDir, 'daemon.pid');
22
+ let _skipDaemon = false;
23
+ try {
24
+ const _xPid = parseInt(readFileSync(_pidPath, 'utf-8').trim(), 10);
25
+ if (!isNaN(_xPid) && _xPid !== process.pid) {
26
+ try { process.kill(_xPid, 0); _skipDaemon = true; daemonStatus = { started: true, pid: _xPid, reused: true }; }
27
+ catch { /* stale PID from dead process — proceed */ }
28
+ }
29
+ } catch { /* no PID file — proceed */ }
30
+ if (!_skipDaemon) {
31
+ // Dynamic import to avoid circular dependencies
32
+ const { startDaemon } = await import('../services/worker-daemon.js');
33
+ const daemon = await startDaemon(process.cwd());""")
34
+
35
+ # Op 2: Write PID after successful start + close guard block
36
+ patch("HK-005b: write PID after daemon start",
37
+ MCP_HOOKS,
38
+ """ const status = daemon.getStatus();
39
+ daemonStatus = {
40
+ started: true,
41
+ pid: status.pid,
42
+ };""",
43
+ """ const status = daemon.getStatus();
44
+ // HK-005: Write PID so other processes detect this daemon
45
+ try {
46
+ if (!existsSync(_pidDir)) { mkdirSync(_pidDir, { recursive: true }); }
47
+ writeFileSync(_pidPath, String(status.pid || process.pid));
48
+ } catch { /* best-effort */ }
49
+ daemonStatus = {
50
+ started: true,
51
+ pid: status.pid,
52
+ };
53
+ } // end HK-005 guard""")
package/patch/137-HK-005-daemon-pid-guard/sentinel ADDED
@@ -0,0 +1,2 @@
1
+ grep "HK-005: PID-file guard" mcp-tools/hooks-tools.js
2
+ grep "HK-005: Write PID" mcp-tools/hooks-tools.js
package/patch/320-SG-004-wizard-parity/README.md ADDED
@@ -0,0 +1,32 @@
1
+ # SG-004: init wizard lacks parity with init
2
+
3
+ **Severity**: High
4
+ **GitHub**: [#1181](https://github.com/ruvnet/claude-flow/issues/1181)
5
+
6
+ ## Root Cause
7
+
8
+ The `wizardCommand.action` in `commands/init.js` was implemented as a
9
+ standalone code path that diverges from the parent `initAction`. It skips the
10
+ already-initialized guard, ignores `--force`, `--start-all`, `--start-daemon`,
11
+ `--codex`, and `--dual` flags, and never shows "Next steps" hints. The wizard
12
+ is conceptually "init with interactive value selection" but behaves as a
13
+ completely separate command.
14
+
15
+ ## Fix
16
+
17
+ Four ops bring the wizard to full parity with `init`:
18
+
19
+ | Op | What it does |
20
+ |----|-------------|
21
+ | SG-004a | Adds the already-initialized guard before prompts + passes `--force` to options |
22
+ | SG-004b | Adds `--codex`/`--dual` handling after executeInit succeeds |
23
+ | SG-004c | Adds `--start-all`/`--start-daemon` service startup + "Next steps" hints |
24
+ | SG-004d | Fixes catch block — catches errors cleanly instead of re-throwing |
25
+
26
+ ## Files Patched
27
+
28
+ - `commands/init.js`
29
+
30
+ ## Ops
31
+
32
+ 4 ops in fix.py
package/patch/320-SG-004-wizard-parity/fix.py ADDED
@@ -0,0 +1,133 @@
1
+ # SG-004: init wizard lacks parity with init
2
+ # GitHub: #1181
3
+ #
4
+ # The wizard was implemented as a standalone code path that ignores
5
+ # --force, --start-all, --start-daemon, --codex, --dual, and skips
6
+ # the already-initialized guard and "Next steps" hints.
7
+ #
8
+ # 4 ops: init-guard + force (a), codex/dual (b), start-all + next-steps (c),
9
+ # catch-block error handling (d)
10
+
11
+ # Op 1: Add already-initialized guard + pass --force to executeInit options
12
+ patch("SG-004a: wizard init-guard + --force",
13
+ INIT_CMD,
14
+ """ try {
15
+ // Start with base options
16
+ const options = { ...DEFAULT_INIT_OPTIONS, targetDir: ctx.cwd };""",
17
+ """ try {
18
+ // SG-004: Check if already initialized (respects --force)
19
+ const force = ctx.flags.force;
20
+ const initialized = isInitialized(ctx.cwd);
21
+ const hasExisting = initialized.claude || initialized.claudeFlow;
22
+ if (hasExisting && !force) {
23
+ output.printWarning('Claude Flow appears to be already initialized');
24
+ if (initialized.claude) output.printInfo(' Found: .claude/settings.json');
25
+ if (initialized.claudeFlow) output.printInfo(' Found: .claude-flow/config.yaml');
26
+ output.printInfo('Use --force to reinitialize');
27
+ const proceed = await confirm({
28
+ message: 'Do you want to reinitialize? This will overwrite existing configuration.',
29
+ default: false,
30
+ });
31
+ if (!proceed) {
32
+ return { success: true, message: 'Wizard cancelled' };
33
+ }
34
+ }
35
+ // Start with base options
36
+ const options = { ...DEFAULT_INIT_OPTIONS, targetDir: ctx.cwd, force: ctx.flags.force };""")
37
+
38
+ # Op 2: Add --codex / --dual handling after executeInit succeeds
39
+ patch("SG-004b: wizard --codex/--dual support",
40
+ INIT_CMD,
41
+ """ spinner.succeed('Setup complete!');
42
+ // Initialize embeddings if enabled
43
+ let embeddingsInitialized = false;""",
44
+ """ spinner.succeed('Setup complete!');
45
+ // SG-004: Respect --codex / --dual in wizard
46
+ const codexMode = ctx.flags.codex;
47
+ const dualMode = ctx.flags.dual;
48
+ if (codexMode || dualMode) {
49
+ try {
50
+ output.writeln(output.dim(' Initializing Codex integration...'));
51
+ await initCodexAction(ctx, { codexMode, dualMode, force: ctx.flags.force, minimal: false, full: false });
52
+ } catch (err) {
53
+ output.printWarning(`Codex initialization: ${err instanceof Error ? err.message : String(err)}`);
54
+ }
55
+ }
56
+ // Initialize embeddings if enabled
57
+ let embeddingsInitialized = false;""")
58
+
59
+ # Op 3: Add --start-all / --start-daemon + "Next steps" hints before final return
60
+ patch("SG-004c: wizard --start-all + next-steps",
61
+ INIT_CMD,
62
+ """ });
63
+ return { success: true, data: result };
64
+ }
65
+ catch (error) {
66
+ if (error instanceof Error && error.message === 'User cancelled') {""",
67
+ """ });
68
+ // SG-004: Respect --start-all / --start-daemon in wizard
69
+ const startAll = ctx.flags['start-all'] || ctx.flags.startAll;
70
+ const startDaemon = ctx.flags['start-daemon'] || ctx.flags.startDaemon || startAll;
71
+ if (startDaemon || startAll) {
72
+ output.writeln();
73
+ output.printInfo('Starting services...');
74
+ const { execSync } = await import('child_process');
75
+ if (startAll) {
76
+ try {
77
+ output.writeln(output.dim(' Initializing memory database...'));
78
+ execSync('npx @claude-flow/cli@latest memory init 2>/dev/null', {
79
+ stdio: 'pipe', cwd: ctx.cwd, timeout: 30000
80
+ });
81
+ output.writeln(output.success(' \\u2713 Memory initialized'));
82
+ } catch { output.writeln(output.dim(' Memory database already exists')); }
83
+ }
84
+ if (startDaemon) {
85
+ try {
86
+ output.writeln(output.dim(' Starting daemon...'));
87
+ execSync('npx @claude-flow/cli@latest daemon start 2>/dev/null &', {
88
+ stdio: 'pipe', cwd: ctx.cwd, timeout: 10000
89
+ });
90
+ output.writeln(output.success(' \\u2713 Daemon started'));
91
+ } catch { output.writeln(output.warning(' Daemon may already be running')); }
92
+ }
93
+ if (startAll) {
94
+ try {
95
+ output.writeln(output.dim(' Initializing swarm...'));
96
+ execSync('npx @claude-flow/cli@latest swarm init --topology hierarchical 2>/dev/null', {
97
+ stdio: 'pipe', cwd: ctx.cwd, timeout: 30000
98
+ });
99
+ output.writeln(output.success(' \\u2713 Swarm initialized'));
100
+ } catch { output.writeln(output.dim(' Swarm initialization skipped')); }
101
+ }
102
+ output.writeln();
103
+ output.printSuccess('All services started');
104
+ }
105
+ else {
106
+ output.writeln(output.bold('Next steps:'));
107
+ output.printList([
108
+ `Run ${output.highlight('claude-flow daemon start')} to start background workers`,
109
+ `Run ${output.highlight('claude-flow memory init')} to initialize memory database`,
110
+ `Run ${output.highlight('claude-flow swarm init')} to initialize a swarm`,
111
+ `Or re-run with ${output.highlight('--start-all')} to do all of the above`,
112
+ ]);
113
+ }
114
+ return { success: true, data: result };
115
+ }
116
+ catch (error) {
117
+ if (error instanceof Error && error.message === 'User cancelled') {""")
118
+
119
+ # Op 4: Fix wizard catch block — re-throws instead of clean error message
120
+ # spinner is declared inside the try block so we can't call spinner.fail() here
121
+ patch("SG-004d: wizard catch block handles errors cleanly",
122
+ INIT_CMD,
123
+ """ if (error instanceof Error && error.message === 'User cancelled') {
124
+ output.printInfo('Setup cancelled');
125
+ return { success: true };
126
+ }
127
+ throw error;""",
128
+ """ if (error instanceof Error && error.message === 'User cancelled') {
129
+ output.printInfo('Setup cancelled');
130
+ return { success: true };
131
+ }
132
+ output.printError(`Failed to initialize: ${error instanceof Error ? error.message : String(error)}`);
133
+ return { success: false, exitCode: 1 };""")
package/patch/320-SG-004-wizard-parity/sentinel ADDED
@@ -0,0 +1 @@
1
+ grep "SG-004" commands/init.js
package/patch/330-SG-005-start-all-subcommand/README.md ADDED
@@ -0,0 +1,32 @@
1
+ # SG-005: add 'start all' subcommand to start everything at once
2
+
3
+ **Severity**: Enhancement
4
+ **GitHub**: [#1177](https://github.com/ruvnet/claude-flow/issues/1177)
5
+
6
+ ## Root Cause
7
+
8
+ There is no single command to start the full Claude Flow stack (memory +
9
+ daemon + swarm + MCP) on an already-initialized project. `claude-flow start`
10
+ only initializes the swarm and MCP server. Users must run `memory init`,
11
+ `daemon start`, and `start` separately, or re-run `init --start-all` which
12
+ also re-creates project files.
13
+
14
+ ## Fix
15
+
16
+ Add an `allCommand` subcommand to the `start` command so that
17
+ `claude-flow start all` initializes memory, starts the daemon, then runs the
18
+ normal `startAction` (swarm + MCP + health checks).
19
+
20
+ | Op | What it does |
21
+ |----|-------------|
22
+ | SG-005a | Adds `allCommand` subcommand definition before `quickCommand` |
23
+ | SG-005b | Registers `allCommand` in the `subcommands` array |
24
+ | SG-005c | Adds `start all` to the examples array for `--help` output |
25
+
26
+ ## Files Patched
27
+
28
+ - `commands/start.js`
29
+
30
+ ## Ops
31
+
32
+ 3 ops in fix.py
package/patch/330-SG-005-start-all-subcommand/fix.py ADDED
@@ -0,0 +1,58 @@
1
+ # SG-005: add 'start all' subcommand to start everything at once
2
+ # GitHub: #1177
3
+
4
+ patch("SG-005a: add allCommand subcommand definition",
5
+ START_CMD,
6
+ """// Quick start subcommand
7
+ const quickCommand = {""",
8
+ """// Start-all subcommand — SG-005
9
+ const allCommand = {
10
+ name: 'all',
11
+ aliases: ['everything'],
12
+ description: 'Start memory, daemon, swarm, and MCP server',
13
+ action: async (ctx) => {
14
+ // Check initialization
15
+ if (!isInitialized(ctx.cwd)) {
16
+ output.printError('Claude Flow is not initialized in this directory');
17
+ output.printInfo('Run "claude-flow init" first, or use "claude-flow start quick"');
18
+ return { success: false, exitCode: 1 };
19
+ }
20
+ output.writeln();
21
+ output.writeln(output.bold('Starting all Claude Flow services'));
22
+ output.writeln();
23
+ const { execSync } = await import('child_process');
24
+ // Step 1: Initialize memory
25
+ try {
26
+ output.writeln(output.dim(' Initializing memory database...'));
27
+ execSync('npx @claude-flow/cli@latest memory init 2>/dev/null', {
28
+ stdio: 'pipe', cwd: ctx.cwd, timeout: 30000
29
+ });
30
+ output.writeln(' \\u2713 Memory initialized');
31
+ } catch { output.writeln(' Memory database already exists'); }
32
+ // Step 2: Start daemon
33
+ try {
34
+ output.writeln(output.dim(' Starting daemon...'));
35
+ execSync('npx @claude-flow/cli@latest daemon start 2>/dev/null &', {
36
+ stdio: 'pipe', cwd: ctx.cwd, timeout: 10000
37
+ });
38
+ output.writeln(' \\u2713 Daemon started');
39
+ } catch { output.writeln(' Daemon may already be running'); }
40
+ // Step 3: Start swarm + MCP via normal startAction
41
+ return startAction(ctx);
42
+ }
43
+ };
44
+ // Quick start subcommand
45
+ const quickCommand = {""")
46
+
47
+ patch("SG-005b: register allCommand in subcommands array",
48
+ START_CMD,
49
+ """ subcommands: [stopCommand, restartCommand, quickCommand],""",
50
+ """ subcommands: [stopCommand, restartCommand, quickCommand, allCommand],""")
51
+
52
+ patch("SG-005c: add 'start all' to examples array",
53
+ START_CMD,
54
+ """ { command: 'claude-flow start stop', description: 'Stop the running system' }
55
+ ],""",
56
+ """ { command: 'claude-flow start stop', description: 'Stop the running system' },
57
+ { command: 'claude-flow start all', description: 'Start memory, daemon, swarm, and MCP' }
58
+ ],""")
package/patch/330-SG-005-start-all-subcommand/sentinel ADDED
@@ -0,0 +1 @@
1
+ grep "allCommand" commands/start.js