@sparkleideas/claude-flow-patch 3.1.0-alpha.44.patch.3 → 3.1.0-alpha.44.patch.5

package/AGENTS.md

@@ -95,7 +95,7 @@ Use `$skill-name` syntax to invoke:
 
 [optional body]
 
-Co-Authored-By: claude-flow <ruv@ruv.net>
+Sparkling Ideas <henrik@sparklingideas.co.uk>
 ```
 
 Types: `feat`, `fix`, `docs`, `style`, `refactor`, `perf`, `test`, `chore`

package/README.md

@@ -1,9 +1,28 @@
 # @sparkleideas/claude-flow-patch
 
+## Contents
+
+- [Quick Start](#quick-start)
+- [CLI Commands](#cli-commands)
+- [How It Works](#how-it-works)
+  - [Sentinel Files](#sentinel-files)
+  - [Target Packages](#target-packages)
+  - [Dependency Order](#dependency-order)
+  - [Key Design Decisions](#key-design-decisions)
+  - [Repository Structure](#repository-structure)
+- [Defect Index](#defect-index)
+- [Init-Script Patches](#init-script-patches)
+- [Compatibility](#compatibility)
+- [Links](#links)
+
+---
+
 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.
 
+<a id="quick-start"></a>
+
 ## Quick Start
 
 **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:
@@ -37,6 +56,8 @@ npx --yes @sparkleideas/claude-flow-patch --global --target ~/my-project   # bot
 
 `npx @claude-flow/cli` uses local `node_modules` if present, otherwise the global npx cache. Use `--target` to patch a project's local install.
 
+<a id="cli-commands"></a>
+
 ## CLI Commands
 
 | Command | Purpose |
@@ -46,6 +67,8 @@ npx --yes @sparkleideas/claude-flow-patch --global --target ~/my-project   # bot
 | `claude-flow-patch check` | Verify patch sentinels and auto-detect drift |
 | `claude-flow-patch repair --target <dir> [--source auto\|local\|global] [--dry-run]` | Rehydrate `.claude/helpers` in projects initialized before patching |
 
+<a id="how-it-works"></a>
+
 ## How It Works
 
 1. `patch-all.sh` locates the `@claude-flow/cli` dist files in the npm/npx cache
@@ -55,6 +78,8 @@ npx --yes @sparkleideas/claude-flow-patch --global --target ~/my-project   # bot
 
 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.
 
+<a id="sentinel-files"></a>
+
 ### Sentinel Files
 
 Each patch directory contains a `sentinel` file that declares how to verify the patch is applied:
@@ -75,6 +100,8 @@ package: ruvector
 
 `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.
 
+<a id="target-packages"></a>
+
 ### Target Packages
 
 | Package | Version | Location | Env var |
@@ -87,6 +114,8 @@ package: ruvector
 `RUVECTOR_CLI` is set by `patch-all.sh` to the ruvector CLI entry point.
 RS-001 locates its own target via `find`.
 
+<a id="dependency-order"></a>
+
 ### Dependency Order
 
 Execution order is controlled by 3-digit numeric prefixes on directory names (e.g. `010-CF-001-*`,
@@ -102,6 +131,8 @@ Two dependency chains exist:
 
 All other patches are independent.
 
+<a id="key-design-decisions"></a>
+
 ### Key Design Decisions
 
 - **Zero-maintenance discovery**: `patch-all.sh`, `check-patches.sh`, and doc generation all discover patches dynamically — no hardcoded lists.
@@ -110,6 +141,8 @@ All other patches are independent.
 - **Platform-aware**: DM-003 is macOS-only (auto-skipped on Linux).
 - **Sentinel-guarded**: `check-patches.sh` reads `sentinel` files from each patch directory to detect cache wipes and auto-reapply.
 
+<a id="repository-structure"></a>
+
 ### Repository Structure
 
 ```
@@ -135,6 +168,8 @@ claude-flow-patch/
     (29 defect directories total)
 ```
 
+<a id="defect-index"></a>
+
 ## Defect Index
 
 <!-- GENERATED:defect-index:begin -->
@@ -237,6 +272,8 @@ claude-flow-patch/
 | [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) |
 <!-- GENERATED:defect-index:end -->
 
+<a id="init-script-patches"></a>
+
 ## Init-Script Patches (Local Project Action Required)
 
 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.
@@ -288,12 +325,16 @@ 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="compatibility"></a>
+
 ## Compatibility
 
 - Tested against `@claude-flow/cli@3.1.0-alpha.41` and `ruv-swarm@1.0.20`
 - Requires Python 3.6+ and Bash
 - Works on Linux and macOS (DM-003 is macOS-only, auto-skipped on Linux)
 
+<a id="links"></a>
+
 ## Links
 
 - Homepage: https://sparklingideas.co.uk/claude-flow/patch

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sparkleideas/claude-flow-patch",
-  "version": "3.1.0-alpha.44.patch.3",
+  "version": "3.1.0-alpha.44.patch.5",
   "description": "Patch toolkit for @claude-flow/cli init/runtime defects with verify and post-init repair commands",
   "scripts": {
     "test": "node --test tests/*.test.mjs",

package/patch/170-IN-001-intelligence-stub/fix.py

@@ -10,15 +10,12 @@
 # 2 ops: upgrade path (line ~398) + writeHelpers path (line ~943)
 
 # Op 1: Upgrade path — when findSourceHelpersDir() returns null
+# old/new strings stop BEFORE generatedCritical to avoid overlap with SG-003j
 patch("IN-001a: upgrade fallback reads real intelligence.cjs",
     EXECUTOR,
     """        else {
             // Source not found (npx with broken paths) — use generated fallbacks
-            const generatedCritical = {
-                'hook-handler.cjs': generateHookHandler(),
-                'intelligence.cjs': generateIntelligenceStub(),
-                'auto-memory-hook.mjs': generateAutoMemoryHook(),
-            };""",
+            const generatedCritical = {""",
     """        else {
             // Source not found (npx with broken paths) — use generated fallbacks
             // IN-001: Try reading real intelligence.cjs from package before using stub
@@ -29,11 +26,7 @@ patch("IN-001a: upgrade fallback reads real intelligence.cjs",
                     intelligenceContent = fs.readFileSync(realPath, 'utf-8');
                 }
             } catch { /* use stub */ }
-            const generatedCritical = {
-                'hook-handler.cjs': generateHookHandler(),
-                'intelligence.cjs': intelligenceContent,
-                'auto-memory-hook.mjs': generateAutoMemoryHook(),
-            };""")
+            const generatedCritical = {""")
 
 # Op 2: writeHelpers path — fresh init when source dir not found
 patch("IN-001b: writeHelpers fallback reads real intelligence.cjs",

package/patch/270-SG-003-init-helpers-all-paths/fix.py

@@ -122,11 +122,12 @@ patch_all("SG-003i: source hook-handler requires memory.cjs",
 
 # Op 6: Fix executeUpgrade() fallback — generatedCritical missing router/session/memory
 # When source helpers aren't found, only 3 files were generated but hook-handler.cjs needs 6
+# Also replaces generateIntelligenceStub() → intelligenceContent (set by IN-001a above)
 patch("SG-003j: upgrade fallback generates router/session/memory",
     EXECUTOR,
     """            const generatedCritical = {
                 'hook-handler.cjs': generateHookHandler(),
-                'intelligence.cjs': intelligenceContent,
+                'intelligence.cjs': generateIntelligenceStub(),
                 'auto-memory-hook.mjs': generateAutoMemoryHook(),
             };""",
     """            const generatedCritical = {