feat: project-scoped instinct isolation

* feat: add project-scoped instinct isolation * fix(continuous-learning-v2): harden instinct loading and promotion safety; sync v2.1 command docs * fix(ci): make copilot-setup-steps a valid GitHub Actions workflow * fix(hooks): stabilize docs warning inline JS regex parsing
2026-03-30 13:43:26 +08:00 · 2026-03-02 04:07:13 +08:00
parent 2d3be88bb5
commit 5818e8adc7
26 changed files with 2476 additions and 713 deletions
--- a/.github/workflows/copilot-setup-steps.yml
+++ b/.github/workflows/copilot-setup-steps.yml
@@ -1,18 +1,30 @@
-steps:
+name: Copilot Setup Steps
-  - name: Setup Go environment
+
-    uses: actions/setup-go@v6.2.0
+on:
-    with:
+  workflow_dispatch:
-      # The Go version to download (if necessary) and use. Supports semver spec and ranges. Be sure to enclose this option in single quotation marks.
+
-      go-version: # optional
+permissions:
-      # Path to the go.mod, go.work, .go-version, or .tool-versions file.
+  contents: read
-      go-version-file: # optional
+
-      # Set this option to true if you want the action to always check for the latest available version that satisfies the version spec
+jobs:
-      check-latest: # optional
+  copilot-setup-steps:
-      # Used to pull Go distributions from go-versions. Since there's a default, this is typically not supplied by the user. When running this action on github.com, the default value is sufficient. When running on GHES, you can pass a personal access token for github.com if you are experiencing rate limiting.
+    runs-on: ubuntu-latest
-      token: # optional, default is ${{ github.server_url == 'https://github.com' && github.token || '' }}
+    timeout-minutes: 10
-      # Used to specify whether caching is needed. Set to true, if you'd like to enable caching.
+    steps:
-      cache: # optional, default is true
+      - name: Checkout repository
-      # Used to specify the path to a dependency file - go.sum
+        uses: actions/checkout@v4
-      cache-dependency-path: # optional
+
-      # Target architecture for Go to use. Examples: x86, x64. Will use system architecture by default.
+      - name: Setup Node.js
-      architecture: # optional
+        uses: actions/setup-node@v4
        with:
          node-version: "20"
          cache: npm
      - name: Install dependencies
        run: npm ci
      - name: Verify environment
        run: |
          node --version
          npm --version
          python3 --version
--- a/.opencode/MIGRATION.md
+++ b/.opencode/MIGRATION.md
@@ -258,6 +258,8 @@ After migration, ALL 23 commands are available:
 | `/instinct-import` | Import instincts |
 | `/instinct-export` | Export instincts |
 | `/evolve` | Cluster instincts into skills |
 | `/promote` | Promote project instincts to global scope |
 | `/projects` | List known projects and instinct stats |
 ## Available Agents
--- a/.opencode/README.md
+++ b/.opencode/README.md
@@ -95,6 +95,8 @@ opencode
 | `/instinct-import` | Import instincts |
 | `/instinct-export` | Export instincts |
 | `/evolve` | Cluster instincts |
 | `/promote` | Promote project instincts |
 | `/projects` | List known projects |
 ### Plugin Hooks
--- a/.opencode/commands/evolve.md
+++ b/.opencode/commands/evolve.md
@@ -1,112 +1,36 @@
 ---
-description: Cluster instincts into skills
+description: Analyze instincts and suggest or generate evolved structures
 agent: build
 ---
 # Evolve Command
-Cluster related instincts into structured skills: $ARGUMENTS
+Analyze and evolve instincts in continuous-learning-v2: $ARGUMENTS
 ## Your Task
-Analyze instincts and promote clusters to skills.
+Run:
-## Evolution Process
+```bash
-
+python3 "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/scripts/instinct-cli.py" evolve $ARGUMENTS
 ### Step 1: Analyze Instincts
 Group instincts by:
 - Trigger similarity
 - Action patterns
 - Category tags
 - Confidence levels
 ### Step 2: Identify Clusters
 ```
 Cluster: Error Handling
 ├── Instinct: Catch specific errors (0.85)
 ├── Instinct: Wrap errors with context (0.82)
 ├── Instinct: Log errors with stack trace (0.78)
 └── Instinct: Return meaningful error messages (0.80)
 ```
-### Step 3: Generate Skill
+If `CLAUDE_PLUGIN_ROOT` is unavailable, use:
-When cluster has:
+```bash
- 3+ instincts
+python3 ~/.claude/skills/continuous-learning-v2/scripts/instinct-cli.py evolve $ARGUMENTS
 - Average confidence > 0.75
 - Cohesive theme
 Generate SKILL.md:
 ```markdown
 # Error Handling Skill
 ## Overview
 Patterns for robust error handling learned from session observations.
 ## Patterns
 ### 1. Catch Specific Errors
 **Trigger**: When catching errors with generic catch
 **Action**: Use specific error types
 ### 2. Wrap Errors with Context
 **Trigger**: When re-throwing errors
 **Action**: Add context with fmt.Errorf or Error.cause
 ### 3. Log with Stack Trace
 **Trigger**: When logging errors
 **Action**: Include stack trace for debugging
 ### 4. Meaningful Messages
 **Trigger**: When returning errors to users
 **Action**: Provide actionable error messages
 ```
-### Step 4: Archive Instincts
+## Supported Args (v2.1)
-Move evolved instincts to `archived/` with reference to skill.
+- no args: analysis only
 - `--generate`: also generate files under `evolved/{skills,commands,agents}`
-## Evolution Report
+## Behavior Notes
-```
+- Uses project + global instincts for analysis.
-Evolution Summary
+- Shows skill/command/agent candidates from trigger and domain clustering.
-=================
+- Shows project -> global promotion candidates.
-
+- With `--generate`, output path is:
-Clusters Found: X
+  - project context: `~/.claude/homunculus/projects/<project-id>/evolved/`
-
+  - global fallback: `~/.claude/homunculus/evolved/`
 Cluster 1: Error Handling
 - Instincts: 5
 - Avg Confidence: 0.82
 - Status: ✅ Promoted to skill
 Cluster 2: Testing Patterns
 - Instincts: 3
 - Avg Confidence: 0.71
 - Status: ⏳ Needs more confidence
 Cluster 3: Git Workflow
 - Instincts: 2
 - Avg Confidence: 0.88
 - Status: ⏳ Needs more instincts
 Skills Created:
 - skills/error-handling/SKILL.md
 Instincts Archived: 5
 Remaining Instincts: 12
 ```
 ## Thresholds
 | Metric | Threshold |
 |--------|-----------|
 | Min instincts per cluster | 3 |
 | Min average confidence | 0.75 |
 | Min cluster cohesion | 0.6 |
 ---
 **TIP**: Run `/evolve` periodically to graduate instincts to skills as confidence grows.
--- a/.opencode/commands/instinct-status.md
+++ b/.opencode/commands/instinct-status.md
@@ -1,75 +1,29 @@
 ---
-description: View learned instincts with confidence scores
+description: Show learned instincts (project + global) with confidence
 agent: build
 ---
 # Instinct Status Command
-Display learned instincts and their confidence scores: $ARGUMENTS
+Show instinct status from continuous-learning-v2: $ARGUMENTS
 ## Your Task
-Read and display instincts from the continuous-learning-v2 system.
+Run:
-## Instinct Location
+```bash
-
+python3 "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/scripts/instinct-cli.py" status
 Global: `~/.claude/instincts/`
 Project: `.claude/instincts/`
 ## Status Display
 ### Instinct Summary
 | Category | Count | Avg Confidence |
 |----------|-------|----------------|
 | Coding | X | 0.XX |
 | Testing | X | 0.XX |
 | Security | X | 0.XX |
 | Git | X | 0.XX |
 ### High Confidence Instincts (>0.8)
 ```
 [trigger] → [action] (confidence: 0.XX)
 ```
-### Learning Progress
+If `CLAUDE_PLUGIN_ROOT` is unavailable, use:
- Total instincts: X
+```bash
- This session: X
+python3 ~/.claude/skills/continuous-learning-v2/scripts/instinct-cli.py status
 - Promoted to skills: X
 ### Recent Instincts
 Last 5 instincts learned:
 1. **[timestamp]** - [trigger] → [action]
 2. **[timestamp]** - [trigger] → [action]
 ...
 ## Instinct Structure
 ```json
 {
  "id": "instinct-123",
  "trigger": "When I see a try-catch without specific error type",
  "action": "Suggest using specific error types for better handling",
  "confidence": 0.75,
  "applications": 5,
  "successes": 4,
  "source": "session-observation",
  "timestamp": "2025-01-15T10:30:00Z"
 }
 ```
-## Confidence Calculation
+## Behavior Notes
-```
+- Output includes both project-scoped and global instincts.
-confidence = (successes + 1) / (applications + 2)
+- Project instincts override global instincts when IDs conflict.
-```
+- Output is grouped by domain with confidence bars.
-
+- This command does not support extra filters in v2.1.
 Bayesian smoothing ensures new instincts don't have extreme confidence.
 ---
 **TIP**: Use `/evolve` to cluster related instincts into skills when confidence is high.
--- a/.opencode/commands/projects.md
+++ b/.opencode/commands/projects.md
@@ -0,0 +1,23 @@
 ---
 description: List registered projects and instinct counts
 agent: build
 ---
 # Projects Command
 Show continuous-learning-v2 project registry and stats: $ARGUMENTS
 ## Your Task
 Run:
 ```bash
 python3 "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/scripts/instinct-cli.py" projects
 ```
 If `CLAUDE_PLUGIN_ROOT` is unavailable, use:
 ```bash
 python3 ~/.claude/skills/continuous-learning-v2/scripts/instinct-cli.py projects
 ```
--- a/.opencode/commands/promote.md
+++ b/.opencode/commands/promote.md
@@ -0,0 +1,23 @@
 ---
 description: Promote project instincts to global scope
 agent: build
 ---
 # Promote Command
 Promote instincts in continuous-learning-v2: $ARGUMENTS
 ## Your Task
 Run:
 ```bash
 python3 "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/scripts/instinct-cli.py" promote $ARGUMENTS
 ```
 If `CLAUDE_PLUGIN_ROOT` is unavailable, use:
 ```bash
 python3 ~/.claude/skills/continuous-learning-v2/scripts/instinct-cli.py promote $ARGUMENTS
 ```
--- a/.opencode/opencode.json
+++ b/.opencode/opencode.json
@@ -303,6 +303,14 @@
    "evolve": {
      "description": "Cluster instincts into skills",
      "template": "{file:.opencode/commands/evolve.md}\n\n$ARGUMENTS"
    },
    "promote": {
      "description": "Promote project instincts to global scope",
      "template": "{file:.opencode/commands/promote.md}\n\n$ARGUMENTS"
    },
    "projects": {
      "description": "List known projects and instinct stats",
      "template": "{file:.opencode/commands/projects.md}\n\n$ARGUMENTS"
    }
  },
  "permission": {
--- a/README.md
+++ b/README.md
@@ -985,6 +985,8 @@ OpenCode's plugin system is MORE sophisticated than Claude Code with 20+ event t
 | `/instinct-import` | Import instincts |
 | `/instinct-export` | Export instincts |
 | `/evolve` | Cluster instincts into skills |
 | `/promote` | Promote project instincts to global scope |
 | `/projects` | List known projects and instinct stats |
 | `/learn-eval` | Extract and evaluate patterns before saving |
 | `/setup-pm` | Configure package manager |
--- a/README.zh-CN.md
+++ b/README.zh-CN.md
@@ -287,6 +287,8 @@ everything-claude-code/
 /instinct-import <file> # 从他人导入直觉
 /instinct-export        # 导出你的直觉以供分享
 /evolve                 # 将相关直觉聚类到技能中
 /promote                # 将项目级直觉提升为全局直觉
 /projects               # 查看已识别项目与直觉统计
 ```
 完整文档见 `skills/continuous-learning-v2/`。
--- a/commands/evolve.md
+++ b/commands/evolve.md
@@ -1,6 +1,6 @@
 ---
 name: evolve
-description: Cluster related instincts into skills, commands, or agents
+description: Analyze instincts and suggest or generate evolved structures
 command: true
 ---
@@ -29,9 +29,7 @@ Analyzes instincts and clusters related ones into higher-level structures:
 ```
 /evolve                    # Analyze all instincts and suggest evolutions
-/evolve --domain testing   # Only evolve instincts in testing domain
+/evolve --generate         # Also generate files under evolved/{skills,commands,agents}
 /evolve --dry-run          # Show what would be created without creating
 /evolve --threshold 5      # Require 5+ related instincts to cluster
 ```
 ## Evolution Rules
@@ -78,63 +76,50 @@ Example:
 ## What to Do
-1. Read all instincts from `~/.claude/homunculus/instincts/`
+1. Detect current project context
-2. Group instincts by:
+2. Read project + global instincts (project takes precedence on ID conflicts)
-   - Domain similarity
+3. Group instincts by trigger/domain patterns
-   - Trigger pattern overlap
+4. Identify:
-   - Action sequence relationship
+   - Skill candidates (trigger clusters with 2+ instincts)
-3. For each cluster of 3+ related instincts:
+   - Command candidates (high-confidence workflow instincts)
-   - Determine evolution type (command/skill/agent)
+   - Agent candidates (larger, high-confidence clusters)
-   - Generate the appropriate file
+5. Show promotion candidates (project -> global) when applicable
-   - Save to `~/.claude/homunculus/evolved/{commands,skills,agents}/`
+6. If `--generate` is passed, write files to:
-4. Link evolved structure back to source instincts
+   - Project scope: `~/.claude/homunculus/projects/<project-id>/evolved/`
   - Global fallback: `~/.claude/homunculus/evolved/`
 ## Output Format
 ```
-🧬 Evolve Analysis
+============================================================
-==================
+  EVOLVE ANALYSIS - 12 instincts
  Project: my-app (a1b2c3d4e5f6)
  Project-scoped: 8 | Global: 4
 ============================================================
-Found 3 clusters ready for evolution:
+High confidence instincts (>=80%): 5
-## Cluster 1: Database Migration Workflow
+## SKILL CANDIDATES
-Instincts: new-table-migration, update-schema, regenerate-types
+1. Cluster: "adding tests"
-Type: Command
+   Instincts: 3
-Confidence: 85% (based on 12 observations)
+   Avg confidence: 82%
   Domains: testing
   Scopes: project
-Would create: /new-table command
+## COMMAND CANDIDATES (2)
-Files:
+  /adding-tests
-  - ~/.claude/homunculus/evolved/commands/new-table.md
+    From: test-first-workflow [project]
    Confidence: 84%
-## Cluster 2: Functional Code Style
+## AGENT CANDIDATES (1)
-Instincts: prefer-functional, use-immutable, avoid-classes, pure-functions
+  adding-tests-agent
-Type: Skill
+    Covers 3 instincts
-Confidence: 78% (based on 8 observations)
+    Avg confidence: 82%
 Would create: functional-patterns skill
 Files:
  - ~/.claude/homunculus/evolved/skills/functional-patterns.md
 ## Cluster 3: Debugging Process
 Instincts: debug-check-logs, debug-isolate, debug-reproduce, debug-verify
 Type: Agent
 Confidence: 72% (based on 6 observations)
 Would create: debugger agent
 Files:
  - ~/.claude/homunculus/evolved/agents/debugger.md
 ---
 Run `/evolve --execute` to create these files.
 ```
 ## Flags
- `--execute`: Actually create the evolved structures (default is preview)
+- `--generate`: Generate evolved files in addition to analysis output
 - `--dry-run`: Preview without creating
 - `--domain <name>`: Only evolve instincts in specified domain
 - `--threshold <n>`: Minimum instincts required to form cluster (default: 3)
 - `--type <command|skill|agent>`: Only create specified type
 ## Generated File Format
--- a/commands/instinct-export.md
+++ b/commands/instinct-export.md
@@ -1,6 +1,6 @@
 ---
 name: instinct-export
-description: Export instincts for sharing with teammates or other projects
+description: Export instincts from project/global scope to a file
 command: /instinct-export
 ---
@@ -18,17 +18,18 @@ Exports instincts to a shareable format. Perfect for:
 /instinct-export --domain testing          # Export only testing instincts
 /instinct-export --min-confidence 0.7      # Only export high-confidence instincts
 /instinct-export --output team-instincts.yaml
 /instinct-export --scope project --output project-instincts.yaml
 ```
 ## What to Do
-1. Read instincts from `~/.claude/homunculus/instincts/personal/`
+1. Detect current project context
-2. Filter based on flags
+2. Load instincts by selected scope:
-3. Strip sensitive information:
+   - `project`: current project only
-   - Remove session IDs
+   - `global`: global only
-   - Remove file paths (keep only patterns)
+   - `all`: project + global merged (default)
-   - Remove timestamps older than "last week"
+3. Apply filters (`--domain`, `--min-confidence`)
-4. Generate export file
+4. Write YAML-style export to file (or stdout if no output path provided)
 ## Output Format
@@ -40,52 +41,26 @@ Creates a YAML file:
 # Source: personal
 # Count: 12 instincts
-version: "2.0"
+---
-exported_by: "continuous-learning-v2"
+id: prefer-functional-style
-export_date: "2025-01-22T10:30:00Z"
+trigger: "when writing new functions"
 confidence: 0.8
 domain: code-style
 source: session-observation
 scope: project
 project_id: a1b2c3d4e5f6
 project_name: my-app
 ---
-instincts:
+# Prefer Functional Style
  - id: prefer-functional-style
    trigger: "when writing new functions"
    action: "Use functional patterns over classes"
    confidence: 0.8
    domain: code-style
    observations: 8
-  - id: test-first-workflow
+## Action
-    trigger: "when adding new functionality"
+Use functional patterns over classes.
    action: "Write test first, then implementation"
    confidence: 0.9
    domain: testing
    observations: 12
  - id: grep-before-edit
    trigger: "when modifying code"
    action: "Search with Grep, confirm with Read, then Edit"
    confidence: 0.7
    domain: workflow
    observations: 6
 ```
 ## Privacy Considerations
 Exports include:
 - ✅ Trigger patterns
 - ✅ Actions
 - ✅ Confidence scores
 - ✅ Domains
 - ✅ Observation counts
 Exports do NOT include:
 - ❌ Actual code snippets
 - ❌ File paths
 - ❌ Session transcripts
 - ❌ Personal identifiers
 ## Flags
 - `--domain <name>`: Export only specified domain
- `--min-confidence <n>`: Minimum confidence threshold (default: 0.3)
+- `--min-confidence <n>`: Minimum confidence threshold
- `--output <file>`: Output file path (default: instincts-export-YYYYMMDD.yaml)
+- `--output <file>`: Output file path (prints to stdout when omitted)
- `--format <yaml|json|md>`: Output format (default: yaml)
+- `--scope <project|global|all>`: Export scope (default: `all`)
 - `--include-evidence`: Include evidence text (default: excluded)
--- a/commands/instinct-import.md
+++ b/commands/instinct-import.md
@@ -1,6 +1,6 @@
 ---
 name: instinct-import
-description: Import instincts from teammates, Skill Creator, or other sources
+description: Import instincts from file or URL into project/global scope
 command: true
 ---
@@ -11,7 +11,7 @@ command: true
 Run the instinct CLI using the plugin root path:
 ```bash
-python3 "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/scripts/instinct-cli.py" import <file-or-url> [--dry-run] [--force] [--min-confidence 0.7]
+python3 "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/scripts/instinct-cli.py" import <file-or-url> [--dry-run] [--force] [--min-confidence 0.7] [--scope project|global]
 ```
 Or if `CLAUDE_PLUGIN_ROOT` is not set (manual installation):
@@ -20,18 +20,15 @@ Or if `CLAUDE_PLUGIN_ROOT` is not set (manual installation):
 python3 ~/.claude/skills/continuous-learning-v2/scripts/instinct-cli.py import <file-or-url>
 ```
-Import instincts from:
+Import instincts from local file paths or HTTP(S) URLs.
 - Teammates' exports
 - Skill Creator (repo analysis)
 - Community collections
 - Previous machine backups
 ## Usage
 ```
 /instinct-import team-instincts.yaml
 /instinct-import https://github.com/org/repo/instincts.yaml
-/instinct-import --from-skill-creator acme/webapp
+/instinct-import team-instincts.yaml --dry-run
 /instinct-import team-instincts.yaml --scope global --force
 ```
 ## What to Do
@@ -40,7 +37,9 @@ Import instincts from:
 2. Parse and validate the format
 3. Check for duplicates with existing instincts
 4. Merge or add new instincts
-5. Save to `~/.claude/homunculus/instincts/inherited/`
+5. Save to inherited instincts directory:
   - Project scope: `~/.claude/homunculus/projects/<project-id>/instincts/inherited/`
   - Global scope: `~/.claude/homunculus/instincts/inherited/`
 ## Import Process
@@ -71,60 +70,33 @@ Already have similar instincts:
     Import: 0.9 confidence
     → Update to import (higher confidence)
-## Conflicting Instincts (1)
+Import 8 new, update 1?
 These contradict local instincts:
  ❌ use-classes-for-services
     Conflicts with: avoid-classes
     → Skip (requires manual resolution)
 ---
 Import 8 new, update 1, skip 3?
 ```
-## Merge Strategies
+## Merge Behavior
-### For Duplicates
+When importing an instinct with an existing ID:
-When importing an instinct that matches an existing one:
+- Higher-confidence import becomes an update candidate
- **Higher confidence wins**: Keep the one with higher confidence
+- Equal/lower-confidence import is skipped
- **Merge evidence**: Combine observation counts
+- User confirms unless `--force` is used
 - **Update timestamp**: Mark as recently validated
 ### For Conflicts
 When importing an instinct that contradicts an existing one:
 - **Skip by default**: Don't import conflicting instincts
 - **Flag for review**: Mark both as needing attention
 - **Manual resolution**: User decides which to keep
 ## Source Tracking
 Imported instincts are marked with:
 ```yaml
-source: "inherited"
+source: inherited
 scope: project
 imported_from: "team-instincts.yaml"
-imported_at: "2025-01-22T10:30:00Z"
+project_id: "a1b2c3d4e5f6"
-original_source: "session-observation"  # or "repo-analysis"
+project_name: "my-project"
 ```
 ## Skill Creator Integration
 When importing from Skill Creator:
 ```
 /instinct-import --from-skill-creator acme/webapp
 ```
 This fetches instincts generated from repo analysis:
 - Source: `repo-analysis`
 - Higher initial confidence (0.7+)
 - Linked to source repository
 ## Flags
 - `--dry-run`: Preview without importing
- `--force`: Import even if conflicts exist
+- `--force`: Skip confirmation prompt
 - `--merge-strategy <higher|local|import>`: How to handle duplicates
 - `--from-skill-creator <owner/repo>`: Import from Skill Creator analysis
 - `--min-confidence <n>`: Only import instincts above threshold
 - `--scope <project|global>`: Select target scope (default: `project`)
 ## Output
@@ -134,7 +106,7 @@ After import:
 Added: 8 instincts
 Updated: 1 instinct
-Skipped: 3 instincts (2 duplicates, 1 conflict)
+Skipped: 3 instincts (equal/higher confidence already exists)
 New instincts saved to: ~/.claude/homunculus/instincts/inherited/
--- a/commands/instinct-status.md
+++ b/commands/instinct-status.md
@@ -1,12 +1,12 @@
 ---
 name: instinct-status
-description: Show all learned instincts with their confidence levels
+description: Show learned instincts (project + global) with confidence
 command: true
 ---
 # Instinct Status Command
-Shows all learned instincts with their confidence scores, grouped by domain.
+Shows learned instincts for the current project plus global instincts, grouped by domain.
 ## Implementation
@@ -26,61 +26,34 @@ python3 ~/.claude/skills/continuous-learning-v2/scripts/instinct-cli.py status
 ```
 /instinct-status
 /instinct-status --domain code-style
 /instinct-status --low-confidence
 ```
 ## What to Do
-1. Read all instinct files from `~/.claude/homunculus/instincts/personal/`
+1. Detect current project context (git remote/path hash)
-2. Read inherited instincts from `~/.claude/homunculus/instincts/inherited/`
+2. Read project instincts from `~/.claude/homunculus/projects/<project-id>/instincts/`
-3. Display them grouped by domain with confidence bars
+3. Read global instincts from `~/.claude/homunculus/instincts/`
 4. Merge with precedence rules (project overrides global when IDs collide)
 5. Display grouped by domain with confidence bars and observation stats
 ## Output Format
 ```
-📊 Instinct Status
+============================================================
-==================
+  INSTINCT STATUS - 12 total
 ============================================================
-## Code Style (4 instincts)
+  Project: my-app (a1b2c3d4e5f6)
  Project instincts: 8
  Global instincts:  4
-### prefer-functional-style
+## PROJECT-SCOPED (my-app)
-Trigger: when writing new functions
+  ### WORKFLOW (3)
-Action: Use functional patterns over classes
+    ███████░░░  70%  grep-before-edit [project]
-Confidence: ████████░░ 80%
+              trigger: when modifying code
 Source: session-observation | Last updated: 2025-01-22
-### use-path-aliases
+## GLOBAL (apply to all projects)
-Trigger: when importing modules
+  ### SECURITY (2)
-Action: Use @/ path aliases instead of relative imports
+    █████████░  85%  validate-user-input [global]
-Confidence: ██████░░░░ 60%
+              trigger: when handling user input
 Source: repo-analysis (github.com/acme/webapp)
 ## Testing (2 instincts)
 ### test-first-workflow
 Trigger: when adding new functionality
 Action: Write test first, then implementation
 Confidence: █████████░ 90%
 Source: session-observation
 ## Workflow (3 instincts)
 ### grep-before-edit
 Trigger: when modifying code
 Action: Search with Grep, confirm with Read, then Edit
 Confidence: ███████░░░ 70%
 Source: session-observation
 ---
 Total: 9 instincts (4 personal, 5 inherited)
 Observer: Running (last analysis: 5 min ago)
 ```
 ## Flags
 - `--domain <name>`: Filter by domain (code-style, testing, git, etc.)
 - `--low-confidence`: Show only instincts with confidence < 0.5
 - `--high-confidence`: Show only instincts with confidence >= 0.7
 - `--source <type>`: Filter by source (session-observation, repo-analysis, inherited)
 - `--json`: Output as JSON for programmatic use
--- a/commands/projects.md
+++ b/commands/projects.md
@@ -0,0 +1,40 @@
 ---
 name: projects
 description: List known projects and their instinct statistics
 command: true
 ---
 # Projects Command
 List project registry entries and per-project instinct/observation counts for continuous-learning-v2.
 ## Implementation
 Run the instinct CLI using the plugin root path:
 ```bash
 python3 "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/scripts/instinct-cli.py" projects
 ```
 Or if `CLAUDE_PLUGIN_ROOT` is not set (manual installation):
 ```bash
 python3 ~/.claude/skills/continuous-learning-v2/scripts/instinct-cli.py projects
 ```
 ## Usage
 ```bash
 /projects
 ```
 ## What to Do
 1. Read `~/.claude/homunculus/projects.json`
 2. For each project, display:
   - Project name, id, root, remote
   - Personal and inherited instinct counts
   - Observation event count
   - Last seen timestamp
 3. Also display global instinct totals
--- a/commands/promote.md
+++ b/commands/promote.md
@@ -0,0 +1,42 @@
 ---
 name: promote
 description: Promote project-scoped instincts to global scope
 command: true
 ---
 # Promote Command
 Promote instincts from project scope to global scope in continuous-learning-v2.
 ## Implementation
 Run the instinct CLI using the plugin root path:
 ```bash
 python3 "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/scripts/instinct-cli.py" promote [instinct-id] [--force] [--dry-run]
 ```
 Or if `CLAUDE_PLUGIN_ROOT` is not set (manual installation):
 ```bash
 python3 ~/.claude/skills/continuous-learning-v2/scripts/instinct-cli.py promote [instinct-id] [--force] [--dry-run]
 ```
 ## Usage
 ```bash
 /promote                      # Auto-detect promotion candidates
 /promote --dry-run            # Preview auto-promotion candidates
 /promote --force              # Promote all qualified candidates without prompt
 /promote grep-before-edit     # Promote one specific instinct from current project
 ```
 ## What to Do
 1. Detect current project
 2. If `instinct-id` is provided, promote only that instinct (if present in current project)
 3. Otherwise, find cross-project candidates that:
   - Appear in at least 2 projects
   - Meet confidence threshold
 4. Write promoted instincts to `~/.claude/homunculus/instincts/personal/` with `scope: global`
--- a/hooks/hooks.json
+++ b/hooks/hooks.json
@@ -37,7 +37,7 @@
        "hooks": [
          {
            "type": "command",
-            "command": "node \"${CLAUDE_PLUGIN_ROOT}/scripts/hooks/pre-write-doc-warn.js\""
+            "command": "node -e \"let d='';process.stdin.on('data',c=>d+=c);process.stdin.on('end',()=>{try{const i=JSON.parse(d);const p=i.tool_input?.file_path||'';if(/\\.(md|txt)$/.test(p)&&!/(README|CLAUDE|AGENTS|CONTRIBUTING|CHANGELOG|LICENSE|SKILL)\\.md$/i.test(p)&&!/\\.claude[\\/\\\\]plans[\\/\\\\]/.test(p)&&!/(^|[\\/\\\\])(docs|skills)[\\/\\\\]/.test(p)){console.error('[Hook] WARNING: Non-standard documentation file detected');console.error('[Hook] File: '+p);console.error('[Hook] Consider consolidating into README.md or docs/ directory')}}catch{}console.log(d)})\""
          }
        ],
        "description": "Doc file warning: warn about non-standard documentation files (exit code 0; warns only)"
@@ -51,6 +51,18 @@
          }
        ],
        "description": "Suggest manual compaction at logical intervals"
      },
      {
        "matcher": "*",
        "hooks": [
          {
            "type": "command",
            "command": "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/hooks/observe.sh",
            "async": true,
            "timeout": 10
          }
        ],
        "description": "Capture tool use observations for continuous learning"
      }
    ],
    "PreCompact": [
@@ -129,6 +141,18 @@
          }
        ],
        "description": "Warn about console.log statements after edits"
      },
      {
        "matcher": "*",
        "hooks": [
          {
            "type": "command",
            "command": "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/hooks/observe.sh",
            "async": true,
            "timeout": 10
          }
        ],
        "description": "Capture tool use results for continuous learning"
      }
    ],
    "Stop": [
--- a/skills/continuous-learning-v2/SKILL.md
+++ b/skills/continuous-learning-v2/SKILL.md
@@ -1,15 +1,16 @@
 ---
 name: continuous-learning-v2
-description: Instinct-based learning system that observes sessions via hooks, creates atomic instincts with confidence scoring, and evolves them into skills/commands/agents.
+description: Instinct-based learning system that observes sessions via hooks, creates atomic instincts with confidence scoring, and evolves them into skills/commands/agents. v2.1 adds project-scoped instincts to prevent cross-project contamination.
 origin: ECC
-version: 2.0.0
+version: 2.1.0
 ---
-# Continuous Learning v2 - Instinct-Based Architecture
+# Continuous Learning v2.1 - Instinct
 -Based Architecture
 An advanced learning system that turns your Claude Code sessions into reusable knowledge through atomic "instincts" - small learned behaviors with confidence scoring.
-Inspired in part by the Homunculus work from [humanplane](https://github.com/humanplane).
+**v2.1** adds **project-scoped instincts** — React patterns stay in your React project, Python conventions stay in your Python project, and universal patterns (like "always validate input") are shared globally.
 ## When to Activate
@@ -18,8 +19,21 @@ Inspired in part by the Homunculus work from [humanplane](https://github.com/hum
 - Tuning confidence thresholds for learned behaviors
 - Reviewing, exporting, or importing instinct libraries
 - Evolving instincts into full skills, commands, or agents
 - Managing project-scoped vs global instincts
 - Promoting instincts from project to global scope
-## What's New in v2
+## What's New in v2.1
 | Feature | v2.0 | v2.1 |
 |---------|------|------|
 | Storage | Global (~/.claude/homunculus/) | Project-scoped (projects/<hash>/) |
 | Scope | All instincts apply everywhere | Project-scoped + global |
 | Detection | None | git remote URL / repo path |
 | Promotion | N/A | Project → global when seen in 2+ projects |
 | Commands | 4 (status/evolve/export/import) | 6 (+promote/projects) |
 | Cross-project | Contamination risk | Isolated by default |
 ## What's New in v2 (vs v1)
 | Feature | v1 | v2 |
 |---------|----|----|
@@ -27,7 +41,7 @@ Inspired in part by the Homunculus work from [humanplane](https://github.com/hum
 | Analysis | Main context | Background agent (Haiku) |
 | Granularity | Full skills | Atomic "instincts" |
 | Confidence | None | 0.3-0.9 weighted |
-| Evolution | Direct to skill | Instincts → cluster → skill/command/agent |
+| Evolution | Direct to skill | Instincts -> cluster -> skill/command/agent |
 | Sharing | None | Export/import instincts |
 ## The Instinct Model
@@ -41,6 +55,9 @@ trigger: "when writing new functions"
 confidence: 0.7
 domain: "code-style"
 source: "session-observation"
 scope: project
 project_id: "a1b2c3d4e5f6"
 project_name: "my-react-app"
 ---
 # Prefer Functional Style
@@ -54,51 +71,69 @@ Use functional patterns over classes when appropriate.
 ```
 **Properties:**
- **Atomic** — one trigger, one action
+- **Atomic** -- one trigger, one action
- **Confidence-weighted** — 0.3 = tentative, 0.9 = near certain
+- **Confidence-weighted** -- 0.3 = tentative, 0.9 = near certain
- **Domain-tagged** — code-style, testing, git, debugging, workflow, etc.
+- **Domain-tagged** -- code-style, testing, git, debugging, workflow, etc.
- **Evidence-backed** — tracks what observations created it
+- **Evidence-backed** -- tracks what observations created it
 - **Scope-aware** -- `project` (default) or `global`
 ## How It Works
 ```
-Session Activity
+Session Activity (in a git repo)
-      │
+      |
-      │ Hooks capture prompts + tool use (100% reliable)
+      | Hooks capture prompts + tool use (100% reliable)
-      ▼
+      | + detect project context (git remote / repo path)
-┌─────────────────────────────────────────┐
+      v
-│         observations.jsonl              │
+---------------------------------------------+
-│   (prompts, tool calls, outcomes)       │
+|  projects/<project-hash>/observations.jsonl  |
-└─────────────────────────────────────────┘
+|   (prompts, tool calls, outcomes, project)   |
-      │
+---------------------------------------------+
-      │ Observer agent reads (background, Haiku)
+      |
-      ▼
+      | Observer agent reads (background, Haiku)
-┌─────────────────────────────────────────┐
+      v
-│          PATTERN DETECTION              │
+---------------------------------------------+
-│   • User corrections → instinct         │
+|          PATTERN DETECTION                   |
-│   • Error resolutions → instinct        │
+|   * User corrections -> instinct             |
-│   • Repeated workflows → instinct       │
+|   * Error resolutions -> instinct            |
-└─────────────────────────────────────────┘
+|   * Repeated workflows -> instinct           |
-      │
+|   * Scope decision: project or global?       |
-      │ Creates/updates
+---------------------------------------------+
-      ▼
+      |
-┌─────────────────────────────────────────┐
+      | Creates/updates
-│         instincts/personal/             │
+      v
-│   • prefer-functional.md (0.7)          │
+---------------------------------------------+
-│   • always-test-first.md (0.9)          │
+|  projects/<project-hash>/instincts/personal/ |
-│   • use-zod-validation.md (0.6)         │
+|   * prefer-functional.yaml (0.7) [project]   |
-└─────────────────────────────────────────┘
+|   * use-react-hooks.yaml (0.9) [project]     |
-      │
+---------------------------------------------+
-      │ /evolve clusters
+|  instincts/personal/  (GLOBAL)               |
-      ▼
+|   * always-validate-input.yaml (0.85) [global]|
-┌─────────────────────────────────────────┐
+|   * grep-before-edit.yaml (0.6) [global]     |
-│              evolved/                   │
+---------------------------------------------+
-│   • commands/new-feature.md             │
+      |
-│   • skills/testing-workflow.md          │
+      | /evolve clusters + /promote
-│   • agents/refactor-specialist.md       │
+      v
-└─────────────────────────────────────────┘
+---------------------------------------------+
 |  projects/<hash>/evolved/ (project-scoped)   |
 |  evolved/ (global)                           |
 |   * commands/new-feature.md                  |
 |   * skills/testing-workflow.md               |
 |   * agents/refactor-specialist.md            |
 +---------------------------------------------+
 ```
 ## Project Detection
 The system automatically detects your current project:
 1. **`CLAUDE_PROJECT_DIR` env var** (highest priority)
 2. **`git remote get-url origin`** -- hashed to create a portable project ID (same repo on different machines gets the same ID)
 3. **`git rev-parse --show-toplevel`** -- fallback using repo path (machine-specific)
 4. **Global fallback** -- if no project is detected, instincts go to global scope
 Each project gets a 12-character hash ID (e.g., `a1b2c3d4e5f6`). A registry file at `~/.claude/homunculus/projects.json` maps IDs to human-readable names.
 ## Quick Start
 ### 1. Enable Observation Hooks
@@ -114,14 +149,14 @@ Add to your `~/.claude/settings.json`.
      "matcher": "*",
      "hooks": [{
        "type": "command",
-        "command": "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/hooks/observe.sh pre"
+        "command": "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/hooks/observe.sh"
      }]
    }],
    "PostToolUse": [{
      "matcher": "*",
      "hooks": [{
        "type": "command",
-        "command": "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/hooks/observe.sh post"
+        "command": "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/hooks/observe.sh"
      }]
    }]
  }
@@ -137,14 +172,14 @@ Add to your `~/.claude/settings.json`.
      "matcher": "*",
      "hooks": [{
        "type": "command",
-        "command": "~/.claude/skills/continuous-learning-v2/hooks/observe.sh pre"
+        "command": "~/.claude/skills/continuous-learning-v2/hooks/observe.sh"
      }]
    }],
    "PostToolUse": [{
      "matcher": "*",
      "hooks": [{
        "type": "command",
-        "command": "~/.claude/skills/continuous-learning-v2/hooks/observe.sh post"
+        "command": "~/.claude/skills/continuous-learning-v2/hooks/observe.sh"
      }]
    }]
  }
@@ -153,92 +188,124 @@ Add to your `~/.claude/settings.json`.
 ### 2. Initialize Directory Structure
-The Python CLI will create these automatically, but you can also create them manually:
+The system creates directories automatically on first use, but you can also create them manually:
 ```bash
-mkdir -p ~/.claude/homunculus/{instincts/{personal,inherited},evolved/{agents,skills,commands}}
+# Global directories
-touch ~/.claude/homunculus/observations.jsonl
+mkdir -p ~/.claude/homunculus/{instincts/{personal,inherited},evolved/{agents,skills,commands},projects}
 # Project directories are auto-created when the hook first runs in a git repo
 ```
 ### 3. Use the Instinct Commands
 ```bash
-/instinct-status     # Show learned instincts with confidence scores
+/instinct-status     # Show learned instincts (project + global)
 /evolve              # Cluster related instincts into skills/commands
-/instinct-export     # Export instincts for sharing
+/instinct-export     # Export instincts to file
 /instinct-import     # Import instincts from others
 /promote             # Promote project instincts to global scope
 /projects            # List all known projects and their instinct counts
 ```
 ## Commands
 | Command | Description |
 |---------|-------------|
-| `/instinct-status` | Show all learned instincts with confidence |
+| `/instinct-status` | Show all instincts (project-scoped + global) with confidence |
-| `/evolve` | Cluster related instincts into skills/commands |
+| `/evolve` | Cluster related instincts into skills/commands, suggest promotions |
-| `/instinct-export` | Export instincts for sharing |
+| `/instinct-export` | Export instincts (filterable by scope/domain) |
-| `/instinct-import <file>` | Import instincts from others |
+| `/instinct-import <file>` | Import instincts with scope control |
 | `/promote [id]` | Promote project instincts to global scope |
 | `/projects` | List all known projects and their instinct counts |
 ## Configuration
-Edit `config.json`:
+Edit `config.json` to control the background observer:
 ```json
 {
-  "version": "2.0",
+  "version": "2.1",
  "observation": {
    "enabled": true,
    "store_path": "~/.claude/homunculus/observations.jsonl",
    "max_file_size_mb": 10,
    "archive_after_days": 7
  },
  "instincts": {
    "personal_path": "~/.claude/homunculus/instincts/personal/",
    "inherited_path": "~/.claude/homunculus/instincts/inherited/",
    "min_confidence": 0.3,
    "auto_approve_threshold": 0.7,
    "confidence_decay_rate": 0.05
  },
  "observer": {
-    "enabled": true,
+    "enabled": false,
    "model": "haiku",
    "run_interval_minutes": 5,
-    "patterns_to_detect": [
+    "min_observations_to_analyze": 20
      "user_corrections",
      "error_resolutions",
      "repeated_workflows",
      "tool_preferences"
    ]
  },
  "evolution": {
    "cluster_threshold": 3,
    "evolved_path": "~/.claude/homunculus/evolved/"
  }
 }
 ```
 | Key | Default | Description |
 |-----|---------|-------------|
 | `observer.enabled` | `false` | Enable the background observer agent |
 | `observer.run_interval_minutes` | `5` | How often the observer analyzes observations |
 | `observer.min_observations_to_analyze` | `20` | Minimum observations before analysis runs |
 Other behavior (observation capture, instinct thresholds, project scoping, promotion criteria) is configured via code defaults in `instinct-cli.py` and `observe.sh`.
 ## File Structure
 ```
 ~/.claude/homunculus/
-├── identity.json           # Your profile, technical level
+-- identity.json           # Your profile, technical level
-├── observations.jsonl      # Current session observations
+-- projects.json           # Registry: project hash -> name/path/remote
-├── observations.archive/   # Processed observations
+-- observations.jsonl      # Global observations (fallback)
-├── instincts/
+-- instincts/
-│   ├── personal/           # Auto-learned instincts
+|   +-- personal/           # Global auto-learned instincts
-│   └── inherited/          # Imported from others
+|   +-- inherited/          # Global imported instincts
-└── evolved/
+-- evolved/
-    ├── agents/             # Generated specialist agents
+|   +-- agents/             # Global generated agents
-    ├── skills/             # Generated skills
+|   +-- skills/             # Global generated skills
-    └── commands/           # Generated commands
+|   +-- commands/           # Global generated commands
 +-- projects/
    +-- a1b2c3d4e5f6/       # Project hash (from git remote URL)
    |   +-- observations.jsonl
    |   +-- observations.archive/
    |   +-- instincts/
    |   |   +-- personal/   # Project-specific auto-learned
    |   |   +-- inherited/  # Project-specific imported
    |   +-- evolved/
    |       +-- skills/
    |       +-- commands/
    |       +-- agents/
    +-- f6e5d4c3b2a1/       # Another project
        +-- ...
 ```
-## Integration with Skill Creator
+## Scope Decision Guide
-When you use the [Skill Creator GitHub App](https://skill-creator.app), it now generates **both**:
+| Pattern Type | Scope | Examples |
- Traditional SKILL.md files (for backward compatibility)
+|-------------|-------|---------|
- Instinct collections (for v2 learning system)
+| Language/framework conventions | **project** | "Use React hooks", "Follow Django REST patterns" |
 | File structure preferences | **project** | "Tests in __tests__/", "Components in src/components/" |
 | Code style | **project** | "Use functional style", "Prefer dataclasses" |
 | Error handling strategies | **project** | "Use Result type for errors" |
 | Security practices | **global** | "Validate user input", "Sanitize SQL" |
 | General best practices | **global** | "Write tests first", "Always handle errors" |
 | Tool workflow preferences | **global** | "Grep before Edit", "Read before Write" |
 | Git practices | **global** | "Conventional commits", "Small focused commits" |
-Instincts from repo analysis have `source: "repo-analysis"` and include the source repository URL.
+## Instinct Promotion (Project -> Global)
 When the same instinct appears in multiple projects with high confidence, it's a candidate for promotion to global scope.
 **Auto-promotion criteria:**
 - Same instinct ID in 2+ projects
 - Average confidence >= 0.8
 **How to promote:**
 ```bash
 # Promote a specific instinct
 python3 instinct-cli.py promote prefer-explicit-errors
 # Auto-promote all qualifying instincts
 python3 instinct-cli.py promote
 # Preview without changes
 python3 instinct-cli.py promote --dry-run
 ```
 The `/evolve` command also suggests promotion candidates.
 ## Confidence Scoring
@@ -263,7 +330,7 @@ Confidence evolves over time:
 ## Why Hooks vs Skills for Observation?
-> "v1 relied on skills to observe. Skills are probabilistic—they fire ~50-80% of the time based on Claude's judgment."
+> "v1 relied on skills to observe. Skills are probabilistic -- they fire ~50-80% of the time based on Claude's judgment."
 Hooks fire **100% of the time**, deterministically. This means:
 - Every tool call is observed
@@ -272,17 +339,19 @@ Hooks fire **100% of the time**, deterministically. This means:
 ## Backward Compatibility
-v2 is fully compatible with v1:
+v2.1 is fully compatible with v2.0 and v1:
- Existing `~/.claude/skills/learned/` skills still work
+- Existing global instincts in `~/.claude/homunculus/instincts/` still work as global instincts
 - Existing `~/.claude/skills/learned/` skills from v1 still work
 - Stop hook still runs (but now also feeds into v2)
- Gradual migration path: run both in parallel
+- Gradual migration: run both in parallel
 ## Privacy
 - Observations stay **local** on your machine
- Only **instincts** (patterns) can be exported
+- Project-scoped instincts are isolated per project
 - Only **instincts** (patterns) can be exported — not raw observations
 - No actual code or conversation content is shared
- You control what gets exported
+- You control what gets exported and promoted
 ## Related
@@ -292,4 +361,4 @@ v2 is fully compatible with v1:
 ---
-*Instinct-based learning: teaching Claude your patterns, one observation at a time.*
+*Instinct-based learning: teaching Claude your patterns, one project at a time.*
--- a/skills/continuous-learning-v2/agents/observer.md
+++ b/skills/continuous-learning-v2/agents/observer.md
@@ -1,8 +1,7 @@
 ---
 name: observer
-description: Background agent that analyzes session observations to detect patterns and create instincts. Uses Haiku for cost-efficiency.
+description: Background agent that analyzes session observations to detect patterns and create instincts. Uses Haiku for cost-efficiency. v2.1 adds project-scoped instincts.
 model: haiku
 run_mode: background
 ---
 # Observer Agent
@@ -11,20 +10,21 @@ A background agent that analyzes observations from Claude Code sessions to detec
 ## When to Run
- After significant session activity (20+ tool calls)
+- After enough observations accumulate (configurable, default 20)
 - When user runs `/analyze-patterns`
 - On a scheduled interval (configurable, default 5 minutes)
- When triggered by observation hook (SIGUSR1)
+- When triggered on demand via SIGUSR1 to the observer process
 ## Input
-Reads observations from `~/.claude/homunculus/observations.jsonl`:
+Reads observations from the **project-scoped** observations file:
 - Project: `~/.claude/homunculus/projects/<project-hash>/observations.jsonl`
 - Global fallback: `~/.claude/homunculus/observations.jsonl`
 ```jsonl
-{"timestamp":"2025-01-22T10:30:00Z","event":"tool_start","session":"abc123","tool":"Edit","input":"..."}
+{"timestamp":"2025-01-22T10:30:00Z","event":"tool_start","session":"abc123","tool":"Edit","input":"...","project_id":"a1b2c3d4e5f6","project_name":"my-react-app"}
-{"timestamp":"2025-01-22T10:30:01Z","event":"tool_complete","session":"abc123","tool":"Edit","output":"..."}
+{"timestamp":"2025-01-22T10:30:01Z","event":"tool_complete","session":"abc123","tool":"Edit","output":"...","project_id":"a1b2c3d4e5f6","project_name":"my-react-app"}
-{"timestamp":"2025-01-22T10:30:05Z","event":"tool_start","session":"abc123","tool":"Bash","input":"npm test"}
+{"timestamp":"2025-01-22T10:30:05Z","event":"tool_start","session":"abc123","tool":"Bash","input":"npm test","project_id":"a1b2c3d4e5f6","project_name":"my-react-app"}
-{"timestamp":"2025-01-22T10:30:10Z","event":"tool_complete","session":"abc123","tool":"Bash","output":"All tests pass"}
+{"timestamp":"2025-01-22T10:30:10Z","event":"tool_complete","session":"abc123","tool":"Bash","output":"All tests pass","project_id":"a1b2c3d4e5f6","project_name":"my-react-app"}
 ```
 ## Pattern Detection
@@ -65,28 +65,75 @@ When certain tools are consistently preferred:
 ## Output
-Creates/updates instincts in `~/.claude/homunculus/instincts/personal/`:
+Creates/updates instincts in the **project-scoped** instincts directory:
 - Project: `~/.claude/homunculus/projects/<project-hash>/instincts/personal/`
 - Global: `~/.claude/homunculus/instincts/personal/` (for universal patterns)
 ### Project-Scoped Instinct (default)
 ```yaml
 ---
-id: prefer-grep-before-edit
+id: use-react-hooks-pattern
-trigger: "when searching for code to modify"
+trigger: "when creating React components"
 confidence: 0.65
-domain: "workflow"
+domain: "code-style"
 source: "session-observation"
 scope: project
 project_id: "a1b2c3d4e5f6"
 project_name: "my-react-app"
 ---
-# Prefer Grep Before Edit
+# Use React Hooks Pattern
 ## Action
-Always use Grep to find the exact location before using Edit.
+Always use functional components with hooks instead of class components.
 ## Evidence
 - Observed 8 times in session abc123
- Pattern: Grep → Read → Edit sequence
+- Pattern: All new components use useState/useEffect
 - Last observed: 2025-01-22
 ```
 ### Global Instinct (universal patterns)
 ```yaml
 ---
 id: always-validate-user-input
 trigger: "when handling user input"
 confidence: 0.75
 domain: "security"
 source: "session-observation"
 scope: global
 ---
 # Always Validate User Input
 ## Action
 Validate and sanitize all user input before processing.
 ## Evidence
 - Observed across 3 different projects
 - Pattern: User consistently adds input validation
 - Last observed: 2025-01-22
 ```
 ## Scope Decision Guide
 When creating instincts, determine scope based on these heuristics:
 | Pattern Type | Scope | Examples |
 |-------------|-------|---------|
 | Language/framework conventions | **project** | "Use React hooks", "Follow Django REST patterns" |
 | File structure preferences | **project** | "Tests in __tests__/", "Components in src/components/" |
 | Code style | **project** | "Use functional style", "Prefer dataclasses" |
 | Error handling strategies | **project** (usually) | "Use Result type for errors" |
 | Security practices | **global** | "Validate user input", "Sanitize SQL" |
 | General best practices | **global** | "Write tests first", "Always handle errors" |
 | Tool workflow preferences | **global** | "Grep before Edit", "Read before Write" |
 | Git practices | **global** | "Conventional commits", "Small focused commits" |
 **When in doubt, default to `scope: project`** — it's safer to be project-specific and promote later than to contaminate the global space.
 ## Confidence Calculation
 Initial confidence based on observation frequency:
@@ -100,6 +147,15 @@ Confidence adjusts over time:
 - -0.1 for each contradicting observation
 - -0.02 per week without observation (decay)
 ## Instinct Promotion (Project → Global)
 An instinct should be promoted from project-scoped to global when:
 1. The **same pattern** (by id or similar trigger) exists in **2+ different projects**
 2. Each instance has confidence **>= 0.8**
 3. The domain is in the global-friendly list (security, general-best-practices, workflow)
 Promotion is handled by the `instinct-cli.py promote` command or the `/evolve` analysis.
 ## Important Guidelines
 1. **Be Conservative**: Only create instincts for clear patterns (3+ observations)
@@ -107,31 +163,36 @@ Confidence adjusts over time:
 3. **Track Evidence**: Always include what observations led to the instinct
 4. **Respect Privacy**: Never include actual code snippets, only patterns
 5. **Merge Similar**: If a new instinct is similar to existing, update rather than duplicate
 6. **Default to Project Scope**: Unless the pattern is clearly universal, make it project-scoped
 7. **Include Project Context**: Always set `project_id` and `project_name` for project-scoped instincts
 ## Example Analysis Session
 Given observations:
 ```jsonl
-{"event":"tool_start","tool":"Grep","input":"pattern: useState"}
+{"event":"tool_start","tool":"Grep","input":"pattern: useState","project_id":"a1b2c3","project_name":"my-app"}
-{"event":"tool_complete","tool":"Grep","output":"Found in 3 files"}
+{"event":"tool_complete","tool":"Grep","output":"Found in 3 files","project_id":"a1b2c3","project_name":"my-app"}
-{"event":"tool_start","tool":"Read","input":"src/hooks/useAuth.ts"}
+{"event":"tool_start","tool":"Read","input":"src/hooks/useAuth.ts","project_id":"a1b2c3","project_name":"my-app"}
-{"event":"tool_complete","tool":"Read","output":"[file content]"}
+{"event":"tool_complete","tool":"Read","output":"[file content]","project_id":"a1b2c3","project_name":"my-app"}
-{"event":"tool_start","tool":"Edit","input":"src/hooks/useAuth.ts..."}
+{"event":"tool_start","tool":"Edit","input":"src/hooks/useAuth.ts...","project_id":"a1b2c3","project_name":"my-app"}
 ```
 Analysis:
 - Detected workflow: Grep → Read → Edit
 - Frequency: Seen 5 times this session
 - **Scope decision**: This is a general workflow pattern (not project-specific) → **global**
 - Create instinct:
  - trigger: "when modifying code"
  - action: "Search with Grep, confirm with Read, then Edit"
  - confidence: 0.6
  - domain: "workflow"
  - scope: "global"
 ## Integration with Skill Creator
 When instincts are imported from Skill Creator (repo analysis), they have:
 - `source: "repo-analysis"`
 - `source_repo: "https://github.com/..."`
 - `scope: "project"` (since they come from a specific repo)
 These should be treated as team/project conventions with higher initial confidence (0.7+).
--- a/skills/continuous-learning-v2/agents/start-observer.sh
+++ b/skills/continuous-learning-v2/agents/start-observer.sh
@@ -4,26 +4,79 @@
 # Starts the background observer agent that analyzes observations
 # and creates instincts. Uses Haiku model for cost efficiency.
 #
 # v2.1: Project-scoped — detects current project and analyzes
 #       project-specific observations into project-scoped instincts.
 #
 # Usage:
-#   start-observer.sh        # Start observer in background
+#   start-observer.sh        # Start observer for current project (or global)
 #   start-observer.sh stop   # Stop running observer
 #   start-observer.sh status # Check if observer is running
 set -e
-CONFIG_DIR="${HOME}/.claude/homunculus"
+# ─────────────────────────────────────────────
-PID_FILE="${CONFIG_DIR}/.observer.pid"
+# Project detection
-LOG_FILE="${CONFIG_DIR}/observer.log"
+# ─────────────────────────────────────────────
 OBSERVATIONS_FILE="${CONFIG_DIR}/observations.jsonl"
-mkdir -p "$CONFIG_DIR"
+SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
 SKILL_ROOT="$(cd "$SCRIPT_DIR/.." && pwd)"
 # Source shared project detection helper
 # This sets: PROJECT_ID, PROJECT_NAME, PROJECT_ROOT, PROJECT_DIR
 source "${SKILL_ROOT}/scripts/detect-project.sh"
 # ─────────────────────────────────────────────
 # Configuration
 # ─────────────────────────────────────────────
 CONFIG_DIR="${HOME}/.claude/homunculus"
 CONFIG_FILE="${SKILL_ROOT}/config.json"
 # PID file is project-scoped so each project can have its own observer
 PID_FILE="${PROJECT_DIR}/.observer.pid"
 LOG_FILE="${PROJECT_DIR}/observer.log"
 OBSERVATIONS_FILE="${PROJECT_DIR}/observations.jsonl"
 INSTINCTS_DIR="${PROJECT_DIR}/instincts/personal"
 # Read config values from config.json
 OBSERVER_INTERVAL_MINUTES=5
 MIN_OBSERVATIONS=20
 OBSERVER_ENABLED=false
 if [ -f "$CONFIG_FILE" ]; then
  _config=$(CLV2_CONFIG="$CONFIG_FILE" python3 -c "
 import json, os
 with open(os.environ['CLV2_CONFIG']) as f:
    cfg = json.load(f)
 obs = cfg.get('observer', {})
 print(obs.get('run_interval_minutes', 5))
 print(obs.get('min_observations_to_analyze', 20))
 print(str(obs.get('enabled', False)).lower())
 " 2>/dev/null || echo "5
 20
 false")
  _interval=$(echo "$_config" | sed -n '1p')
  _min_obs=$(echo "$_config" | sed -n '2p')
  _enabled=$(echo "$_config" | sed -n '3p')
  if [ "$_interval" -gt 0 ] 2>/dev/null; then
    OBSERVER_INTERVAL_MINUTES="$_interval"
  fi
  if [ "$_min_obs" -gt 0 ] 2>/dev/null; then
    MIN_OBSERVATIONS="$_min_obs"
  fi
  if [ "$_enabled" = "true" ]; then
    OBSERVER_ENABLED=true
  fi
 fi
 OBSERVER_INTERVAL_SECONDS=$((OBSERVER_INTERVAL_MINUTES * 60))
 echo "Project: ${PROJECT_NAME} (${PROJECT_ID})"
 echo "Storage: ${PROJECT_DIR}"
 case "${1:-start}" in
  stop)
    if [ -f "$PID_FILE" ]; then
      pid=$(cat "$PID_FILE")
      if kill -0 "$pid" 2>/dev/null; then
-        echo "Stopping observer (PID: $pid)..."
+        echo "Stopping observer for ${PROJECT_NAME} (PID: $pid)..."
        kill "$pid"
        rm -f "$PID_FILE"
        echo "Observer stopped."
@@ -44,6 +97,9 @@ case "${1:-start}" in
        echo "Observer is running (PID: $pid)"
        echo "Log: $LOG_FILE"
        echo "Observations: $(wc -l < "$OBSERVATIONS_FILE" 2>/dev/null || echo 0) lines"
        # Also show instinct count
        instinct_count=$(find "$INSTINCTS_DIR" -name "*.yaml" 2>/dev/null | wc -l)
        echo "Instincts: $instinct_count"
        exit 0
      else
        echo "Observer not running (stale PID file)"
@@ -57,17 +113,24 @@ case "${1:-start}" in
    ;;
  start)
    # Check if observer is disabled in config
    if [ "$OBSERVER_ENABLED" != "true" ]; then
      echo "Observer is disabled in config.json (observer.enabled: false)."
      echo "Set observer.enabled to true in config.json to enable."
      exit 1
    fi
    # Check if already running
    if [ -f "$PID_FILE" ]; then
      pid=$(cat "$PID_FILE")
      if kill -0 "$pid" 2>/dev/null; then
-        echo "Observer already running (PID: $pid)"
+        echo "Observer already running for ${PROJECT_NAME} (PID: $pid)"
        exit 0
      fi
      rm -f "$PID_FILE"
    fi
-    echo "Starting observer agent..."
+    echo "Starting observer agent for ${PROJECT_NAME}..."
    # The observer loop
    (
@@ -79,18 +142,43 @@ case "${1:-start}" in
          return
        fi
        obs_count=$(wc -l < "$OBSERVATIONS_FILE" 2>/dev/null || echo 0)
-        if [ "$obs_count" -lt 10 ]; then
+        if [ "$obs_count" -lt "$MIN_OBSERVATIONS" ]; then
          return
        fi
-        echo "[$(date)] Analyzing $obs_count observations..." >> "$LOG_FILE"
+        echo "[$(date)] Analyzing $obs_count observations for project ${PROJECT_NAME}..." >> "$LOG_FILE"
        # Use Claude Code with Haiku to analyze observations
-        # This spawns a quick analysis session
+        # The prompt now specifies project-scoped instinct creation
        if command -v claude &> /dev/null; then
          exit_code=0
-          claude --model haiku --max-turns 3 --print \
+          claude --model haiku --print \
-            "Read $OBSERVATIONS_FILE and identify patterns. If you find 3+ occurrences of the same pattern, create an instinct file in $CONFIG_DIR/instincts/personal/ following the format in the observer agent spec. Be conservative - only create instincts for clear patterns." \
+            "Read $OBSERVATIONS_FILE and identify patterns for the project '${PROJECT_NAME}'.
 If you find 3+ occurrences of the same pattern, create an instinct file in $INSTINCTS_DIR/ following this format:
 ---
 id: <kebab-case-id>
 trigger: \"<when this happens>\"
 confidence: <0.3-0.9>
 domain: <code-style|testing|git|debugging|workflow|etc>
 source: session-observation
 scope: project
 project_id: ${PROJECT_ID}
 project_name: ${PROJECT_NAME}
 ---
 # <Title>
 ## Action
 <What to do>
 ## Evidence
 <What observations led to this>
 Be conservative - only create instincts for clear patterns.
 If a pattern seems universal (not project-specific), set scope to 'global' instead of 'project'.
 Examples of global patterns: 'always validate user input', 'prefer explicit error handling'.
 Examples of project patterns: 'use React functional components', 'follow Django REST framework conventions'." \
            >> "$LOG_FILE" 2>&1 || exit_code=$?
          if [ "$exit_code" -ne 0 ]; then
            echo "[$(date)] Claude analysis failed (exit $exit_code)" >> "$LOG_FILE"
@@ -101,10 +189,9 @@ case "${1:-start}" in
        # Archive processed observations
        if [ -f "$OBSERVATIONS_FILE" ]; then
-          archive_dir="${CONFIG_DIR}/observations.archive"
+          archive_dir="${PROJECT_DIR}/observations.archive"
          mkdir -p "$archive_dir"
-          mv "$OBSERVATIONS_FILE" "$archive_dir/processed-$(date +%Y%m%d-%H%M%S).jsonl" 2>/dev/null || true
+          mv "$OBSERVATIONS_FILE" "$archive_dir/processed-$(date +%Y%m%d-%H%M%S)-$$.jsonl" 2>/dev/null || true
          touch "$OBSERVATIONS_FILE"
        fi
      }
@@ -112,11 +199,11 @@ case "${1:-start}" in
      trap 'analyze_observations' USR1
      echo "$$" > "$PID_FILE"
-      echo "[$(date)] Observer started (PID: $$)" >> "$LOG_FILE"
+      echo "[$(date)] Observer started for ${PROJECT_NAME} (PID: $$)" >> "$LOG_FILE"
      while true; do
-        # Check every 5 minutes
+        # Check at configured interval (default: 5 minutes)
-        sleep 300
+        sleep "$OBSERVER_INTERVAL_SECONDS"
        analyze_observations
      done
--- a/skills/continuous-learning-v2/config.json
+++ b/skills/continuous-learning-v2/config.json
@@ -1,41 +1,8 @@
 {
-  "version": "2.0",
+  "version": "2.1",
  "observation": {
    "enabled": true,
    "store_path": "~/.claude/homunculus/observations.jsonl",
    "max_file_size_mb": 10,
    "archive_after_days": 7,
    "capture_tools": ["Edit", "Write", "Bash", "Read", "Grep", "Glob"],
    "ignore_tools": ["TodoWrite"]
  },
  "instincts": {
    "personal_path": "~/.claude/homunculus/instincts/personal/",
    "inherited_path": "~/.claude/homunculus/instincts/inherited/",
    "min_confidence": 0.3,
    "auto_approve_threshold": 0.7,
    "confidence_decay_rate": 0.02,
    "max_instincts": 100
  },
  "observer": {
    "enabled": false,
    "model": "haiku",
    "run_interval_minutes": 5,
-    "min_observations_to_analyze": 20,
+    "min_observations_to_analyze": 20
    "patterns_to_detect": [
      "user_corrections",
      "error_resolutions",
      "repeated_workflows",
      "tool_preferences",
      "file_patterns"
    ]
  },
  "evolution": {
    "cluster_threshold": 3,
    "evolved_path": "~/.claude/homunculus/evolved/",
    "auto_evolve": false
  },
  "integration": {
    "skill_creator_api": "https://skill-creator.app/api",
    "backward_compatible_v1": true
  }
 }
--- a/skills/continuous-learning-v2/hooks/observe.sh
+++ b/skills/continuous-learning-v2/hooks/observe.sh
@@ -4,52 +4,20 @@
 # Captures tool use events for pattern analysis.
 # Claude Code passes hook data via stdin as JSON.
 #
-# Hook config (in ~/.claude/settings.json):
+# v2.1: Project-scoped observations — detects current project context
 #       and writes observations to project-specific directory.
 #
-# If installed as a plugin, use ${CLAUDE_PLUGIN_ROOT}:
+# Registered via plugin hooks/hooks.json (auto-loaded when plugin is enabled).
-# {
+# Can also be registered manually in ~/.claude/settings.json.
 #   "hooks": {
 #     "PreToolUse": [{
 #       "matcher": "*",
 #       "hooks": [{ "type": "command", "command": "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/hooks/observe.sh pre" }]
 #     }],
 #     "PostToolUse": [{
 #       "matcher": "*",
 #       "hooks": [{ "type": "command", "command": "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/hooks/observe.sh post" }]
 #     }]
 #   }
 # }
 #
 # If installed manually to ~/.claude/skills:
 # {
 #   "hooks": {
 #     "PreToolUse": [{
 #       "matcher": "*",
 #       "hooks": [{ "type": "command", "command": "~/.claude/skills/continuous-learning-v2/hooks/observe.sh pre" }]
 #     }],
 #     "PostToolUse": [{
 #       "matcher": "*",
 #       "hooks": [{ "type": "command", "command": "~/.claude/skills/continuous-learning-v2/hooks/observe.sh post" }]
 #     }]
 #   }
 # }
 set -e
 # Hook phase from CLI argument: "pre" (PreToolUse) or "post" (PostToolUse)
 HOOK_PHASE="${1:-post}"
-CONFIG_DIR="${HOME}/.claude/homunculus"
+# ─────────────────────────────────────────────
-OBSERVATIONS_FILE="${CONFIG_DIR}/observations.jsonl"
+# Read stdin first (before project detection)
-MAX_FILE_SIZE_MB=10
+# ─────────────────────────────────────────────
 # Ensure directory exists
 mkdir -p "$CONFIG_DIR"
 # Skip if disabled
 if [ -f "$CONFIG_DIR/disabled" ]; then
  exit 0
 fi
 # Read JSON from stdin (Claude Code hook format)
 INPUT_JSON=$(cat)
@@ -59,6 +27,51 @@ if [ -z "$INPUT_JSON" ]; then
  exit 0
 fi
 # ─────────────────────────────────────────────
 # Extract cwd from stdin for project detection
 # ─────────────────────────────────────────────
 # Extract cwd from the hook JSON to use for project detection.
 # This avoids spawning a separate git subprocess when cwd is available.
 STDIN_CWD=$(echo "$INPUT_JSON" | python3 -c '
 import json, sys
 try:
    data = json.load(sys.stdin)
    cwd = data.get("cwd", "")
    print(cwd)
 except(KeyError, TypeError, ValueError):
    print("")
 ' 2>/dev/null || echo "")
 # If cwd was provided in stdin, use it for project detection
 if [ -n "$STDIN_CWD" ] && [ -d "$STDIN_CWD" ]; then
  export CLAUDE_PROJECT_DIR="$STDIN_CWD"
 fi
 # ─────────────────────────────────────────────
 # Project detection
 # ─────────────────────────────────────────────
 SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
 SKILL_ROOT="$(cd "$SCRIPT_DIR/.." && pwd)"
 # Source shared project detection helper
 # This sets: PROJECT_ID, PROJECT_NAME, PROJECT_ROOT, PROJECT_DIR
 source "${SKILL_ROOT}/scripts/detect-project.sh"
 # ─────────────────────────────────────────────
 # Configuration
 # ─────────────────────────────────────────────
 CONFIG_DIR="${HOME}/.claude/homunculus"
 OBSERVATIONS_FILE="${PROJECT_DIR}/observations.jsonl"
 MAX_FILE_SIZE_MB=10
 # Skip if disabled
 if [ -f "$CONFIG_DIR/disabled" ]; then
  exit 0
 fi
 # Parse using python via stdin pipe (safe for all JSON payloads)
 # Pass HOOK_PHASE via env var since Claude Code does not include hook type in stdin JSON
 PARSED=$(echo "$INPUT_JSON" | HOOK_PHASE="$HOOK_PHASE" python3 -c '
@@ -80,6 +93,8 @@ try:
    tool_input = data.get("tool_input", data.get("input", {}))
    tool_output = data.get("tool_output", data.get("output", ""))
    session_id = data.get("session_id", "unknown")
    tool_use_id = data.get("tool_use_id", "")
    cwd = data.get("cwd", "")
    # Truncate large inputs/outputs
    if isinstance(tool_input, dict):
@@ -88,24 +103,26 @@ try:
        tool_input_str = str(tool_input)[:5000]
    if isinstance(tool_output, dict):
-        tool_output_str = json.dumps(tool_output)[:5000]
+        tool_response_str = json.dumps(tool_output)[:5000]
    else:
-        tool_output_str = str(tool_output)[:5000]
+        tool_response_str = str(tool_output)[:5000]
    print(json.dumps({
        "parsed": True,
        "event": event,
        "tool": tool_name,
        "input": tool_input_str if event == "tool_start" else None,
-        "output": tool_output_str if event == "tool_complete" else None,
+        "output": tool_response_str if event == "tool_complete" else None,
-        "session": session_id
+        "session": session_id,
        "tool_use_id": tool_use_id,
        "cwd": cwd
    }))
 except Exception as e:
    print(json.dumps({"parsed": False, "error": str(e)}))
 ')
 # Check if parsing succeeded
-PARSED_OK=$(echo "$PARSED" | python3 -c "import json,sys; print(json.load(sys.stdin).get('parsed', False))")
+PARSED_OK=$(echo "$PARSED" | python3 -c "import json,sys; print(json.load(sys.stdin).get('parsed', False))" 2>/dev/null || echo "False")
 if [ "$PARSED_OK" != "True" ]; then
  # Fallback: log raw input for debugging
@@ -119,20 +136,23 @@ print(json.dumps({'timestamp': os.environ['TIMESTAMP'], 'event': 'parse_error',
  exit 0
 fi
-# Archive if file too large
+# Archive if file too large (atomic: rename with unique suffix to avoid race)
 if [ -f "$OBSERVATIONS_FILE" ]; then
  file_size_mb=$(du -m "$OBSERVATIONS_FILE" 2>/dev/null | cut -f1)
  if [ "${file_size_mb:-0}" -ge "$MAX_FILE_SIZE_MB" ]; then
-    archive_dir="${CONFIG_DIR}/observations.archive"
+    archive_dir="${PROJECT_DIR}/observations.archive"
    mkdir -p "$archive_dir"
-    mv "$OBSERVATIONS_FILE" "$archive_dir/observations-$(date +%Y%m%d-%H%M%S).jsonl"
+    mv "$OBSERVATIONS_FILE" "$archive_dir/observations-$(date +%Y%m%d-%H%M%S)-$$.jsonl" 2>/dev/null || true
  fi
 fi
-# Build and write observation
+# Build and write observation (now includes project context)
 timestamp=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
 export PROJECT_ID_ENV="$PROJECT_ID"
 export PROJECT_NAME_ENV="$PROJECT_NAME"
 export TIMESTAMP="$timestamp"
 echo "$PARSED" | python3 -c "
 import json, sys, os
@@ -141,10 +161,12 @@ observation = {
    'timestamp': os.environ['TIMESTAMP'],
    'event': parsed['event'],
    'tool': parsed['tool'],
-    'session': parsed['session']
+    'session': parsed['session'],
    'project_id': os.environ.get('PROJECT_ID_ENV', 'global'),
    'project_name': os.environ.get('PROJECT_NAME_ENV', 'global')
 }
-if parsed['input'] is not None:
+if parsed['input']:
    observation['input'] = parsed['input']
 if parsed['output'] is not None:
    observation['output'] = parsed['output']
@@ -152,13 +174,14 @@ if parsed['output'] is not None:
 print(json.dumps(observation))
 " >> "$OBSERVATIONS_FILE"
-# Signal observer if running
+# Signal observer if running (check both project-scoped and global observer)
-OBSERVER_PID_FILE="${CONFIG_DIR}/.observer.pid"
+for pid_file in "${PROJECT_DIR}/.observer.pid" "${CONFIG_DIR}/.observer.pid"; do
-if [ -f "$OBSERVER_PID_FILE" ]; then
+  if [ -f "$pid_file" ]; then
-  observer_pid=$(cat "$OBSERVER_PID_FILE")
+    observer_pid=$(cat "$pid_file")
-  if kill -0 "$observer_pid" 2>/dev/null; then
+    if kill -0 "$observer_pid" 2>/dev/null; then
-    kill -USR1 "$observer_pid" 2>/dev/null || true
+      kill -USR1 "$observer_pid" 2>/dev/null || true
    fi
  fi
-fi
+done
 exit 0
--- a/skills/continuous-learning-v2/scripts/detect-project.sh
+++ b/skills/continuous-learning-v2/scripts/detect-project.sh
@@ -0,0 +1,141 @@
 #!/bin/bash
 # Continuous Learning v2 - Project Detection Helper
 #
 # Shared logic for detecting current project context.
 # Sourced by observe.sh and start-observer.sh.
 #
 # Exports:
 #   _CLV2_PROJECT_ID     - Short hash identifying the project (or "global")
 #   _CLV2_PROJECT_NAME   - Human-readable project name
 #   _CLV2_PROJECT_ROOT   - Absolute path to project root
 #   _CLV2_PROJECT_DIR    - Project-scoped storage directory under homunculus
 #
 # Also sets unprefixed convenience aliases:
 #   PROJECT_ID, PROJECT_NAME, PROJECT_ROOT, PROJECT_DIR
 #
 # Detection priority:
 #   1. CLAUDE_PROJECT_DIR env var (if set)
 #   2. git remote URL (hashed for uniqueness across machines)
 #   3. git repo root path (fallback, machine-specific)
 #   4. "global" (no project context detected)
 _CLV2_HOMUNCULUS_DIR="${HOME}/.claude/homunculus"
 _CLV2_PROJECTS_DIR="${_CLV2_HOMUNCULUS_DIR}/projects"
 _CLV2_REGISTRY_FILE="${_CLV2_HOMUNCULUS_DIR}/projects.json"
 _clv2_detect_project() {
  local project_root=""
  local project_name=""
  local project_id=""
  local source_hint=""
  # 1. Try CLAUDE_PROJECT_DIR env var
  if [ -n "$CLAUDE_PROJECT_DIR" ] && [ -d "$CLAUDE_PROJECT_DIR" ]; then
    project_root="$CLAUDE_PROJECT_DIR"
    source_hint="env"
  fi
  # 2. Try git repo root from CWD (only if git is available)
  if [ -z "$project_root" ] && command -v git &>/dev/null; then
    project_root=$(git rev-parse --show-toplevel 2>/dev/null || true)
    if [ -n "$project_root" ]; then
      source_hint="git"
    fi
  fi
  # 3. No project detected — fall back to global
  if [ -z "$project_root" ]; then
    _CLV2_PROJECT_ID="global"
    _CLV2_PROJECT_NAME="global"
    _CLV2_PROJECT_ROOT=""
    _CLV2_PROJECT_DIR="${_CLV2_HOMUNCULUS_DIR}"
    return 0
  fi
  # Derive project name from directory basename
  project_name=$(basename "$project_root")
  # Derive project ID: prefer git remote URL hash (portable across machines),
  # fall back to path hash (machine-specific but still useful)
  local remote_url=""
  if command -v git &>/dev/null; then
    if [ "$source_hint" = "git" ] || [ -d "${project_root}/.git" ]; then
      remote_url=$(git -C "$project_root" remote get-url origin 2>/dev/null || true)
    fi
  fi
  local hash_input="${remote_url:-$project_root}"
  # Use SHA256 via python3 (portable across macOS/Linux, no shasum/sha256sum divergence)
  project_id=$(printf '%s' "$hash_input" | python3 -c "import sys,hashlib; print(hashlib.sha256(sys.stdin.buffer.read()).hexdigest()[:12])" 2>/dev/null)
  # Fallback if python3 failed
  if [ -z "$project_id" ]; then
    project_id=$(printf '%s' "$hash_input" | shasum -a 256 2>/dev/null | cut -c1-12 || \
                 printf '%s' "$hash_input" | sha256sum 2>/dev/null | cut -c1-12 || \
                 echo "fallback")
  fi
  # Export results
  _CLV2_PROJECT_ID="$project_id"
  _CLV2_PROJECT_NAME="$project_name"
  _CLV2_PROJECT_ROOT="$project_root"
  _CLV2_PROJECT_DIR="${_CLV2_PROJECTS_DIR}/${project_id}"
  # Ensure project directory structure exists
  mkdir -p "${_CLV2_PROJECT_DIR}/instincts/personal"
  mkdir -p "${_CLV2_PROJECT_DIR}/instincts/inherited"
  mkdir -p "${_CLV2_PROJECT_DIR}/observations.archive"
  mkdir -p "${_CLV2_PROJECT_DIR}/evolved/skills"
  mkdir -p "${_CLV2_PROJECT_DIR}/evolved/commands"
  mkdir -p "${_CLV2_PROJECT_DIR}/evolved/agents"
  # Update project registry (lightweight JSON mapping)
  _clv2_update_project_registry "$project_id" "$project_name" "$project_root" "$remote_url"
 }
 _clv2_update_project_registry() {
  local pid="$1"
  local pname="$2"
  local proot="$3"
  local premote="$4"
  mkdir -p "$(dirname "$_CLV2_REGISTRY_FILE")"
  # Pass values via env vars to avoid shell→python injection.
  # python3 reads them with os.environ, which is safe for any string content.
  _CLV2_REG_PID="$pid" \
  _CLV2_REG_PNAME="$pname" \
  _CLV2_REG_PROOT="$proot" \
  _CLV2_REG_PREMOTE="$premote" \
  _CLV2_REG_FILE="$_CLV2_REGISTRY_FILE" \
  python3 -c '
 import json, os
 from datetime import datetime, timezone
 registry_path = os.environ["_CLV2_REG_FILE"]
 try:
    with open(registry_path) as f:
        registry = json.load(f)
 except (FileNotFoundError, json.JSONDecodeError):
    registry = {}
 registry[os.environ["_CLV2_REG_PID"]] = {
    "name": os.environ["_CLV2_REG_PNAME"],
    "root": os.environ["_CLV2_REG_PROOT"],
    "remote": os.environ["_CLV2_REG_PREMOTE"],
    "last_seen": datetime.now(timezone.utc).isoformat().replace("+00:00", "Z")
 }
 with open(registry_path, "w") as f:
    json.dump(registry, f, indent=2)
 ' 2>/dev/null || true
 }
 # Auto-detect on source
 _clv2_detect_project
 # Convenience aliases for callers (short names pointing to prefixed vars)
 PROJECT_ID="$_CLV2_PROJECT_ID"
 PROJECT_NAME="$_CLV2_PROJECT_NAME"
 PROJECT_ROOT="$_CLV2_PROJECT_ROOT"
 PROJECT_DIR="$_CLV2_PROJECT_DIR"
--- a/skills/continuous-learning-v2/scripts/instinct-cli.py
+++ b/skills/continuous-learning-v2/scripts/instinct-cli.py
--- a/skills/continuous-learning-v2/scripts/test_parse_instinct.py
+++ b/skills/continuous-learning-v2/scripts/test_parse_instinct.py
@@ -1,7 +1,26 @@
-"""Tests for parse_instinct_file() — verifies content after frontmatter is preserved."""
+"""Tests for continuous-learning-v2 instinct-cli.py
 Covers:
  - parse_instinct_file() — content preservation, edge cases
  - _validate_file_path() — path traversal blocking
  - detect_project() — project detection with mocked git/env
  - load_all_instincts() — loading from project + global dirs, dedup
  - _load_instincts_from_dir() — directory scanning
  - cmd_projects() — listing projects from registry
  - cmd_status() — status display
  - _promote_specific() — single instinct promotion
  - _promote_auto() — auto-promotion across projects
 """
 import importlib.util
 import json
 import os
 import sys
 from pathlib import Path
 from types import SimpleNamespace
 from unittest import mock
 import pytest
 # Load instinct-cli.py (hyphenated filename requires importlib)
 _spec = importlib.util.spec_from_file_location(
@@ -10,8 +29,125 @@ _spec = importlib.util.spec_from_file_location(
 )
 _mod = importlib.util.module_from_spec(_spec)
 _spec.loader.exec_module(_mod)
 parse_instinct_file = _mod.parse_instinct_file
 parse_instinct_file = _mod.parse_instinct_file
 _validate_file_path = _mod._validate_file_path
 detect_project = _mod.detect_project
 load_all_instincts = _mod.load_all_instincts
 load_project_only_instincts = _mod.load_project_only_instincts
 _load_instincts_from_dir = _mod._load_instincts_from_dir
 cmd_status = _mod.cmd_status
 cmd_projects = _mod.cmd_projects
 _promote_specific = _mod._promote_specific
 _promote_auto = _mod._promote_auto
 _find_cross_project_instincts = _mod._find_cross_project_instincts
 load_registry = _mod.load_registry
 _validate_instinct_id = _mod._validate_instinct_id
 _update_registry = _mod._update_registry
 # ─────────────────────────────────────────────
 # Fixtures
 # ─────────────────────────────────────────────
 SAMPLE_INSTINCT_YAML = """\
 ---
 id: test-instinct
 trigger: "when writing tests"
 confidence: 0.8
 domain: testing
 scope: project
 ---
 ## Action
 Always write tests first.
 ## Evidence
 TDD leads to better design.
 """
 SAMPLE_GLOBAL_INSTINCT_YAML = """\
 ---
 id: global-instinct
 trigger: "always"
 confidence: 0.9
 domain: security
 scope: global
 ---
 ## Action
 Validate all user input.
 """
@pytest.fixture
 def project_tree(tmp_path):
    """Create a realistic project directory tree for testing."""
    homunculus = tmp_path / ".claude" / "homunculus"
    projects_dir = homunculus / "projects"
    global_personal = homunculus / "instincts" / "personal"
    global_inherited = homunculus / "instincts" / "inherited"
    global_evolved = homunculus / "evolved"
    for d in [
        global_personal, global_inherited,
        global_evolved / "skills", global_evolved / "commands", global_evolved / "agents",
        projects_dir,
    ]:
        d.mkdir(parents=True, exist_ok=True)
    return {
        "root": tmp_path,
        "homunculus": homunculus,
        "projects_dir": projects_dir,
        "global_personal": global_personal,
        "global_inherited": global_inherited,
        "global_evolved": global_evolved,
        "registry_file": homunculus / "projects.json",
    }
@pytest.fixture
 def patch_globals(project_tree, monkeypatch):
    """Patch module-level globals to use tmp_path-based directories."""
    monkeypatch.setattr(_mod, "HOMUNCULUS_DIR", project_tree["homunculus"])
    monkeypatch.setattr(_mod, "PROJECTS_DIR", project_tree["projects_dir"])
    monkeypatch.setattr(_mod, "REGISTRY_FILE", project_tree["registry_file"])
    monkeypatch.setattr(_mod, "GLOBAL_PERSONAL_DIR", project_tree["global_personal"])
    monkeypatch.setattr(_mod, "GLOBAL_INHERITED_DIR", project_tree["global_inherited"])
    monkeypatch.setattr(_mod, "GLOBAL_EVOLVED_DIR", project_tree["global_evolved"])
    monkeypatch.setattr(_mod, "GLOBAL_OBSERVATIONS_FILE", project_tree["homunculus"] / "observations.jsonl")
    return project_tree
 def _make_project(tree, pid="abc123", pname="test-project"):
    """Create project directory structure and return a project dict."""
    project_dir = tree["projects_dir"] / pid
    personal_dir = project_dir / "instincts" / "personal"
    inherited_dir = project_dir / "instincts" / "inherited"
    for d in [personal_dir, inherited_dir,
              project_dir / "evolved" / "skills",
              project_dir / "evolved" / "commands",
              project_dir / "evolved" / "agents",
              project_dir / "observations.archive"]:
        d.mkdir(parents=True, exist_ok=True)
    return {
        "id": pid,
        "name": pname,
        "root": str(tree["root"] / "fake-repo"),
        "remote": "https://github.com/test/test-project.git",
        "project_dir": project_dir,
        "instincts_personal": personal_dir,
        "instincts_inherited": inherited_dir,
        "evolved_dir": project_dir / "evolved",
        "observations_file": project_dir / "observations.jsonl",
    }
 # ─────────────────────────────────────────────
 # parse_instinct_file tests
 # ─────────────────────────────────────────────
 MULTI_SECTION = """\
 ---
@@ -80,3 +216,741 @@ domain: general
    result = parse_instinct_file(content)
    assert len(result) == 1
    assert result[0]["content"] == ""
 def test_parse_no_id_skipped():
    """Instincts without an 'id' field should be silently dropped."""
    content = """\
 ---
 trigger: "when doing nothing"
 confidence: 0.5
 ---
 No id here.
 """
    result = parse_instinct_file(content)
    assert len(result) == 0
 def test_parse_confidence_is_float():
    content = """\
 ---
 id: float-check
 trigger: "when parsing"
 confidence: 0.42
 domain: general
 ---
 Body.
 """
    result = parse_instinct_file(content)
    assert isinstance(result[0]["confidence"], float)
    assert result[0]["confidence"] == pytest.approx(0.42)
 def test_parse_trigger_strips_quotes():
    content = """\
 ---
 id: quote-check
 trigger: "when quoting"
 confidence: 0.5
 domain: general
 ---
 Body.
 """
    result = parse_instinct_file(content)
    assert result[0]["trigger"] == "when quoting"
 def test_parse_empty_string():
    result = parse_instinct_file("")
    assert result == []
 def test_parse_garbage_input():
    result = parse_instinct_file("this is not yaml at all\nno frontmatter here")
    assert result == []
 # ─────────────────────────────────────────────
 # _validate_file_path tests
 # ─────────────────────────────────────────────
 def test_validate_normal_path(tmp_path):
    test_file = tmp_path / "test.yaml"
    test_file.write_text("hello")
    result = _validate_file_path(str(test_file), must_exist=True)
    assert result == test_file.resolve()
 def test_validate_rejects_etc():
    with pytest.raises(ValueError, match="system directory"):
        _validate_file_path("/etc/passwd")
 def test_validate_rejects_var_log():
    with pytest.raises(ValueError, match="system directory"):
        _validate_file_path("/var/log/syslog")
 def test_validate_rejects_usr():
    with pytest.raises(ValueError, match="system directory"):
        _validate_file_path("/usr/local/bin/foo")
 def test_validate_rejects_proc():
    with pytest.raises(ValueError, match="system directory"):
        _validate_file_path("/proc/self/status")
 def test_validate_must_exist_fails(tmp_path):
    with pytest.raises(ValueError, match="does not exist"):
        _validate_file_path(str(tmp_path / "nonexistent.yaml"), must_exist=True)
 def test_validate_home_expansion(tmp_path):
    """Tilde expansion should work."""
    result = _validate_file_path("~/test.yaml")
    assert str(result).startswith(str(Path.home()))
 def test_validate_relative_path(tmp_path, monkeypatch):
    """Relative paths should be resolved."""
    monkeypatch.chdir(tmp_path)
    test_file = tmp_path / "rel.yaml"
    test_file.write_text("content")
    result = _validate_file_path("rel.yaml", must_exist=True)
    assert result == test_file.resolve()
 # ─────────────────────────────────────────────
 # detect_project tests
 # ─────────────────────────────────────────────
 def test_detect_project_global_fallback(patch_globals, monkeypatch):
    """When no git and no env var, should return global project."""
    monkeypatch.delenv("CLAUDE_PROJECT_DIR", raising=False)
    # Mock subprocess.run to simulate git not available
    def mock_run(*args, **kwargs):
        raise FileNotFoundError("git not found")
    monkeypatch.setattr("subprocess.run", mock_run)
    project = detect_project()
    assert project["id"] == "global"
    assert project["name"] == "global"
 def test_detect_project_from_env(patch_globals, monkeypatch, tmp_path):
    """CLAUDE_PROJECT_DIR env var should be used as project root."""
    fake_repo = tmp_path / "my-repo"
    fake_repo.mkdir()
    monkeypatch.setenv("CLAUDE_PROJECT_DIR", str(fake_repo))
    # Mock git remote to return a URL
    def mock_run(cmd, **kwargs):
        if "rev-parse" in cmd:
            return SimpleNamespace(returncode=0, stdout=str(fake_repo) + "\n", stderr="")
        if "get-url" in cmd:
            return SimpleNamespace(returncode=0, stdout="https://github.com/test/my-repo.git\n", stderr="")
        return SimpleNamespace(returncode=1, stdout="", stderr="")
    monkeypatch.setattr("subprocess.run", mock_run)
    project = detect_project()
    assert project["id"] != "global"
    assert project["name"] == "my-repo"
 def test_detect_project_git_timeout(patch_globals, monkeypatch):
    """Git timeout should fall through to global."""
    monkeypatch.delenv("CLAUDE_PROJECT_DIR", raising=False)
    import subprocess as sp
    def mock_run(cmd, **kwargs):
        raise sp.TimeoutExpired(cmd, 5)
    monkeypatch.setattr("subprocess.run", mock_run)
    project = detect_project()
    assert project["id"] == "global"
 def test_detect_project_creates_directories(patch_globals, monkeypatch, tmp_path):
    """detect_project should create the project dir structure."""
    fake_repo = tmp_path / "structured-repo"
    fake_repo.mkdir()
    monkeypatch.setenv("CLAUDE_PROJECT_DIR", str(fake_repo))
    def mock_run(cmd, **kwargs):
        if "rev-parse" in cmd:
            return SimpleNamespace(returncode=0, stdout=str(fake_repo) + "\n", stderr="")
        if "get-url" in cmd:
            return SimpleNamespace(returncode=1, stdout="", stderr="no remote")
        return SimpleNamespace(returncode=1, stdout="", stderr="")
    monkeypatch.setattr("subprocess.run", mock_run)
    project = detect_project()
    assert project["instincts_personal"].exists()
    assert project["instincts_inherited"].exists()
    assert (project["evolved_dir"] / "skills").exists()
 # ─────────────────────────────────────────────
 # _load_instincts_from_dir tests
 # ─────────────────────────────────────────────
 def test_load_from_empty_dir(tmp_path):
    result = _load_instincts_from_dir(tmp_path, "personal", "project")
    assert result == []
 def test_load_from_nonexistent_dir(tmp_path):
    result = _load_instincts_from_dir(tmp_path / "does-not-exist", "personal", "project")
    assert result == []
 def test_load_annotates_metadata(tmp_path):
    """Loaded instincts should have _source_file, _source_type, _scope_label."""
    yaml_file = tmp_path / "test.yaml"
    yaml_file.write_text(SAMPLE_INSTINCT_YAML)
    result = _load_instincts_from_dir(tmp_path, "personal", "project")
    assert len(result) == 1
    assert result[0]["_source_file"] == str(yaml_file)
    assert result[0]["_source_type"] == "personal"
    assert result[0]["_scope_label"] == "project"
 def test_load_defaults_scope_from_label(tmp_path):
    """If an instinct has no 'scope' in frontmatter, it should default to scope_label."""
    no_scope_yaml = """\
 ---
 id: no-scope
 trigger: "test"
 confidence: 0.5
 domain: general
 ---
 Body.
 """
    (tmp_path / "no-scope.yaml").write_text(no_scope_yaml)
    result = _load_instincts_from_dir(tmp_path, "inherited", "global")
    assert result[0]["scope"] == "global"
 def test_load_preserves_explicit_scope(tmp_path):
    """If frontmatter has explicit scope, it should be preserved."""
    yaml_file = tmp_path / "test.yaml"
    yaml_file.write_text(SAMPLE_INSTINCT_YAML)
    result = _load_instincts_from_dir(tmp_path, "personal", "global")
    # Frontmatter says scope: project, scope_label is global
    # The explicit scope should be preserved (not overwritten)
    assert result[0]["scope"] == "project"
 def test_load_handles_corrupt_file(tmp_path, capsys):
    """Corrupt YAML files should be warned about but not crash."""
    # A file that will cause parse_instinct_file to return empty
    (tmp_path / "good.yaml").write_text(SAMPLE_INSTINCT_YAML)
    (tmp_path / "bad.yaml").write_text("not yaml\nno frontmatter")
    result = _load_instincts_from_dir(tmp_path, "personal", "project")
    # bad.yaml has no valid instincts (no id), so only good.yaml contributes
    assert len(result) == 1
    assert result[0]["id"] == "test-instinct"
 def test_load_supports_yml_extension(tmp_path):
    yml_file = tmp_path / "test.yml"
    yml_file.write_text(SAMPLE_INSTINCT_YAML)
    result = _load_instincts_from_dir(tmp_path, "personal", "project")
    ids = {i["id"] for i in result}
    assert "test-instinct" in ids
 def test_load_supports_md_extension(tmp_path):
    md_file = tmp_path / "legacy-instinct.md"
    md_file.write_text(SAMPLE_INSTINCT_YAML)
    result = _load_instincts_from_dir(tmp_path, "personal", "project")
    ids = {i["id"] for i in result}
    assert "test-instinct" in ids
 # ─────────────────────────────────────────────
 # load_all_instincts tests
 # ─────────────────────────────────────────────
 def test_load_all_project_and_global(patch_globals):
    """Should load from both project and global directories."""
    tree = patch_globals
    project = _make_project(tree)
    # Write a project instinct
    (project["instincts_personal"] / "proj.yaml").write_text(SAMPLE_INSTINCT_YAML)
    # Write a global instinct
    (tree["global_personal"] / "glob.yaml").write_text(SAMPLE_GLOBAL_INSTINCT_YAML)
    result = load_all_instincts(project)
    ids = {i["id"] for i in result}
    assert "test-instinct" in ids
    assert "global-instinct" in ids
 def test_load_all_project_overrides_global(patch_globals):
    """When project and global have same ID, project wins."""
    tree = patch_globals
    project = _make_project(tree)
    # Same ID but different confidence
    proj_yaml = SAMPLE_INSTINCT_YAML.replace("id: test-instinct", "id: shared-id")
    proj_yaml = proj_yaml.replace("confidence: 0.8", "confidence: 0.9")
    glob_yaml = SAMPLE_GLOBAL_INSTINCT_YAML.replace("id: global-instinct", "id: shared-id")
    glob_yaml = glob_yaml.replace("confidence: 0.9", "confidence: 0.3")
    (project["instincts_personal"] / "shared.yaml").write_text(proj_yaml)
    (tree["global_personal"] / "shared.yaml").write_text(glob_yaml)
    result = load_all_instincts(project)
    shared = [i for i in result if i["id"] == "shared-id"]
    assert len(shared) == 1
    assert shared[0]["_scope_label"] == "project"
    assert shared[0]["confidence"] == 0.9
 def test_load_all_global_only(patch_globals):
    """Global project should only load global instincts."""
    tree = patch_globals
    (tree["global_personal"] / "glob.yaml").write_text(SAMPLE_GLOBAL_INSTINCT_YAML)
    global_project = {
        "id": "global",
        "name": "global",
        "root": "",
        "project_dir": tree["homunculus"],
        "instincts_personal": tree["global_personal"],
        "instincts_inherited": tree["global_inherited"],
        "evolved_dir": tree["global_evolved"],
        "observations_file": tree["homunculus"] / "observations.jsonl",
    }
    result = load_all_instincts(global_project)
    assert len(result) == 1
    assert result[0]["id"] == "global-instinct"
 def test_load_project_only_excludes_global(patch_globals):
    """load_project_only_instincts should NOT include global instincts."""
    tree = patch_globals
    project = _make_project(tree)
    (project["instincts_personal"] / "proj.yaml").write_text(SAMPLE_INSTINCT_YAML)
    (tree["global_personal"] / "glob.yaml").write_text(SAMPLE_GLOBAL_INSTINCT_YAML)
    result = load_project_only_instincts(project)
    ids = {i["id"] for i in result}
    assert "test-instinct" in ids
    assert "global-instinct" not in ids
 def test_load_project_only_global_fallback_loads_global(patch_globals):
    """Global fallback should return global instincts for project-only queries."""
    tree = patch_globals
    (tree["global_personal"] / "glob.yaml").write_text(SAMPLE_GLOBAL_INSTINCT_YAML)
    global_project = {
        "id": "global",
        "name": "global",
        "root": "",
        "project_dir": tree["homunculus"],
        "instincts_personal": tree["global_personal"],
        "instincts_inherited": tree["global_inherited"],
        "evolved_dir": tree["global_evolved"],
        "observations_file": tree["homunculus"] / "observations.jsonl",
    }
    result = load_project_only_instincts(global_project)
    assert len(result) == 1
    assert result[0]["id"] == "global-instinct"
 def test_load_all_empty(patch_globals):
    """No instincts at all should return empty list."""
    tree = patch_globals
    project = _make_project(tree)
    result = load_all_instincts(project)
    assert result == []
 # ─────────────────────────────────────────────
 # cmd_status tests
 # ─────────────────────────────────────────────
 def test_cmd_status_no_instincts(patch_globals, monkeypatch, capsys):
    """Status with no instincts should print fallback message."""
    tree = patch_globals
    project = _make_project(tree)
    monkeypatch.setattr(_mod, "detect_project", lambda: project)
    args = SimpleNamespace()
    ret = cmd_status(args)
    assert ret == 0
    out = capsys.readouterr().out
    assert "No instincts found." in out
 def test_cmd_status_with_instincts(patch_globals, monkeypatch, capsys):
    """Status should show project and global instinct counts."""
    tree = patch_globals
    project = _make_project(tree)
    monkeypatch.setattr(_mod, "detect_project", lambda: project)
    (project["instincts_personal"] / "proj.yaml").write_text(SAMPLE_INSTINCT_YAML)
    (tree["global_personal"] / "glob.yaml").write_text(SAMPLE_GLOBAL_INSTINCT_YAML)
    args = SimpleNamespace()
    ret = cmd_status(args)
    assert ret == 0
    out = capsys.readouterr().out
    assert "INSTINCT STATUS" in out
    assert "Project instincts: 1" in out
    assert "Global instincts:  1" in out
    assert "PROJECT-SCOPED" in out
    assert "GLOBAL" in out
 def test_cmd_status_returns_int(patch_globals, monkeypatch):
    """cmd_status should always return an int."""
    tree = patch_globals
    project = _make_project(tree)
    monkeypatch.setattr(_mod, "detect_project", lambda: project)
    args = SimpleNamespace()
    ret = cmd_status(args)
    assert isinstance(ret, int)
 # ─────────────────────────────────────────────
 # cmd_projects tests
 # ─────────────────────────────────────────────
 def test_cmd_projects_empty_registry(patch_globals, capsys):
    """No projects should print helpful message."""
    args = SimpleNamespace()
    ret = cmd_projects(args)
    assert ret == 0
    out = capsys.readouterr().out
    assert "No projects registered yet." in out
 def test_cmd_projects_with_registry(patch_globals, capsys):
    """Should list projects from registry."""
    tree = patch_globals
    # Create a project dir with instincts
    pid = "test123abc"
    project = _make_project(tree, pid=pid, pname="my-app")
    (project["instincts_personal"] / "inst.yaml").write_text(SAMPLE_INSTINCT_YAML)
    # Write registry
    registry = {
        pid: {
            "name": "my-app",
            "root": "/home/user/my-app",
            "remote": "https://github.com/user/my-app.git",
            "last_seen": "2025-01-15T12:00:00Z",
        }
    }
    tree["registry_file"].write_text(json.dumps(registry))
    args = SimpleNamespace()
    ret = cmd_projects(args)
    assert ret == 0
    out = capsys.readouterr().out
    assert "my-app" in out
    assert pid in out
    assert "1 personal" in out
 # ─────────────────────────────────────────────
 # _promote_specific tests
 # ─────────────────────────────────────────────
 def test_promote_specific_not_found(patch_globals, capsys):
    """Promoting nonexistent instinct should fail."""
    tree = patch_globals
    project = _make_project(tree)
    ret = _promote_specific(project, "nonexistent", force=True)
    assert ret == 1
    out = capsys.readouterr().out
    assert "not found" in out
 def test_promote_specific_rejects_invalid_id(patch_globals, capsys):
    """Path-like instinct IDs should be rejected before file writes."""
    tree = patch_globals
    project = _make_project(tree)
    ret = _promote_specific(project, "../escape", force=True)
    assert ret == 1
    err = capsys.readouterr().err
    assert "Invalid instinct ID" in err
 def test_promote_specific_already_global(patch_globals, capsys):
    """Promoting an instinct that already exists globally should fail."""
    tree = patch_globals
    project = _make_project(tree)
    # Write same-id instinct in both project and global
    (project["instincts_personal"] / "shared.yaml").write_text(SAMPLE_INSTINCT_YAML)
    global_yaml = SAMPLE_INSTINCT_YAML  # same id: test-instinct
    (tree["global_personal"] / "shared.yaml").write_text(global_yaml)
    ret = _promote_specific(project, "test-instinct", force=True)
    assert ret == 1
    out = capsys.readouterr().out
    assert "already exists in global" in out
 def test_promote_specific_success(patch_globals, capsys):
    """Promote a project instinct to global with --force."""
    tree = patch_globals
    project = _make_project(tree)
    (project["instincts_personal"] / "inst.yaml").write_text(SAMPLE_INSTINCT_YAML)
    ret = _promote_specific(project, "test-instinct", force=True)
    assert ret == 0
    out = capsys.readouterr().out
    assert "Promoted" in out
    # Verify file was created in global dir
    promoted_file = tree["global_personal"] / "test-instinct.yaml"
    assert promoted_file.exists()
    content = promoted_file.read_text()
    assert "scope: global" in content
    assert "promoted_from: abc123" in content
 # ─────────────────────────────────────────────
 # _promote_auto tests
 # ─────────────────────────────────────────────
 def test_promote_auto_no_candidates(patch_globals, capsys):
    """Auto-promote with no cross-project instincts should say so."""
    tree = patch_globals
    project = _make_project(tree)
    # Empty registry
    tree["registry_file"].write_text("{}")
    ret = _promote_auto(project, force=True, dry_run=False)
    assert ret == 0
    out = capsys.readouterr().out
    assert "No instincts qualify" in out
 def test_promote_auto_dry_run(patch_globals, capsys):
    """Dry run should list candidates but not write files."""
    tree = patch_globals
    # Create two projects with the same high-confidence instinct
    p1 = _make_project(tree, pid="proj1", pname="project-one")
    p2 = _make_project(tree, pid="proj2", pname="project-two")
    high_conf_yaml = """\
 ---
 id: cross-project-instinct
 trigger: "when reviewing"
 confidence: 0.95
 domain: security
 scope: project
 ---
 ## Action
 Always review for injection.
 """
    (p1["instincts_personal"] / "cross.yaml").write_text(high_conf_yaml)
    (p2["instincts_personal"] / "cross.yaml").write_text(high_conf_yaml)
    # Write registry
    registry = {
        "proj1": {"name": "project-one", "root": "/a", "remote": "", "last_seen": "2025-01-01T00:00:00Z"},
        "proj2": {"name": "project-two", "root": "/b", "remote": "", "last_seen": "2025-01-01T00:00:00Z"},
    }
    tree["registry_file"].write_text(json.dumps(registry))
    project = p1
    ret = _promote_auto(project, force=True, dry_run=True)
    assert ret == 0
    out = capsys.readouterr().out
    assert "DRY RUN" in out
    assert "cross-project-instinct" in out
    # Verify no file was created
    assert not (tree["global_personal"] / "cross-project-instinct.yaml").exists()
 def test_promote_auto_writes_file(patch_globals, capsys):
    """Auto-promote with force should write global instinct file."""
    tree = patch_globals
    p1 = _make_project(tree, pid="proj1", pname="project-one")
    p2 = _make_project(tree, pid="proj2", pname="project-two")
    high_conf_yaml = """\
 ---
 id: universal-pattern
 trigger: "when coding"
 confidence: 0.85
 domain: general
 scope: project
 ---
 ## Action
 Use descriptive variable names.
 """
    (p1["instincts_personal"] / "uni.yaml").write_text(high_conf_yaml)
    (p2["instincts_personal"] / "uni.yaml").write_text(high_conf_yaml)
    registry = {
        "proj1": {"name": "project-one", "root": "/a", "remote": "", "last_seen": "2025-01-01T00:00:00Z"},
        "proj2": {"name": "project-two", "root": "/b", "remote": "", "last_seen": "2025-01-01T00:00:00Z"},
    }
    tree["registry_file"].write_text(json.dumps(registry))
    ret = _promote_auto(p1, force=True, dry_run=False)
    assert ret == 0
    promoted = tree["global_personal"] / "universal-pattern.yaml"
    assert promoted.exists()
    content = promoted.read_text()
    assert "scope: global" in content
    assert "auto-promoted" in content
 def test_promote_auto_skips_invalid_id(patch_globals, capsys):
    tree = patch_globals
    p1 = _make_project(tree, pid="proj1", pname="project-one")
    p2 = _make_project(tree, pid="proj2", pname="project-two")
    bad_id_yaml = """\
 ---
 id: ../escape
 trigger: "when coding"
 confidence: 0.9
 domain: general
 scope: project
 ---
 ## Action
 Invalid id should be skipped.
 """
    (p1["instincts_personal"] / "bad.yaml").write_text(bad_id_yaml)
    (p2["instincts_personal"] / "bad.yaml").write_text(bad_id_yaml)
    registry = {
        "proj1": {"name": "project-one", "root": "/a", "remote": "", "last_seen": "2025-01-01T00:00:00Z"},
        "proj2": {"name": "project-two", "root": "/b", "remote": "", "last_seen": "2025-01-01T00:00:00Z"},
    }
    tree["registry_file"].write_text(json.dumps(registry))
    ret = _promote_auto(p1, force=True, dry_run=False)
    assert ret == 0
    err = capsys.readouterr().err
    assert "Skipping invalid instinct ID" in err
    assert not (tree["global_personal"] / "../escape.yaml").exists()
 # ─────────────────────────────────────────────
 # _find_cross_project_instincts tests
 # ─────────────────────────────────────────────
 def test_find_cross_project_empty_registry(patch_globals):
    tree = patch_globals
    tree["registry_file"].write_text("{}")
    result = _find_cross_project_instincts()
    assert result == {}
 def test_find_cross_project_single_project(patch_globals):
    """Single project should return nothing (need 2+)."""
    tree = patch_globals
    p1 = _make_project(tree, pid="proj1", pname="project-one")
    (p1["instincts_personal"] / "inst.yaml").write_text(SAMPLE_INSTINCT_YAML)
    registry = {"proj1": {"name": "project-one", "root": "/a", "remote": "", "last_seen": "2025-01-01T00:00:00Z"}}
    tree["registry_file"].write_text(json.dumps(registry))
    result = _find_cross_project_instincts()
    assert result == {}
 def test_find_cross_project_shared_instinct(patch_globals):
    """Same instinct ID in 2 projects should be found."""
    tree = patch_globals
    p1 = _make_project(tree, pid="proj1", pname="project-one")
    p2 = _make_project(tree, pid="proj2", pname="project-two")
    (p1["instincts_personal"] / "shared.yaml").write_text(SAMPLE_INSTINCT_YAML)
    (p2["instincts_personal"] / "shared.yaml").write_text(SAMPLE_INSTINCT_YAML)
    registry = {
        "proj1": {"name": "project-one", "root": "/a", "remote": "", "last_seen": "2025-01-01T00:00:00Z"},
        "proj2": {"name": "project-two", "root": "/b", "remote": "", "last_seen": "2025-01-01T00:00:00Z"},
    }
    tree["registry_file"].write_text(json.dumps(registry))
    result = _find_cross_project_instincts()
    assert "test-instinct" in result
    assert len(result["test-instinct"]) == 2
 # ─────────────────────────────────────────────
 # load_registry tests
 # ─────────────────────────────────────────────
 def test_load_registry_missing_file(patch_globals):
    result = load_registry()
    assert result == {}
 def test_load_registry_corrupt_json(patch_globals):
    tree = patch_globals
    tree["registry_file"].write_text("not json at all {{{")
    result = load_registry()
    assert result == {}
 def test_load_registry_valid(patch_globals):
    tree = patch_globals
    data = {"abc": {"name": "test", "root": "/test"}}
    tree["registry_file"].write_text(json.dumps(data))
    result = load_registry()
    assert result == data
 def test_validate_instinct_id():
    assert _validate_instinct_id("good-id_1.0")
    assert not _validate_instinct_id("../bad")
    assert not _validate_instinct_id("bad/name")
    assert not _validate_instinct_id(".hidden")
 def test_update_registry_atomic_replaces_file(patch_globals):
    tree = patch_globals
    _update_registry("abc123", "demo", "/repo", "https://example.com/repo.git")
    data = json.loads(tree["registry_file"].read_text())
    assert "abc123" in data
    leftovers = list(tree["registry_file"].parent.glob(".projects.json.tmp.*"))
    assert leftovers == []
--- a/tests/hooks/hooks.test.js
+++ b/tests/hooks/hooks.test.js
@@ -1183,7 +1183,7 @@ async function runTests() {
    assert.ok(hooks.hooks.PreCompact, 'Should have PreCompact hooks');
  })) passed++; else failed++;
-  if (test('all hook commands use node', () => {
+  if (test('all hook commands use node or are skill shell scripts', () => {
    const hooksPath = path.join(__dirname, '..', '..', 'hooks', 'hooks.json');
    const hooks = JSON.parse(fs.readFileSync(hooksPath, 'utf8'));
@@ -1191,9 +1191,14 @@ async function runTests() {
      for (const entry of hookArray) {
        for (const hook of entry.hooks) {
          if (hook.type === 'command') {
            const isNode = hook.command.startsWith('node');
            const isSkillScript = hook.command.includes('/skills/') && (
              /^(bash|sh)\s/.test(hook.command) ||
              hook.command.startsWith('${CLAUDE_PLUGIN_ROOT}/skills/')
            );
            assert.ok(
-              hook.command.startsWith('node'),
+              isNode || isSkillScript,
-              `Hook command should start with 'node': ${hook.command.substring(0, 50)}...`
+              `Hook command should start with 'node' or be a skill shell script: ${hook.command.substring(0, 80)}...`
            );
          }
        }