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 @@
+name: Copilot Setup Steps
+
+on:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  copilot-setup-steps:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
    steps:
-  - name: Setup Go environment
-    uses: actions/setup-go@v6.2.0
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
        with:
-      # 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
-      # Path to the go.mod, go.work, .go-version, or .tool-versions file.
-      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
-      check-latest: # optional
-      # 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.
-      token: # optional, default is ${{ github.server_url == 'https://github.com' && github.token || '' }}
-      # Used to specify whether caching is needed. Set to true, if you'd like to enable caching.
-      cache: # optional, default is true
-      # Used to specify the path to a dependency file - go.sum
-      cache-dependency-path: # optional
-      # Target architecture for Go to use. Examples: x86, x64. Will use system architecture by default.
-      architecture: # optional
+          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
-
-### 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)
+```bash
+python3 "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/scripts/instinct-cli.py" evolve $ARGUMENTS
 ```

-### Step 3: Generate Skill
+If `CLAUDE_PLUGIN_ROOT` is unavailable, use:

-When cluster has:
- 3+ instincts
- 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
+```bash
+python3 ~/.claude/skills/continuous-learning-v2/scripts/instinct-cli.py evolve $ARGUMENTS
 ```

-### 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

-```
-Evolution Summary
-=================
-
-Clusters Found: X
-
-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.
+- Uses project + global instincts for analysis.
+- Shows skill/command/agent candidates from trigger and domain clustering.
+- Shows project -> global promotion candidates.
+- With `--generate`, output path is:
+  - project context: `~/.claude/homunculus/projects/<project-id>/evolved/`
+  - global fallback: `~/.claude/homunculus/evolved/`
--- 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
-
-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)
+```bash
+python3 "${CLAUDE_PLUGIN_ROOT}/skills/continuous-learning-v2/scripts/instinct-cli.py" status
 ```

-### Learning Progress
+If `CLAUDE_PLUGIN_ROOT` is unavailable, use:

- Total instincts: X
- This session: X
- 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"
-}
+```bash
+python3 ~/.claude/skills/continuous-learning-v2/scripts/instinct-cli.py status
 ```

-## Confidence Calculation
+## Behavior Notes

-```
-confidence = (successes + 1) / (applications + 2)
-```
-
-Bayesian smoothing ensures new instincts don't have extreme confidence.
-
---
-
-**TIP**: Use `/evolve` to cluster related instincts into skills when confidence is high.
+- Output includes both project-scoped and global instincts.
+- 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.
--- 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 --dry-run          # Show what would be created without creating
-/evolve --threshold 5      # Require 5+ related instincts to cluster
+/evolve --generate         # Also generate files under evolved/{skills,commands,agents}
 ```

 ## Evolution Rules
@@ -78,63 +76,50 @@ Example:

 ## What to Do

-1. Read all instincts from `~/.claude/homunculus/instincts/`
-2. Group instincts by:
-   - Domain similarity
-   - Trigger pattern overlap
-   - Action sequence relationship
-3. For each cluster of 3+ related instincts:
-   - Determine evolution type (command/skill/agent)
-   - Generate the appropriate file
-   - Save to `~/.claude/homunculus/evolved/{commands,skills,agents}/`
-4. Link evolved structure back to source instincts
+1. Detect current project context
+2. Read project + global instincts (project takes precedence on ID conflicts)
+3. Group instincts by trigger/domain patterns
+4. Identify:
+   - Skill candidates (trigger clusters with 2+ instincts)
+   - Command candidates (high-confidence workflow instincts)
+   - Agent candidates (larger, high-confidence clusters)
+5. Show promotion candidates (project -> global) when applicable
+6. If `--generate` is passed, write files to:
+   - 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
-Instincts: new-table-migration, update-schema, regenerate-types
-Type: Command
-Confidence: 85% (based on 12 observations)
+## SKILL CANDIDATES
+1. Cluster: "adding tests"
+   Instincts: 3
+   Avg confidence: 82%
+   Domains: testing
+   Scopes: project

-Would create: /new-table command
-Files:
-  - ~/.claude/homunculus/evolved/commands/new-table.md
+## COMMAND CANDIDATES (2)
+  /adding-tests
+    From: test-first-workflow [project]
+    Confidence: 84%

-## Cluster 2: Functional Code Style
-Instincts: prefer-functional, use-immutable, avoid-classes, pure-functions
-Type: Skill
-Confidence: 78% (based on 8 observations)
-
-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.
+## AGENT CANDIDATES (1)
+  adding-tests-agent
+    Covers 3 instincts
+    Avg confidence: 82%
 ```

 ## Flags

- `--execute`: Actually create the evolved structures (default is preview)
- `--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
+- `--generate`: Generate evolved files in addition to analysis output

 ## 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/`
-2. Filter based on flags
-3. Strip sensitive information:
-   - Remove session IDs
-   - Remove file paths (keep only patterns)
-   - Remove timestamps older than "last week"
-4. Generate export file
+1. Detect current project context
+2. Load instincts by selected scope:
+   - `project`: current project only
+   - `global`: global only
+   - `all`: project + global merged (default)
+3. Apply filters (`--domain`, `--min-confidence`)
+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"
-export_date: "2025-01-22T10:30:00Z"
-
-instincts:
-  - id: 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
+source: session-observation
+scope: project
+project_id: a1b2c3d4e5f6
+project_name: my-app
+---

-  - id: test-first-workflow
-    trigger: "when adding new functionality"
-    action: "Write test first, then implementation"
-    confidence: 0.9
-    domain: testing
-    observations: 12
+# Prefer Functional Style

-  - id: grep-before-edit
-    trigger: "when modifying code"
-    action: "Search with Grep, confirm with Read, then Edit"
-    confidence: 0.7
-    domain: workflow
-    observations: 6
+## Action
+Use functional patterns over classes.
 ```

-## 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)
- `--output <file>`: Output file path (default: instincts-export-YYYYMMDD.yaml)
- `--format <yaml|json|md>`: Output format (default: yaml)
- `--include-evidence`: Include evidence text (default: excluded)
+- `--min-confidence <n>`: Minimum confidence threshold
+- `--output <file>`: Output file path (prints to stdout when omitted)
+- `--scope <project|global|all>`: Export scope (default: `all`)
--- 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:
- Teammates' exports
- Skill Creator (repo analysis)
- Community collections
- Previous machine backups
+Import instincts from local file paths or HTTP(S) URLs.

 ## 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)
-These contradict local instincts:
-  ❌ use-classes-for-services
-     Conflicts with: avoid-classes
-     → Skip (requires manual resolution)
-
---
-Import 8 new, update 1, skip 3?
+Import 8 new, update 1?
 ```

-## Merge Strategies
+## Merge Behavior

-### For Duplicates
-When importing an instinct that matches an existing one:
- **Higher confidence wins**: Keep the one with higher confidence
- **Merge evidence**: Combine observation counts
- **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
+When importing an instinct with an existing ID:
+- Higher-confidence import becomes an update candidate
+- Equal/lower-confidence import is skipped
+- User confirms unless `--force` is used

 ## 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"
-original_source: "session-observation"  # or "repo-analysis"
+project_id: "a1b2c3d4e5f6"
+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
- `--merge-strategy <higher|local|import>`: How to handle duplicates
- `--from-skill-creator <owner/repo>`: Import from Skill Creator analysis
+- `--force`: Skip confirmation prompt
 - `--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/`
-2. Read inherited instincts from `~/.claude/homunculus/instincts/inherited/`
-3. Display them grouped by domain with confidence bars
+1. Detect current project context (git remote/path hash)
+2. Read project instincts from `~/.claude/homunculus/projects/<project-id>/instincts/`
+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
-Trigger: when writing new functions
-Action: Use functional patterns over classes
-Confidence: ████████░░ 80%
-Source: session-observation | Last updated: 2025-01-22
+## PROJECT-SCOPED (my-app)
+  ### WORKFLOW (3)
+    ███████░░░  70%  grep-before-edit [project]
+              trigger: when modifying code

-### use-path-aliases
-Trigger: when importing modules
-Action: Use @/ path aliases instead of relative imports
-Confidence: ██████░░░░ 60%
-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)
+## GLOBAL (apply to all projects)
+  ### SECURITY (2)
+    █████████░  85%  validate-user-input [global]
+              trigger: when handling user input
 ```
-
-## 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
- **Confidence-weighted** — 0.3 = tentative, 0.9 = near certain
- **Domain-tagged** — code-style, testing, git, debugging, workflow, etc.
- **Evidence-backed** — tracks what observations created it
+- **Atomic** -- one trigger, one action
+- **Confidence-weighted** -- 0.3 = tentative, 0.9 = near certain
+- **Domain-tagged** -- code-style, testing, git, debugging, workflow, etc.
+- **Evidence-backed** -- tracks what observations created it
+- **Scope-aware** -- `project` (default) or `global`

 ## How It Works

 ```
-Session Activity
-      │
-      │ Hooks capture prompts + tool use (100% reliable)
-      ▼
-┌─────────────────────────────────────────┐
-│         observations.jsonl              │
-│   (prompts, tool calls, outcomes)       │
-└─────────────────────────────────────────┘
-      │
-      │ Observer agent reads (background, Haiku)
-      ▼
-┌─────────────────────────────────────────┐
-│          PATTERN DETECTION              │
-│   • User corrections → instinct         │
-│   • Error resolutions → instinct        │
-│   • Repeated workflows → instinct       │
-└─────────────────────────────────────────┘
-      │
-      │ Creates/updates
-      ▼
-┌─────────────────────────────────────────┐
-│         instincts/personal/             │
-│   • prefer-functional.md (0.7)          │
-│   • always-test-first.md (0.9)          │
-│   • use-zod-validation.md (0.6)         │
-└─────────────────────────────────────────┘
-      │
-      │ /evolve clusters
-      ▼
-┌─────────────────────────────────────────┐
-│              evolved/                   │
-│   • commands/new-feature.md             │
-│   • skills/testing-workflow.md          │
-│   • agents/refactor-specialist.md       │
-└─────────────────────────────────────────┘
+Session Activity (in a git repo)
+      |
+      | Hooks capture prompts + tool use (100% reliable)
+      | + detect project context (git remote / repo path)
+      v
+---------------------------------------------+
+|  projects/<project-hash>/observations.jsonl  |
+|   (prompts, tool calls, outcomes, project)   |
+---------------------------------------------+
+      |
+      | Observer agent reads (background, Haiku)
+      v
+---------------------------------------------+
+|          PATTERN DETECTION                   |
+|   * User corrections -> instinct             |
+|   * Error resolutions -> instinct            |
+|   * Repeated workflows -> instinct           |
+|   * Scope decision: project or global?       |
+---------------------------------------------+
+      |
+      | Creates/updates
+      v
+---------------------------------------------+
+|  projects/<project-hash>/instincts/personal/ |
+|   * prefer-functional.yaml (0.7) [project]   |
+|   * use-react-hooks.yaml (0.9) [project]     |
+---------------------------------------------+
+|  instincts/personal/  (GLOBAL)               |
+|   * always-validate-input.yaml (0.85) [global]|
+|   * grep-before-edit.yaml (0.6) [global]     |
+---------------------------------------------+
+      |
+      | /evolve clusters + /promote
+      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}}
-touch ~/.claude/homunculus/observations.jsonl
+# Global directories
+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 |
-| `/evolve` | Cluster related instincts into skills/commands |
-| `/instinct-export` | Export instincts for sharing |
-| `/instinct-import <file>` | Import instincts from others |
+| `/instinct-status` | Show all instincts (project-scoped + global) with confidence |
+| `/evolve` | Cluster related instincts into skills/commands, suggest promotions |
+| `/instinct-export` | Export instincts (filterable by scope/domain) |
+| `/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",
-  "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
-  },
+  "version": "2.1",
  "observer": {
-    "enabled": true,
-    "model": "haiku",
+    "enabled": false,
    "run_interval_minutes": 5,
-    "patterns_to_detect": [
-      "user_corrections",
-      "error_resolutions",
-      "repeated_workflows",
-      "tool_preferences"
-    ]
-  },
-  "evolution": {
-    "cluster_threshold": 3,
-    "evolved_path": "~/.claude/homunculus/evolved/"
+    "min_observations_to_analyze": 20
  }
 }
 ```

+| 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
-├── observations.jsonl      # Current session observations
-├── observations.archive/   # Processed observations
-├── instincts/
-│   ├── personal/           # Auto-learned instincts
-│   └── inherited/          # Imported from others
-└── evolved/
-    ├── agents/             # Generated specialist agents
-    ├── skills/             # Generated skills
-    └── commands/           # Generated commands
+-- identity.json           # Your profile, technical level
+-- projects.json           # Registry: project hash -> name/path/remote
+-- observations.jsonl      # Global observations (fallback)
+-- instincts/
+|   +-- personal/           # Global auto-learned instincts
+|   +-- inherited/          # Global imported instincts
+-- evolved/
+|   +-- agents/             # Global generated agents
+|   +-- skills/             # Global generated skills
+|   +-- 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**:
- Traditional SKILL.md files (for backward compatibility)
- Instinct collections (for v2 learning system)
+| 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** | "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:
- Existing `~/.claude/skills/learned/` skills still work
+v2.1 is fully compatible with v2.0 and v1:
+- 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)
- When user runs `/analyze-patterns`
+- After enough observations accumulate (configurable, default 20)
 - 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":"2025-01-22T10:30:01Z","event":"tool_complete","session":"abc123","tool":"Edit","output":"..."}
-{"timestamp":"2025-01-22T10:30:05Z","event":"tool_start","session":"abc123","tool":"Bash","input":"npm test"}
-{"timestamp":"2025-01-22T10:30:10Z","event":"tool_complete","session":"abc123","tool":"Bash","output":"All tests pass"}
+{"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":"...","project_id":"a1b2c3d4e5f6","project_name":"my-react-app"}
+{"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","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
-trigger: "when searching for code to modify"
+id: use-react-hooks-pattern
+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_complete","tool":"Grep","output":"Found in 3 files"}
-{"event":"tool_start","tool":"Read","input":"src/hooks/useAuth.ts"}
-{"event":"tool_complete","tool":"Read","output":"[file content]"}
-{"event":"tool_start","tool":"Edit","input":"src/hooks/useAuth.ts..."}
+{"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","project_id":"a1b2c3","project_name":"my-app"}
+{"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]","project_id":"a1b2c3","project_name":"my-app"}
+{"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"
-LOG_FILE="${CONFIG_DIR}/observer.log"
-OBSERVATIONS_FILE="${CONFIG_DIR}/observations.jsonl"
+# ─────────────────────────────────────────────
+# Project detection
+# ─────────────────────────────────────────────

-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 \
-            "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." \
+          claude --model haiku --print \
+            "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-$(date +%Y%m%d-%H%M%S).jsonl" 2>/dev/null || true
-          touch "$OBSERVATIONS_FILE"
+          mv "$OBSERVATIONS_FILE" "$archive_dir/processed-$(date +%Y%m%d-%H%M%S)-$$.jsonl" 2>/dev/null || true
        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
-        sleep 300
+        # Check at configured interval (default: 5 minutes)
+        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",
-  "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
-  },
+  "version": "2.1",
  "observer": {
    "enabled": false,
-    "model": "haiku",
    "run_interval_minutes": 5,
-    "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
+    "min_observations_to_analyze": 20
  }
 }
--- 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 ${CLAUDE_PLUGIN_ROOT}:
-# {
-#   "hooks": {
-#     "PreToolUse": [{
-#       "matcher": "*",
-#       "hooks": [{ "type": "command", "command": "${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" }]
-#     }]
-#   }
-# }
+# Registered via plugin hooks/hooks.json (auto-loaded when plugin is enabled).
+# Can also be registered manually in ~/.claude/settings.json.

 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"
-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 stdin first (before project detection)
+# ─────────────────────────────────────────────

 # 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,
-        "session": session_id
+        "output": tool_response_str if event == "tool_complete" else None,
+        "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
-OBSERVER_PID_FILE="${CONFIG_DIR}/.observer.pid"
-if [ -f "$OBSERVER_PID_FILE" ]; then
-  observer_pid=$(cat "$OBSERVER_PID_FILE")
+# Signal observer if running (check both project-scoped and global observer)
+for pid_file in "${PROJECT_DIR}/.observer.pid" "${CONFIG_DIR}/.observer.pid"; do
+  if [ -f "$pid_file" ]; then
+    observer_pid=$(cat "$pid_file")
    if kill -0 "$observer_pid" 2>/dev/null; then
      kill -USR1 "$observer_pid" 2>/dev/null || true
    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'),
-              `Hook command should start with 'node': ${hook.command.substring(0, 50)}...`
+              isNode || isSkillScript,
+              `Hook command should start with 'node' or be a skill shell script: ${hook.command.substring(0, 80)}...`
            );
          }
        }