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

.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/`

.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.

.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
+```
+

.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
+```
+