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

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")
-  if kill -0 "$observer_pid" 2>/dev/null; then
-    kill -USR1 "$observer_pid" 2>/dev/null || true
+# 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
-fi
+done
 
 exit 0