fix: add support for gitserver/owner/repo#number issue ref format

Add third pattern to parse_issue_ref_from_message() to support the mixed
format 'gitserver/owner/repo#number' (e.g., git.fbrns.co/shoko/kugetsu#116).

Previously only two formats were supported:
1. Full URL: #116
2. Short format: shoko/kugetsu#116

Now supports:
3. Mixed format: git.fbrns.co/shoko/kugetsu#116

Fixes #144

.github/ISSUES/fix-queue-daemon-excess-agents.md

@@ -0,0 +1,67 @@
+# Fix: Queue daemon spawning excess agents due to race condition
+
+## Problem
+
+When enqueueing multiple tasks (e.g., 6 tasks), the queue daemon was spawning many more subagents than expected, eventually exhausting container memory.
+
+**Root Cause:** The combination of:
+1. `process_queue()` calling `opencode run` directly instead of `kugetsu start`, bypassing all concurrency logic
+2. `count_active_dev_sessions()` counting `pm-agent.json` toward `MAX_CONCURRENT_AGENTS`, reducing effective dev agent slots
+3. No atomic locking around session count check + session file creation (TOCTOU race condition)
+4. Background spawning of multiple concurrent processes in `process_queue()`
+
+**Expected behavior:** With `MAX_CONCURRENT_AGENTS=3` and 6 tasks:
+- Tasks should be processed sequentially via `kugetsu start`
+- Only 3 dev agents should run at a time
+- Tasks should queue and wait for slots to free up
+
+## Solution
+
+### 1. `count_active_dev_sessions()` - Exclude pm-agent
+Only count actual dev agent session files (exclude `pm-agent.json`).
+
+### 2. `process_queue()` - Call `kugetsu start` directly + retry logic
+- Call `kugetsu start` directly (foreground, sequential) instead of spawning `opencode run` background process
+- Dynamic batch size = available slots (removes need for `QUEUE_DAEMON_BATCH_SIZE`)
+- Retry logic (max 3 attempts) on failure
+- On failure: cleanup worktree/session and revert to `pending` state
+- Save `fork_pid` to queue item for timeout handling
+
+### 3. `cmd_start()` - Add flock
+- Add flock around critical section (count check + fork)
+- Track `fork_pid` for queue item timeout handling
+
+### 4. Notification System
+New notification types:
+| Event | Type |
+|-------|------|
+| Task enqueued | `task_queued` |
+| Task dequeued | `task_dequeued` |
+| Task started | `task_started` |
+| Task completed | `task_completed` |
+| Task error | `task_error` |
+
+### 5. Config
+- Remove `QUEUE_DAEMON_BATCH_SIZE` (no longer needed - batch size is now dynamic)
+
+## Notification Flow
+
+| Event | Location | Type |
+|-------|----------|------|
+| Task enqueued | `enqueue_task()` | `task_queued` |
+| Task dequeued | `process_queue()` after state change to `notified` | `task_dequeued` |
+| Task started | `cmd_start()` after session file created | `task_started` |
+| Task completed | `update_queue_item_state()` | `task_completed` |
+| Task error | `update_queue_item_state()` | `task_error` |
+
+## Out of Scope
+
+- Re-check loop in cmd_start (checking if session DB is reliable) - deferred to separate research issue
+- Buffer mechanism for excess forking (safety failsafe only)
+
+## Status
+
+- [x] Issue created
+- [x] Implementation
+- [x] PR created (#147)
+- [ ] Merged

skills/kugetsu/SKILL.md

@@ -50,7 +50,6 @@ A default config file is created during `kugetsu init` with commented examples:
 | `KUGETSU_TEMP_DIR` | `~/.local/share/opencode/tool-output` | Temp directory for subagent tool output (useful in headless environments where /tmp is restricted) |
 | `KUGETSU_VERBOSITY` | `default` | PM agent verbosity level: `verbose`, `default`, or `quiet` |
 | `QUEUE_DAEMON_INTERVAL_MINUTES` | 5 | How often daemon polls queue (in minutes) |
-| `QUEUE_DAEMON_BATCH_SIZE` | 2 | How many tasks daemon picks per poll |
 | `QUEUE_CLEANUP_AGE_DAYS` | 7 | Auto-cleanup completed/error items older than N days |
 
 ### Environment Variables for Agents

skills/kugetsu/scripts/kugetsu

@@ -23,8 +23,8 @@ QUEUE_DAEMON_PID_FILE="${QUEUE_DAEMON_PID_FILE:-$QUEUE_DIR/daemon.pid}"
 QUEUE_DAEMON_LOCK_FILE="${QUEUE_DAEMON_LOCK_FILE:-$QUEUE_DIR/daemon.lock}"
 QUEUE_DAEMON_LOG_FILE="${QUEUE_DAEMON_LOG_FILE:-$QUEUE_DIR/daemon.log}"
 QUEUE_DAEMON_INTERVAL_MINUTES="${QUEUE_DAEMON_INTERVAL_MINUTES:-5}"
-QUEUE_DAEMON_BATCH_SIZE="${QUEUE_DAEMON_BATCH_SIZE:-2}"
 QUEUE_CLEANUP_AGE_DAYS="${QUEUE_CLEANUP_AGE_DAYS:-7}"
+TASK_TIMEOUT_HOURS="${TASK_TIMEOUT_HOURS:-1}"
 
 # Load user config overrides (~/.kugetsu/config)
 if [ -f "$KUGETSU_DIR/config" ]; then
@@ -62,7 +62,7 @@ count_active_dev_sessions() {
         for session_file in "$SESSIONS_DIR"/*.json; do
             if [ -f "$session_file" ]; then
                 local filename=$(basename "$session_file")
-                if [ "$filename" != "base.json" ]; then
+                if [ "$filename" != "base.json" ] && [ "$filename" != "pm-agent.json" ]; then
                     count=$((count + 1))
                 fi
             fi
@@ -531,6 +531,8 @@ with open("$QUEUE_ITEMS_DIR/${queue_id}.json", "w") as f:
 
 print(f"Enqueued: $queue_id")
 PYEOF
+
+    kugetsu_add_notification "task_queued" "Task queued: $issue_ref" "$issue_ref"
 }
 
 get_pending_tasks() {
@@ -576,6 +578,8 @@ get_queue_stats() {
 update_queue_item_state() {
     local queue_id="$1"
     local new_state="$2"
+    local session_id="${3:-}"
+    local pid="${4:-}"
     
     local item_file="$QUEUE_ITEMS_DIR/${queue_id}.json"
     if [ ! -f "$item_file" ]; then
@@ -585,22 +589,33 @@ update_queue_item_state() {
     
     python3 << PYEOF
 import json
+import os
 from datetime import datetime
 
 item_file = "$item_file"
 new_state = "$new_state"
+session_id = "$session_id"
+pid = "$pid"
 
 with open(item_file, 'r') as f:
     item = json.load(f)
 
+issue_ref = item.get('issue_ref', '')
+
 item['state'] = new_state
 
 if new_state == "notified":
     item['notified_at'] = datetime.now().isoformat() + "Z"
+    if session_id:
+        item['opencode_session_id'] = session_id
+    if pid:
+        item['pid'] = int(pid) if pid.isdigit() else None
 elif new_state == "completed":
     item['completed_at'] = datetime.now().isoformat() + "Z"
+    os.system(f"kugetsu_add_notification 'task_completed' 'Task completed: {issue_ref}' '{issue_ref}'")
 elif new_state == "error":
     item['error'] = datetime.now().isoformat() + "Z"
+    os.system(f"kugetsu_add_notification 'task_error' 'Task error: {issue_ref}' '{issue_ref}'")
 
 with open(item_file, 'w') as f:
     json.dump(item, f, indent=2)
@@ -609,6 +624,83 @@ print(f"Updated $queue_id to state: $new_state")
 PYEOF
 }
 
+check_task_timeouts() {
+    if [ ! -d "$QUEUE_ITEMS_DIR" ]; then
+        return
+    fi
+    
+    local timeout_hours="${TASK_TIMEOUT_HOURS:-1}"
+    
+    for item in "$QUEUE_ITEMS_DIR"/*.json; do
+        [ -f "$item" ] || continue
+        
+        local state=$(python3 -c "import json; print(json.load(open('$item')).get('state', ''))" 2>/dev/null)
+        if [ "$state" != "notified" ]; then
+            continue
+        fi
+        
+        local notified_at=$(python3 -c "import json; print(json.load(open('$item')).get('notified_at', ''))" 2>/dev/null)
+        if [ -z "$notified_at" ]; then
+            continue
+        fi
+        
+        local queue_id=$(basename "$item" .json)
+        local pid=$(python3 -c "import json; print(json.load(open('$item')).get('pid', ''))" 2>/dev/null)
+        local session_id=$(python3 -c "import json; print(json.load(open('$item')).get('opencode_session_id', ''))" 2>/dev/null)
+        
+        local notified_epoch=$(date -d "$notified_at" +%s 2>/dev/null || echo "0")
+        local now_epoch=$(date +%s)
+        local hours_elapsed=$(( (now_epoch - notified_epoch) / 3600 ))
+        
+        if [ "$hours_elapsed" -ge "$timeout_hours" ]; then
+            echo "Task $queue_id timed out after ${hours_elapsed}h (limit: ${timeout_hours}h)"
+            
+            if [ -n "$pid" ] && kill -0 "$pid" 2>/dev/null; then
+                echo "Killing process $pid"
+                kill "$pid" 2>/dev/null || true
+            fi
+            
+            if [ -n "$session_id" ]; then
+                local worktree_path=""
+                for session_file in "$SESSIONS_DIR"/*.json; do
+                    [ -f "$session_file" ] || continue
+                    local sess_id=$(python3 -c "import json; print(json.load(open('$session_file')).get('opencode_session_id', ''))" 2>/dev/null)
+                    if [ "$sess_id" = "$session_id" ]; then
+                        worktree_path=$(python3 -c "import json; print(json.load(open('$session_file')).get('worktree_path', ''))" 2>/dev/null)
+                        break
+                    fi
+                done
+                
+                if [ -n "$worktree_path" ]; then
+                    pkill -f "opencode.*$worktree_path" 2>/dev/null || true
+                fi
+            fi
+            
+            update_queue_item_state "$queue_id" "error"
+            
+            local issue_ref=$(python3 -c "import json; print(json.load(open('$item')).get('issue_ref', ''))" 2>/dev/null)
+            if [ -n "$issue_ref" ]; then
+                local session_file=$(get_session_for_issue "$issue_ref")
+                if [ -n "$session_file" ] && [ "$session_file" != "null" ]; then
+                    python3 << PYEOF
+import json
+session_path = "$SESSIONS_DIR/$session_file"
+try:
+    with open(session_path, 'r') as f:
+        session = json.load(f)
+    session['state'] = 'timeout'
+    with open(session_path, 'w') as f:
+        json.dump(session, f, indent=2)
+    print(f"Marked session for $issue_ref as timeout")
+except Exception as e:
+    print(f"Error marking session: {e}")
+PYEOF
+                fi
+            fi
+        fi
+    done
+}
+
 cleanup_old_queue_items() {
     local days="${QUEUE_CLEANUP_AGE_DAYS:-7}"
     
@@ -1053,6 +1145,11 @@ parse_issue_ref_from_message() {
         owner=$(echo "$full_path" | cut -d'/' -f2)
         repo=$(echo "$full_path" | cut -d'/' -f3)
         issue_number=$(echo "$full_path" | grep -oE '[0-9]+$' | head -1)
+    elif echo "$message" | grep -qE '[a-zA-Z0-9.-]+\.[a-zA-Z]{2,}/[a-zA-Z0-9_.-]+/[a-zA-Z0-9_.-]+#[0-9]+'; then
+        gitserver=$(echo "$message" | grep -oE '[a-zA-Z0-9.-]+\.[a-zA-Z]{2,}/[a-zA-Z0-9_.-]+/[a-zA-Z0-9_.-]+' | head -1)
+        owner=$(echo "$gitserver" | cut -d'/' -f2)
+        repo=$(echo "$gitserver" | cut -d'/' -f3)
+        issue_number=$(echo "$message" | grep -oE '#[0-9]+' | grep -oE '[0-9]+' | head -1)
     elif echo "$message" | grep -qE '[a-zA-Z0-9_.-]+/[a-zA-Z0-9_.-]+#([0-9]+)'; then
         owner=$(echo "$message" | grep -oE '[a-zA-Z0-9_.-]+/[a-zA-Z0-9_.-]+#' | sed 's/#$//' | cut -d'/' -f1)
         repo=$(echo "$message" | grep -oE '[a-zA-Z0-9_.-]+/[a-zA-Z0-9_.-]+#' | sed 's/#$//' | cut -d'/' -f2)
@@ -1267,6 +1364,7 @@ queue_daemon_loop() {
             exit 0
         fi
         
+        check_task_timeouts
         process_queue
     done
 }
@@ -1279,22 +1377,15 @@ process_queue() {
     fi
     
     local available_slots=$((MAX_CONCURRENT_AGENTS - active_count))
-    local batch_size=$QUEUE_DAEMON_BATCH_SIZE
-    [ "$batch_size" -gt "$available_slots" ] && batch_size=$available_slots
     
-    if [ "$batch_size" -le 0 ]; then
-        return
-    fi
-    
-    local pm_session=$(get_pm_agent_session_id)
-    if [ -z "$pm_session" ] || [ "$pm_session" = "null" ]; then
+    if [ "$available_slots" -le 0 ]; then
         return
     fi
     
     local count=0
     for item in $(ls -t "$QUEUE_ITEMS_DIR"/*.json 2>/dev/null | head -20); do
+        [ $count -ge "$available_slots" ] && break
         [ -f "$item" ] || continue
-        [ $count -ge "$batch_size" ] && break
         
         local state=$(python3 -c "import json; print(json.load(open('$item')).get('state', ''))" 2>/dev/null)
         if [ "$state" != "pending" ]; then
@@ -1302,30 +1393,49 @@ process_queue() {
         fi
         
         local queue_id=$(basename "$item" .json)
-        local issue_ref=$(python3 -c "import json; print(json.load(open('$item')).get('issue_ref', '')" 2>/dev/null)
-        local message=$(python3 -c "import json; print(json.load(open('$item')).get('message', '')" 2>/dev/null)
+        local issue_ref=$(python3 -c "import json; print(json.load(open('$item')).get('issue_ref', ''))" 2>/dev/null)
+        local message=$(python3 -c "import json; print(json.load(open('$item')).get('message', ''))" 2>/dev/null)
         
         if [ -z "$issue_ref" ] || [ -z "$message" ]; then
             continue
         fi
         
         update_queue_item_state "$queue_id" "notified"
+        kugetsu_add_notification "task_dequeued" "Task dequeued: $issue_ref" "$issue_ref"
         
         local log_file="$LOGS_DIR/delegate-${queue_id}.log"
         mkdir -p "$LOGS_DIR"
         
-        local env_sh="set -a; "
-        if [ -f "$ENV_DIR/pm-agent.env" ]; then
-            env_sh="${env_sh}source '$ENV_DIR/pm-agent.env'; "
-        elif [ -f "$ENV_DIR/default.env" ]; then
-            env_sh="${env_sh}source '$ENV_DIR/default.env'; "
+        local max_retries=3
+        local attempt=1
+        local success=false
+        local fork_pid=""
+        
+        while [ $attempt -le $max_retries ]; do
+            if kugetsu start "$issue_ref" "$message" >> "$log_file" 2>&1; then
+                success=true
+                break
+            fi
+            
+            echo "Attempt $attempt failed for $queue_id, cleaning up..." >> "$log_file"
+            
+            local session_file="$(issue_ref_to_filename "$issue_ref").json"
+            local worktree_path=$(issue_ref_to_worktree_path "$issue_ref" "$PWD")
+            
+            [ -f "$SESSIONS_DIR/$session_file" ] && rm -f "$SESSIONS_DIR/$session_file"
+            worktree_exists "$issue_ref" "$PWD" && remove_worktree_for_issue "$issue_ref" "$PWD"
+            remove_issue_from_index "$issue_ref" 2>/dev/null || true
+            
+            attempt=$((attempt + 1))
+        done
+        
+        if [ "$success" = true ]; then
+            echo "Started task $queue_id: $issue_ref"
+            count=$((count + 1))
+        else
+            echo "Failed to start task $queue_id after $max_retries attempts"
+            update_queue_item_state "$queue_id" "pending"
         fi
-        env_sh="${env_sh}set +a; "
-        
-        nohup sh -c "${env_sh}opencode run 'Delegate task: ${message}' --continue --session '$pm_session'" >> "$log_file" 2>&1 &
-        
-        echo "Queued task $queue_id for PM agent"
-        count=$((count + 1))
     done
 }
 
@@ -1971,20 +2081,10 @@ cmd_start() {
     create_worktree "$issue_ref" "$parent_dir"
 
     local session_file="$(issue_ref_to_filename "$issue_ref").json"
-
-    echo "Forking session for '$issue_ref'..."
-    
-    # Session-counting: count actual dev sessions, reject if at limit
-    local active_count=$(count_active_dev_sessions)
-    if [ "$active_count" -ge "$MAX_CONCURRENT_AGENTS" ]; then
-        echo "Error: Max concurrent agents ($MAX_CONCURRENT_AGENTS) reached" >&2
-        echo "Active sessions: $active_count" >&2
-        remove_worktree_for_issue "$issue_ref" "$parent_dir"
-        exit 1
-    fi
-     
     local fork_log="$SESSIONS_DIR/$session_file.fork.log"
     local opencode_db="${OPENCODE_DB:-$HOME/.local/share/opencode/opencode.db}"
+    local lock_file="$KUGETSU_DIR/.session_lock"
+    local lock_fd=200
     
     > "$fork_log"
     
@@ -1997,25 +2097,38 @@ ${previous_context}
 ## YOUR TASK
 $message"
     
-    fix_session_permissions
-    
-    if [ "$DEBUG_MODE" = true ]; then
-        (cd "$worktree_path" && opencode run "$full_message" --fork --session "$base_session_id" --dir "$worktree_path" 2>&1) | tee "$fork_log" &
-    else
-        (cd "$worktree_path" && opencode run "$full_message" --fork --session "$base_session_id" --dir "$worktree_path" 2>&1) >> "$fork_log" &
-    fi
-
-    local fork_pid=$!
-    
-    local max_attempts=10
-    local attempt=1
-    local new_session_id=""
-    local fork_log_output=""
-    
-    while [ $attempt -le $max_attempts ]; do
-        sleep 1
+    (
+        flock -x $lock_fd
         
-        new_session_id=$(python3 -c "
+        local active_count=$(count_active_dev_sessions)
+        if [ "$active_count" -ge "$MAX_CONCURRENT_AGENTS" ]; then
+            echo "Error: Max concurrent agents ($MAX_CONCURRENT_AGENTS) reached" >&2
+            echo "Active sessions: $active_count" >&2
+            remove_worktree_for_issue "$issue_ref" "$parent_dir"
+            exit 1
+        fi
+        
+        echo "Forking session for '$issue_ref'..."
+        
+        fix_session_permissions
+        
+        if [ "$DEBUG_MODE" = true ]; then
+            (cd "$worktree_path" && opencode run "$full_message" --fork --session "$base_session_id" --dir "$worktree_path" 2>&1) | tee "$fork_log" &
+        else
+            (cd "$worktree_path" && opencode run "$full_message" --fork --session "$base_session_id" --dir "$worktree_path" 2>&1) >> "$fork_log" &
+        fi
+
+        local fork_pid=$!
+        
+        local max_attempts=10
+        local attempt=1
+        local new_session_id=""
+        local fork_log_output=""
+        
+        while [ $attempt -le $max_attempts ]; do
+            sleep 1
+            
+            new_session_id=$(python3 -c "
 import sqlite3
 conn = sqlite3.connect('$opencode_db')
 cursor = conn.cursor()
@@ -2024,31 +2137,31 @@ result = cursor.fetchone()
 if result:
     print(result[0])
 " 2>/dev/null || echo "")
-        
-        if [ -n "$new_session_id" ] && [ "$new_session_id" != "$base_session_id" ] && [ "$new_session_id" != "$pm_agent_session_id" ]; then
-            break
-        fi
-        
-        if ! kill -0 $fork_pid 2>/dev/null; then
-            fork_log_output=$(tail -20 "$fork_log" 2>/dev/null || echo "(log empty or unavailable)")
-            break
-        fi
-        
-        attempt=$((attempt + 1))
-    done
+            
+            if [ -n "$new_session_id" ] && [ "$new_session_id" != "$base_session_id" ] && [ "$new_session_id" != "$pm_agent_session_id" ]; then
+                break
+            fi
+            
+            if ! kill -0 $fork_pid 2>/dev/null; then
+                fork_log_output=$(tail -20 "$fork_log" 2>/dev/null || echo "(log empty or unavailable)")
+                break
+            fi
+            
+            attempt=$((attempt + 1))
+        done
 
-    if [ -z "$new_session_id" ]; then
-        echo "Error: Could not find newly created session after ${max_attempts}s" >&2
-        if [ -n "$fork_log_output" ]; then
-            echo "Fork log output:" >&2
-            echo "$fork_log_output" >&2
+        if [ -z "$new_session_id" ]; then
+            echo "Error: Could not find newly created session after ${max_attempts}s" >&2
+            if [ -n "$fork_log_output" ]; then
+                echo "Fork log output:" >&2
+                echo "$fork_log_output" >&2
+            fi
+            remove_worktree_for_issue "$issue_ref"
+            exit 1
         fi
-        remove_worktree_for_issue "$issue_ref"
-        exit 1
-    fi
 
-    echo "Updating permissions for new session: $new_session_id"
-    python3 -c "
+        echo "Updating permissions for new session: $new_session_id"
+        python3 -c "
 import sqlite3
 conn = sqlite3.connect('$opencode_db')
 cursor = conn.cursor()
@@ -2058,9 +2171,9 @@ conn.commit()
 print('[OK] Session permissions updated')
 "
 
-    if [ "$DEBUG_MODE" = true ]; then
-        echo "[DEBUG] Forked session permissions check:"
-        python3 -c "
+        if [ "$DEBUG_MODE" = true ]; then
+            echo "[DEBUG] Forked session permissions check:"
+            python3 -c "
 import sqlite3
 conn = sqlite3.connect('$opencode_db')
 cursor = conn.cursor()
@@ -2070,11 +2183,11 @@ for row in cursor.fetchall():
     print('  Directory:', row[1])
     print('  Permission:', row[2])
 " 2>/dev/null || echo "  (failed to query DB)"
-    fi
+        fi
 
-    local branch_name=$(issue_ref_to_branch_name "$issue_ref")
-    
-    python3 << PYEOF > "$SESSIONS_DIR/$session_file"
+        local branch_name=$(issue_ref_to_branch_name "$issue_ref")
+        
+        python3 << PYEOF > "$SESSIONS_DIR/$session_file"
 import json
 
 session = {
@@ -2092,12 +2205,15 @@ with open("$SESSIONS_DIR/$session_file", "w") as f:
     json.dump(session, f, indent=2)
 PYEOF
 
-    add_issue_to_index "$issue_ref" "$session_file"
-    
-    kugetsu_context_dump "$issue_ref" "$message" "$branch_name"
+        add_issue_to_index "$issue_ref" "$session_file"
+        
+        kugetsu_context_dump "$issue_ref" "$message" "$branch_name"
+        
+        kugetsu_add_notification "task_started" "Task started: $issue_ref" "$issue_ref"
 
-    echo "Session started for '$issue_ref': $new_session_id"
-    echo "Worktree: $worktree_path"
+        echo "Session started for '$issue_ref': $new_session_id"
+        echo "Worktree: $worktree_path"
+    ) 200>"$lock_file"
 }
 
 cmd_continue() {