fix: queue daemon crashes on every task - 3 bugs

Fix 3 bugs from issue #174 that caused silent failure loop:

1. kugetsu-log.sh: Fix json.loads with newlines
   - Previously, notifications JSON was embedded in a single-quoted Python
     string literal, but newlines in the JSON broke the Python parser.
   - Fix: Pass JSON via stdin to Python instead of embedding in string.

2. kugetsu-queue-daemon.sh: Create logs directory during init
   - The logs/ directory ($LOGS_DIR) was never created during kugetsu init.
   - Fix: Add mkdir -p for LOGS_DIR, WORKTREES_DIR, QUEUE_DIR, and
     QUEUE_ITEMS_DIR to ensure_dirs() and ensure_queue_dirs().

3. kugetsu: Fix parse_issue_ref_from_message URL parsing
   - The function used buggy grep/sed to parse URLs like
     #158
   - Fix: Use bash regex (=~) for reliable URL parsing with proper
     capture groups.

Additional improvements:
   - ensure_dirs() now creates all necessary directories instead of just
     SESSIONS_DIR
   - ensure_queue_dirs() now also creates QUEUE_DIR and LOGS_DIR
   - parse_issue_ref_from_message uses consistent bash regex approach
     for all URL patterns

skills/kugetsu/scripts/kugetsu-log.sh

@@ -43,15 +43,24 @@ kugetsu_add_notification() {
         notifications=$(cat "$NOTIFICATIONS_FILE")
     fi
     
-    local new_notification=$(python3 -c "import json; print(json.dumps({
-        'type': '$notification_type',
-        'message': '$message',
-        'issue_ref': '$issue_ref',
-        'timestamp': '$timestamp',
-        'read': False
-    }))")
-    
-    notifications=$(python3 -c "import json; n=json.loads('$notifications'); n.append(json.loads('$new_notification')); print(json.dumps(n[-50:] if len(n)>50 else n, indent=2))")
+    notifications=$(echo "$notifications" | python3 -c "
+import json
+import sys
+
+notifications = json.load(sys.stdin)
+new_notification = {
+    'type': '$notification_type',
+    'message': '''$message'''.replace('\"', '\"'),
+    'issue_ref': '$issue_ref' if '$issue_ref' else None,
+    'timestamp': '$timestamp',
+    'read': False
+}
+
+notifications.append(new_notification)
+notifications = notifications[-50:] if len(notifications) > 50 else notifications
+
+print(json.dumps(notifications, indent=2))
+")
     
     echo "$notifications" > "$NOTIFICATIONS_FILE"
 }