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

@@ -854,6 +854,11 @@ EOF
 }
 
 parse_issue_ref_from_message() {
+    # DEPRECATED: This function is not called anywhere.
+    # The active implementation is extract_issue_ref_from_message()
+    # in kugetsu-session.sh which is used by cmd_delegate.
+    # This function is kept for backwards compatibility and will
+    # be removed in a future release.
     local message="$1"
     
     local gitserver=""