fix(deploy): resolve SQL timeouts, YAML drift, and orphaned tmux sessions

- lib.sh: update atomic_dump_yaml to sync with YAML on any active session status change; set reader timeouts to 60.0s
- create_session.sh: add exit trap cleanup_tmux_on_error to rollback spawned tmux sessions on initialization failures
- reconcile.sh, update_yaml_resumed.sh, status.sh, stop_session.sh: align SQLite connection timeout values to 60.0s

.agents/skills/lib.sh

@@ -115,7 +115,7 @@ yaml_path = os.environ['YAML_PATH']
 db_path = os.path.splitext(yaml_path)[0] + '.db'
 try:
     if os.path.exists(db_path):
-        conn = sqlite3.connect(db_path, timeout=10.0)
+        conn = sqlite3.connect(db_path, timeout=60.0)
         try:
             row = conn.execute('SELECT data FROM sessions WHERE name=?', (name,)).fetchone()
             if row:
@@ -315,6 +315,9 @@ def _validate(d):
 def get_terminal_set(d):
     return {s.get('name'): s.get('status') for s in d.get('tmux_sessions', []) if s.get('status') in ('stopped', 'terminated', 'archived')}
 
+def get_all_sessions_status(d):
+    return {s.get('name'): s.get('status') for s in d.get('tmux_sessions', [])}
+
 os.makedirs(os.path.dirname(db_path) or '.', exist_ok=True)
 conn = sqlite3.connect(db_path, timeout=60.0)
 
@@ -367,7 +370,7 @@ try:
     elif 'tmux_sessions' not in d:
         d['tmux_sessions'] = []
 
-    old_terminals = get_terminal_set(d)
+    old_sessions = get_all_sessions_status(d)
     old_roles = {s.get('name'): s.get('role') for s in db_sessions if s.get('role')}
 
     # --- caller mutation (module scope: sees d, yaml, os, glob, subprocess) ---
@@ -400,13 +403,12 @@ try:
     else:
         conn.execute('DELETE FROM sessions')
 
-    new_terminals = get_terminal_set(d)
+    new_sessions = get_all_sessions_status(d)
 
     conn.commit()
     
-    # Write to YAML ONLY when a session transitions to a finished state
-    # (Moved after conn.commit() per Claude's feedback)
-    if new_terminals != old_terminals:
+    # Write to YAML when sessions status or session list changes (e.g. create/stop/resume)
+    if new_sessions != old_sessions:
         if os.path.exists(yaml_path):
             try:
                 shutil.copy2(yaml_path, yaml_path + '.bak')
@@ -509,7 +511,7 @@ def emit(u):
 sessions = []
 try:
     if os.path.exists(db_path):
-        conn = sqlite3.connect(db_path, timeout=10.0)
+        conn = sqlite3.connect(db_path, timeout=60.0)
         has_sessions_table = False
         try:
             cursor = conn.execute('SELECT data FROM sessions WHERE pane_cwd=?', (ws,))
@@ -621,7 +623,7 @@ elif agent == 'cline':
 ai = {}
 try:
     if os.path.exists(db_path):
-        conn = sqlite3.connect(db_path, timeout=10.0)
+        conn = sqlite3.connect(db_path, timeout=60.0)
         row = conn.execute('SELECT data FROM state WHERE id=1').fetchone()
         if row:
             ai = json.loads(row[0]).get('agent_identities', {})
@@ -687,7 +689,7 @@ yaml_path = os.environ['YAML_PATH']
 db_path = os.path.splitext(yaml_path)[0] + '.db'
 try:
     if os.path.exists(db_path):
-        conn = sqlite3.connect(db_path, timeout=10.0)
+        conn = sqlite3.connect(db_path, timeout=60.0)
         has_sessions_table = False
         try:
             row = conn.execute('SELECT status, data FROM sessions WHERE name=?', (name,)).fetchone()