fix(lib): hardening and edge-case bugfixes (FW-12, FW-16 round)

- Restored .bak generation to maintain P0-B backup invariants
- Fixed stale NFS warning message to reflect SQLite DELETE fallback
- Replaced vulnerable yaml.replace with os.path.splitext globally
- Ensured YAML dump occurs after conn.commit() to prevent partial syncs
- Re-applied chmod 0600 on SQLite -wal and -shm files

skills/lib.sh

@@ -112,7 +112,7 @@ resolve_tmux_server() {
 import os, sys, sqlite3, json, yaml
 name = os.environ['SESSION_NAME']
 yaml_path = os.environ['YAML_PATH']
-db_path = yaml_path.replace('.yaml', '.db')
+db_path = os.path.splitext(yaml_path)[0] + '.db'
 d = {}
 try:
     if os.path.exists(db_path):
@@ -124,13 +124,13 @@ try:
         with open(yaml_path) as f:
             d = yaml.safe_load(f) or {}
     for s in d.get('tmux_sessions', []):
-            if s.get('name') == name:
-                server = s.get('tmux_server')
-                if server:
-                    print(server)
-                    sys.exit(0)
-    except Exception:
-        pass
+        if s.get('name') == name:
+            server = s.get('tmux_server')
+            if server:
+                print(server)
+                sys.exit(0)
+except Exception:
+    pass
 # Fallback
 print(os.environ.get('TMUX_SERVER_NAME', 'default'))
 PYEOF
@@ -208,7 +208,7 @@ _atomic_dump_yaml_check_nfs() {
   if mount | grep -q "$mountpoint.*nfs\|$mountpoint.*cifs\|$mountpoint.*fuse.sshfs"; then
     echo "WARNING: $mountpoint appears to be a network filesystem (NFS/CIFS/SSHFS)." >&2
     echo "WARNING: fcntl.flock-based atomic writes are unreliable on network filesystems." >&2
-    echo "WARNING: Consider migrating to SQLite WAL for registry storage (see FUTURE_WORKS.md FW-02)." >&2
+    echo "WARNING: SQLite journal_mode automatically falls back to DELETE." >&2
   fi
 }
 
@@ -228,7 +228,7 @@ from datetime import datetime, timezone
 import yaml
 
 yaml_path = os.environ['YAML_PATH']
-db_path = yaml_path.replace('.yaml', '.db')
+db_path = os.path.splitext(yaml_path)[0] + '.db'
 
 def _validate(d):
     if not isinstance(d, dict):
@@ -305,14 +305,16 @@ try:
 
     new_terminals = get_terminal_set(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:
         if os.path.exists(yaml_path):
             try:
                 shutil.copy2(yaml_path, yaml_path + '.bak')
             except Exception:
                 pass
-
         dir_ = os.path.dirname(yaml_path) or '.'
         fd, tmp = tempfile.mkstemp(dir=dir_, prefix='.agent-sessions.', suffix='.tmp')
         try:
@@ -324,9 +326,7 @@ try:
             if os.path.exists(tmp):
                 os.remove(tmp)
             raise
-    conn.commit()
         
-    if new_terminals != old_terminals:
         try:
             conn.execute('PRAGMA wal_checkpoint(TRUNCATE)')
         except Exception:
@@ -336,6 +336,16 @@ except Exception:
     raise
 finally:
     conn.close()
+    
+    # H3: Re-apply chmod 0600 after close to cover newly created -wal / -shm files
+    try:
+        os.chmod(db_path, 0o600)
+        wal = db_path + '-wal'
+        if os.path.exists(wal): os.chmod(wal, 0o600)
+        shm = db_path + '-shm'
+        if os.path.exists(shm): os.chmod(shm, 0o600)
+    except Exception:
+        pass
 PYEOF
 }
 
@@ -364,7 +374,7 @@ ws = os.environ['WS_ABS']
 agent = os.environ['AGENT']
 home = os.environ['HOME_DIR']
 yaml_path = os.environ['YAML_PATH']
-db_path = yaml_path.replace('.yaml', '.db')
+db_path = os.path.splitext(yaml_path)[0] + '.db'
 claude_project_dir = os.environ.get('CLAUDE_PROJECT_DIR', f"{home}/.claude/projects")
 
 d = {}
@@ -483,7 +493,7 @@ is_already_stopped() {
 import os, yaml, sqlite3, json
 name = os.environ['SESSION_NAME']
 yaml_path = os.environ['YAML_PATH']
-db_path = yaml_path.replace('.yaml', '.db')
+db_path = os.path.splitext(yaml_path)[0] + '.db'
 d = {}
 try:
     if os.path.exists(db_path):

skills/tmux-agent-orchestrate-monitor/scripts/reconcile.sh

@@ -238,7 +238,7 @@ try:
     d
 except NameError:
     import sqlite3
-    db_path = yaml_path.replace('.yaml', '.db')
+    db_path = os.path.splitext(yaml_path)[0] + '.db'
     d = {}
     try:
         if os.path.exists(db_path):

skills/tmux-agent-orchestrate-status/scripts/status.sh

@@ -37,7 +37,7 @@ home = os.environ['HOME_DIR']
 claude_project_dir = os.environ.get('CLAUDE_PROJECT_DIR', f"{home}/.claude/projects")
 drift = json.loads(os.environ['DRIFT_JSON'])
 
-db_path = yaml_path.replace('.yaml', '.db')
+db_path = os.path.splitext(yaml_path)[0] + '.db'
 d = {}
 import sqlite3
 try: