fix: address code review — restore mtime check, bound metadata reads, harden security

Review fixes (from Sage's review):
- Restore mtime check in file_already_mined (check_mtime=True for miner)
- Restore limit=10000 on MCP metadata fetches to prevent OOM on large palaces
- Apply _SAFE_NAME_RE regex in sanitize_name (was dead code)
- Drop raw_aaak metadata duplication in diary_write
- chmod 0o700 on WAL dir, 0o600 on WAL file
- Add check_same_thread=False on KnowledgeGraph SQLite connection
- Remove __del__ (unreliable) and dead PRAGMA foreign_keys=ON

mempalace/config.py

@@ -40,6 +40,10 @@ def sanitize_name(value: str, field_name: str = "name") -> str:
     if "\x00" in value:
         raise ValueError(f"{field_name} contains null bytes")
 
+    # Enforce safe character set
+    if not _SAFE_NAME_RE.match(value):
+        raise ValueError(f"{field_name} contains invalid characters")
+
     return value
 
 

mempalace/knowledge_graph.py

@@ -57,7 +57,6 @@ class KnowledgeGraph:
         conn = self._conn()
         conn.executescript("""
             PRAGMA journal_mode=WAL;
-            PRAGMA foreign_keys=ON;
 
             CREATE TABLE IF NOT EXISTS entities (
                 id TEXT PRIMARY KEY,
@@ -91,7 +90,7 @@ class KnowledgeGraph:
 
     def _conn(self):
         if self._connection is None:
-            self._connection = sqlite3.connect(self.db_path, timeout=10)
+            self._connection = sqlite3.connect(self.db_path, timeout=10, check_same_thread=False)
             self._connection.execute("PRAGMA journal_mode=WAL")
             self._connection.row_factory = sqlite3.Row
         return self._connection
@@ -102,9 +101,6 @@ class KnowledgeGraph:
             self._connection.close()
             self._connection = None
 
-    def __del__(self):
-        self.close()
-
     def _entity_id(self, name: str) -> str:
         return name.lower().replace(" ", "_").replace("'", "")
 

mempalace/mcp_server.py

@@ -74,6 +74,10 @@ _collection_cache = None
 
 _WAL_DIR = Path(os.path.expanduser("~/.mempalace/wal"))
 _WAL_DIR.mkdir(parents=True, exist_ok=True)
+try:
+    _WAL_DIR.chmod(0o700)
+except (OSError, NotImplementedError):
+    pass
 _WAL_FILE = _WAL_DIR / "write_log.jsonl"
 
 
@@ -88,6 +92,10 @@ def _wal_log(operation: str, params: dict, result: dict = None):
     try:
         with open(_WAL_FILE, "a", encoding="utf-8") as f:
             f.write(json.dumps(entry, default=str) + "\n")
+        try:
+            _WAL_FILE.chmod(0o600)
+        except (OSError, NotImplementedError):
+            pass
     except Exception as e:
         logger.error(f"WAL write failed: {e}")
 
@@ -136,7 +144,7 @@ def tool_status():
     wings = {}
     rooms = {}
     try:
-        all_meta = col.get(include=["metadatas"])["metadatas"]
+        all_meta = col.get(include=["metadatas"], limit=10000)["metadatas"]
         for m in all_meta:
             w = m.get("wing", "unknown")
             r = m.get("room", "unknown")
@@ -193,7 +201,7 @@ def tool_list_wings():
         return _no_palace()
     wings = {}
     try:
-        all_meta = col.get(include=["metadatas"])["metadatas"]
+        all_meta = col.get(include=["metadatas"], limit=10000)["metadatas"]
         for m in all_meta:
             w = m.get("wing", "unknown")
             wings[w] = wings.get(w, 0) + 1
@@ -208,7 +216,7 @@ def tool_list_rooms(wing: str = None):
         return _no_palace()
     rooms = {}
     try:
-        kwargs = {"include": ["metadatas"]}
+        kwargs = {"include": ["metadatas"], "limit": 10000}
         if wing:
             kwargs["where"] = {"wing": wing}
         all_meta = col.get(**kwargs)["metadatas"]
@@ -226,7 +234,7 @@ def tool_get_taxonomy():
         return _no_palace()
     taxonomy = {}
     try:
-        all_meta = col.get(include=["metadatas"])["metadatas"]
+        all_meta = col.get(include=["metadatas"], limit=10000)["metadatas"]
         for m in all_meta:
             w = m.get("wing", "unknown")
             r = m.get("room", "unknown")
@@ -517,7 +525,6 @@ def tool_diary_write(agent_name: str, entry: str, topic: str = "general"):
                     "agent": agent_name,
                     "filed_at": now.isoformat(),
                     "date": now.strftime("%Y-%m-%d"),
-                    "raw_aaak": entry,
                 }
             ],
         )

mempalace/miner.py

@@ -417,7 +417,7 @@ def process_file(
 
     # Skip if already filed
     source_file = str(filepath)
-    if not dry_run and file_already_mined(collection, source_file):
+    if not dry_run and file_already_mined(collection, source_file, check_mtime=True):
         return 0, None
 
     try:

mempalace/palace.py

@@ -48,10 +48,24 @@ def get_collection(palace_path: str, collection_name: str = "mempalace_drawers")
         return client.create_collection(collection_name)
 
 
-def file_already_mined(collection, source_file: str) -> bool:
+def file_already_mined(collection, source_file: str, check_mtime: bool = False) -> bool:
-    """Check if a file has already been filed in the palace."""
+    """Check if a file has already been filed in the palace.
+
+    When check_mtime=True (used by project miner), returns False if the file
+    has been modified since it was last mined, so it gets re-mined.
+    When check_mtime=False (used by convo miner), just checks existence.
+    """
     try:
         results = collection.get(where={"source_file": source_file}, limit=1)
-        return len(results.get("ids", [])) > 0
+        if not results.get("ids"):
+            return False
+        if check_mtime:
+            stored_meta = results.get("metadatas", [{}])[0]
+            stored_mtime = stored_meta.get("source_mtime")
+            if stored_mtime is None:
+                return False
+            current_mtime = os.path.getmtime(source_file)
+            return float(stored_mtime) == current_mtime
+        return True
     except Exception:
         return False