fix: skip _fix_blob_seq_ids sqlite open on already-migrated palaces (#1090)

Opening chroma.sqlite3 via Python's sqlite3.connect() against a live
ChromaDB 1.5.x WAL-mode database leaves state that segfaults the next
PersistentClient call — the same failure mode tracked at #1090.

_fix_blob_seq_ids runs unconditionally on every make_client() call, so
every fresh process (MCP server, stop hook, CLI) re-triggers the sqlite
open → corrupt → segfault cycle on palaces that have already completed
the 0.6.x → 1.5.x seq_id migration.

Guard with a .blob_seq_ids_migrated marker file in the palace directory:
- If marker exists, return immediately — skip sqlite entirely
- After successful migration (or confirmation that no BLOBs remain),
  write the marker so subsequent opens take the fast path
- Palaces that never had BLOB seq_ids also get the marker on first open,
  so they too avoid the redundant sqlite open after that
- Already-migrated palaces can touch the marker manually to opt in

Test plan: Direct test — run _fix_blob_seq_ids twice against a fresh
palace; second call returns immediately because marker exists. 1094
existing tests pass.

Author: jphein

mempalace/backends/chroma.py

@@ -131,6 +131,9 @@ def quarantine_stale_hnsw(palace_path: str, stale_seconds: float = 3600.0) -> li
     return moved
 
 
+_BLOB_FIX_MARKER = ".blob_seq_ids_migrated"
+
+
 def _fix_blob_seq_ids(palace_path: str) -> None:
     """Fix ChromaDB 0.6.x -> 1.5.x migration bug: BLOB seq_ids -> INTEGER.
 
@@ -140,10 +143,20 @@ def _fix_blob_seq_ids(palace_path: str) -> None:
     type INTEGER) is not compatible with SQL type BLOB".
 
     Must run BEFORE PersistentClient is created (the compactor fires on init).
+
+    Opening a Python sqlite3 connection against a ChromaDB 1.5.x WAL-mode
+    database leaves state that segfaults the next PersistentClient call. After
+    the migration has run once successfully, a marker file is written so
+    subsequent opens skip the sqlite connection entirely. Already-migrated
+    palaces can touch the marker manually to opt into the fast path.
     """
     db_path = os.path.join(palace_path, "chroma.sqlite3")
     if not os.path.isfile(db_path):
         return
+    marker = os.path.join(palace_path, _BLOB_FIX_MARKER)
+    if os.path.isfile(marker):
+        return
+    migrated = False
     try:
         with sqlite3.connect(db_path) as conn:
             for table in ("embeddings", "max_seq_id"):
@@ -158,9 +171,18 @@ def _fix_blob_seq_ids(palace_path: str) -> None:
                 updates = [(int.from_bytes(blob, byteorder="big"), rowid) for rowid, blob in rows]
                 conn.executemany(f"UPDATE {table} SET seq_id = ? WHERE rowid = ?", updates)
                 logger.info("Fixed %d BLOB seq_ids in %s", len(updates), table)
+                migrated = True
             conn.commit()
     except Exception:
         logger.exception("Could not fix BLOB seq_ids in %s", db_path)
+        return
+    # Write marker whether or not rows needed migration — the palace is now
+    # confirmed to be in the INTEGER-seq_id state and future opens can skip the
+    # sqlite3.connect() entirely.
+    try:
+        open(marker, "a").close()
+    except OSError:
+        logger.exception("Could not write migration marker %s", marker)
 
 
 # ---------------------------------------------------------------------------