chore(rebase): reconcile with develop and apply ruff format

After rebasing onto current develop:
- chroma.py: keep develop's quarantine_stale_hnsw + UnsupportedFilterError
  validation alongside this PR's _pin_hnsw_threads retrofit.
- tests/test_backends.py: combine quarantine_stale_hnsw and
  _pin_hnsw_threads test sections; ruff format.
- miner.py: propagate the new `files=` kwarg (added on develop in #1183
  for the init -> mine flow) through _mine_impl so the caller can pass
  a pre-scanned file list under the global lock.

mempalace/backends/chroma.py

@@ -153,9 +153,7 @@ def _pin_hnsw_threads(collection) -> None:
         return
     try:
         collection.modify(
-            configuration=UpdateCollectionConfiguration(
+            configuration=UpdateCollectionConfiguration(hnsw=UpdateHNSWConfiguration(num_threads=1))
-                hnsw=UpdateHNSWConfiguration(num_threads=1)
-            )
         )
     except Exception:
         logger.debug("_pin_hnsw_threads modify failed", exc_info=True)

mempalace/miner.py

@@ -1005,6 +1005,7 @@ def mine(
             dry_run=dry_run,
             respect_gitignore=respect_gitignore,
             include_ignored=include_ignored,
+            files=files,
         )
 
     try:
@@ -1018,6 +1019,7 @@ def mine(
                 dry_run=dry_run,
                 respect_gitignore=respect_gitignore,
                 include_ignored=include_ignored,
+                files=files,
             )
     except MineAlreadyRunning:
         print(
@@ -1037,6 +1039,7 @@ def _mine_impl(
     dry_run: bool = False,
     respect_gitignore: bool = True,
     include_ignored: list = None,
+    files: list = None,
 ):
     project_path = Path(project_dir).expanduser().resolve()
     config = load_config(project_dir)

tests/test_backends.py

@@ -483,9 +483,7 @@ def test_get_collection_applies_retrofit_on_existing_palace(tmp_path):
 
     # Simulate a legacy palace: create collection without num_threads
     bootstrap_client = chromadb.PersistentClient(path=str(palace_path))
-    bootstrap_client.create_collection(
+    bootstrap_client.create_collection("mempalace_drawers", metadata={"hnsw:space": "cosine"})
-        "mempalace_drawers", metadata={"hnsw:space": "cosine"}
-    )
     del bootstrap_client  # drop reference so a fresh client reopens cleanly
 
     wrapper = ChromaBackend().get_collection(
@@ -494,6 +492,4 @@ def test_get_collection_applies_retrofit_on_existing_palace(tmp_path):
         create=False,
     )
 
-    assert (
+    assert wrapper._collection.configuration_json["hnsw"]["num_threads"] == 1
-        wrapper._collection.configuration_json["hnsw"]["num_threads"] == 1
-    )