From d4302c01e5226c61a8fe0ff463042740001e5e7f Mon Sep 17 00:00:00 2001
From: ww2283 <ww2283@columbia.edu>
Date: Wed, 19 Aug 2026 18:46:48 -0400
Subject: [PATCH] fix(cli): copy chunk metadata before id assignment to break
 dict aliasing (#7)

---
 packages/leann-core/src/leann/cli.py |  4 ++--
 tests/test_incremental_build.py      | 34 ++++++++++++++++++++++++++++
 2 files changed, 36 insertions(+), 2 deletions(-)

diff --git a/packages/leann-core/src/leann/cli.py b/packages/leann-core/src/leann/cli.py
index f37e1ca9..58e81faf 100644
--- a/packages/leann-core/src/leann/cli.py
+++ b/packages/leann-core/src/leann/cli.py
@@ -2081,7 +2081,7 @@ def _assign_chunk_ids(chunks: list[dict]) -> None:
         for path_key, path_chunks in by_path.items():
             for idx, c in enumerate(path_chunks):
                 sid = hashlib.sha256(f"{path_key}:{idx}".encode()).hexdigest()[:16]
-                c.setdefault("metadata", {})["id"] = sid
+                c["metadata"] = {**c.get("metadata", {}), "id": sid}
                 c["id"] = sid
 
     @staticmethod
@@ -2089,7 +2089,7 @@ def _assign_unique_chunk_ids(chunks: list[dict]) -> None:
         """Assign unique IDs for incremental (avoids collision when path lookup misses some old ids)."""
         for c in chunks:
             sid = uuid.uuid4().hex[:16]
-            c.setdefault("metadata", {})["id"] = sid
+            c["metadata"] = {**c.get("metadata", {}), "id": sid}
             c["id"] = sid
 
     def _chunks_for_paths(self, all_texts: list[dict], paths: set[str]) -> list[dict]:
diff --git a/tests/test_incremental_build.py b/tests/test_incremental_build.py
index 63ec0ea2..e9cb366a 100644
--- a/tests/test_incremental_build.py
+++ b/tests/test_incremental_build.py
@@ -371,3 +371,37 @@ def test_ivf_multiple_incremental_no_duplicates(tmp_path):
     assert len(stale_ids) == 0, (
         f"passages.jsonl has {len(stale_ids)} stale entries not in offset_map: {stale_ids[:5]}"
     )
+
+
+def test_assign_unique_chunk_ids_with_shared_metadata_dict():
+    from leann.cli import LeannCLI
+
+    # Arrange
+    shared = {"file_path": "a.md"}
+    chunks = [{"text": t, "metadata": shared} for t in ("one", "two", "three")]
+
+    # Act
+    LeannCLI._assign_unique_chunk_ids(chunks)
+
+    # Assert
+    metadata_ids = [c["metadata"]["id"] for c in chunks]
+    assert len(set(metadata_ids)) == len(chunks)
+    for c in chunks:
+        assert c["metadata"]["id"] == c["id"]
+
+
+def test_assign_chunk_ids_with_shared_metadata_dict():
+    from leann.cli import LeannCLI
+
+    # Arrange
+    shared = {"file_path": "a.md"}
+    chunks = [{"text": t, "metadata": shared} for t in ("one", "two", "three")]
+
+    # Act
+    LeannCLI._assign_chunk_ids(chunks)
+
+    # Assert
+    metadata_ids = [c["metadata"]["id"] for c in chunks]
+    assert len(set(metadata_ids)) == len(chunks)
+    for c in chunks:
+        assert c["metadata"]["id"] == c["id"]