[BUG] Documents persist in user_data after UI deletion
Description
When deleting documents through the Kotaemon UI, while the documents are removed from the interface, they continue to persist in the actual file system under the user_data directory. Specifically, the documents remain stored in the LanceDB data directory (/ktem_app_data/user_data/docstore/index_1.lance/data). This creates a discrepancy between the UI state and the actual data storage, potentially leading to storage bloat and inconsistent state management
Reproduction steps
Start Kotaemon application
# optional (setup env)
conda create -n kotaemon python=3.10
conda activate kotaemon
pip install -e "libs/kotaemon[all]"
pip install -e "libs/ktem"
python app.py
Upload any document through the UI
Delete the document using the UI delete function
Check the contents of /ktem_app_data/user_data/docstore/index_1.lance/data
Observe that the document data still exists in the directory despite being deleted from the UI
Screenshots

Logs
no logs. no error message.
Browsers
Chrome
OS
MacOS
Additional information
When a document is deleted through the UI, it should be completely removed from both the UI and the underlying storage system The /ktem_app_data/user_data/docstore/index_1.lance/data directory should be properly cleaned up
I have the same bug! already fix?
Related https://github.com/Cinnamon/kotaemon/issues/493. Planned fixes will be in the next release.
does it affect qdrant/milvus too?