* fix(rag): skip hidden and junk directories when indexing (#5559)
index_personal_documents walked the whole tree with no pruning, so
pointing RAG at a real-world folder silently swept in .obsidian/ plugin
JS, .git/ internals, node_modules/, and __pycache__/ — multiplying
indexing time and polluting retrieval with junk chunks.
Prune hidden directories and well-known junk directories from the walk,
and skip hidden files. The explicitly passed root is exempt, so a user
who deliberately indexes a hidden directory still gets its contents.
* fix(rag): prune hidden/junk dirs in the keyword index too, via a shared helper
The #5559 fix pruned only VectorRAG.index_personal_documents (the vector index).
The parallel keyword index built by PersonalDocsManager.refresh_index ->
load_personal_index walked the same tree unpruned, so .obsidian/, .git/,
node_modules/ etc. still swept into keyword retrieval and the file listing —
the 'end-to-end' guarantee was only half true.
Single-source the pruning policy in src/index_walk (prune_index_dirs +
is_indexable_file) and use it from both walkers so they cannot drift again.
The junk-dir match is now case-insensitive, so a Node_Modules on a
case-insensitive filesystem is pruned too.
Tests: keyword-path regressions covering hidden/junk dirs, hidden files, junk
at depth (not just top level), case-insensitive junk, and the explicit-hidden-
root exemption. The existing vector tests still pass against the shared helper.
Removing one RAG directory destroyed the whole shared ChromaDB collection
(all owners + base index) instead of just that directory's chunks. Shared
root cause: PersonalDocsManager.remove_directory called rebuild_index()
(delete_collection + recreate) then re-indexed only the remaining tracked
dirs (ownerless, never personal_dir). The targeted VectorRAG.remove_directory
that should have been used was itself broken (where={"source":{"$contains":dir}}
selects nothing on scalar metadata and would over-delete siblings), and the
dead do_manage_rag path fired a second unconditional rebuild.
- VectorRAG.remove_directory: select chunks in Python by a path-boundary match
on the stored absolute `source` (dir or dir+os.sep), abspath-normalized.
Keys on `source` (always written), never `owner` -- no migration.
- PersonalDocsManager.remove_directory: call the targeted remove instead of
rebuild_index() + partial reindex.
- do_manage_rag (dead code): drop the second rebuild_index() (hygiene).
- rag_server.py add path: abspath so indexed `source` matches the remove.
No schema change. Prevents future wipes (does not recover already-wiped
vectors). Adds hermetic regression tests at three layers.
Fixes#1660
Co-authored-by: Ethan <23321960+0xLeathery@users.noreply.github.com>
add_directory cleared exclusions with a raw path.startswith(directory)
test, which also matched sibling directories sharing a name prefix —
adding /docs would silently un-exclude files under /docs2. Match the
directory itself or paths under it (directory + os.sep) instead.
Office documents were dropped server-side: .docx fell through to
"[Attached document file]", .xlsx/.pptx weren't recognized at all, and
the personal-docs RAG index only covered txt/md/json/pdf.
Wire the optional markitdown dependency (MIT, Microsoft) into both the
chat-attachment path (build_user_content) and the RAG indexer
(personal_docs), converting .docx/.xlsx/.pptx/.xls/.epub to Markdown.
It is lazy-imported with graceful fallback (mirrors src/pdf_runtime.py):
without it those formats show an "install to extract" banner and the
MIT core is unaffected. pypdf stays the default PDF path.
- src/markitdown_runtime.py: optional-dep loader + convert_to_markdown
- upload_handler: recognize Office/EPUB extensions + MIME types
- document_processor: extract Office docs in the chat else-branch
- personal_docs: index Office docs (DEFAULT_EXTENSIONS + dispatch)
- requirements-optional.txt + ACKNOWLEDGMENTS.md: pinned markitdown 0.1.5
- tests: markitdown_runtime + office index coverage
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
