Update prompt assertion in decomposer test and field assertions in query endpoint tests to match extracted_questions rename.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
- Add page_number and chunk_file_path to SourceMetadata model and query router
- Add GET /chunks/{file_path}/pdf endpoint with path traversal protection
- Add View PDF links in ResponsePanel source cards and ChunkList component
- Update TypeScript types and API helper for chunk PDF URLs
- Add backend tests (5) and frontend ChunkList tests (7)
- Update enhancement plan: all 3 features complete
PDF uploads now use parse_pdf_by_page() -> chunk_pages() -> extract page PDFs -> enhanced metadata with page_number, chunk_file_path, and document_id. Same-filename replacement deletes old chunks and PDFs before re-ingest. DOCX/TXT keep original flat flow with document_id added. RAGService.ingest_document() accepts optional document_id parameter.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
New pdf_extractor.py with extract_page_as_pdf() and extract_pages_as_pdf() for extracting individual PDF pages as separate files. Adds document_chunk_path setting to config and document_chunk/ to .gitignore.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Enhance extract_metadata() with three new optional fields for page-aware chunking support. Validates list length mismatches. Fully backward compatible — existing callers unaffected.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Add chunk_pages() to TokenChunkingStrategy: one chunk per page with 200-token overlap from adjacent pages. Uses original page text for main content, decoded tokens for overlap. Never splits a page regardless of size.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Add parse_pdf_by_page() that returns List[Tuple[int, str]] with 1-indexed page numbers. Pages with no extractable text are skipped. Follows same error handling as existing parse_pdf().
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Add 4 REST endpoints for RAG database management: GET /documents, GET /documents/{id}/chunks, DELETE /documents/{id}, DELETE /chunks/{id}. Register documents router in main.py. 8 unit tests covering all CRUD operations.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
The LLM (Qwen3.5 via OpenRouter) returns JSON wrapped in markdown code blocks:
```json
["project manager", "limits", ...]
```
But the code was trying to parse this directly with json.loads(), causing:
- QueryDecomposer to return empty keywords
- RelevanceFilter to fail with "Expecting value: line 1 column 1"
Changes:
- Added _extract_json_from_markdown() helper function to both modules
- Strips markdown code block markers (```json and ```) before JSON parsing
- Added unit tests for markdown code block handling
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus \u003cclio-agent@sisyphuslabs.ai\u003e
Woody