Replace numeric [1] labels with [filename, page N] format in context chunks.
Update LLM prompt to instruct inline citation using bracket labels.
Enables traceable source references in generated answers.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
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>
- Add react-router-dom with NavBar component (LTT + RAG Database tabs)
- Extract AppContent into LTTPage, add RAGDatabasePage placeholder
- Refactor App.tsx to BrowserRouter + Routes layout
- Switch ResponsePanel to react-markdown for rich formatting
- Fix ResponsePanel test for markdown rendering
- Update RAG prompt to cite source name instead of number
- Save Phase 1 enhancement plan (.plans/phase1_enhancement_plan.md)
- LLMClient.complete() now accepts step_name parameter to identify processing step
- Logs prompt preview (first 100 + last 100 chars) at INFO level
- Logs processing time in milliseconds with token usage stats
- Updated QueryDecomposer, RelevanceFilter, and RAGService to pass step names
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>