Add incremental indexing with deleted file detection

- Add file_mtime to chunk metadata for change detection
- Add get_indexed_files() and get_existing_sources() methods
- Add filter_new_chunks() to skip unchanged files
- Add remove_chunks_by_source() to delete orphaned chunks
- Update server to detect and remove deleted files on incremental index
- Fix clear() to recreate ChromaVectorStore wrapper

src/knowledge_rag/chunker.py

@@ -49,6 +49,9 @@ class MarkdownChunker:
         # Get relative path for context
         rel_path = os.path.relpath(file_path)
 
+        # Get file modification time for change detection
+        file_mtime = os.path.getmtime(file_path)
+
         # Split into sections based on headings
         sections = self._split_by_headings(body)
 
@@ -64,6 +67,7 @@ class MarkdownChunker:
                 metadata={
                     "source": rel_path,
                     "file_name": os.path.basename(file_path),
+                    "file_mtime": file_mtime,
                     "heading": section.get("heading", ""),
                     "section_index": i,
                     "wiki_links": ",".join(wiki_links) if wiki_links else "",
@@ -105,9 +109,7 @@ class MarkdownChunker:
 
         return all_chunks
 
-    def _extract_frontmatter(
-        self, content: str
-    ) -> tuple[Optional[dict], str]:
+    def _extract_frontmatter(self, content: str) -> tuple[Optional[dict], str]:
         """Extract YAML frontmatter from markdown."""
         if not content.startswith("---"):
             return None, content