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(
+    def _extract_frontmatter(self, content: str) -> tuple[Optional[dict], str]:
-        self, content: str
-    ) -> tuple[Optional[dict], str]:
         """Extract YAML frontmatter from markdown."""
         if not content.startswith("---"):
             return None, content

src/knowledge_rag/server.py

@@ -35,9 +35,7 @@ class KnowledgeMCPServer:
 
     def __init__(self, vault_path: str | None = None):
         # Get vault path from environment or use default
-        self.vault_path = vault_path or os.environ.get(
+        self.vault_path = vault_path or os.environ.get("VAULT_PATH", "/data/vault")
-            "VAULT_PATH", "/data/vault"
-        )
 
         # Ensure vault path exists
         if not Path(self.vault_path).exists():
@@ -45,9 +43,7 @@ class KnowledgeMCPServer:
 
         # Initialize components
         self.embedding_model = get_embedding_model()
-        self.vector_store = KnowledgeVectorStore(
+        self.vector_store = KnowledgeVectorStore(embedding_model=self.embedding_model)
-            embedding_model=self.embedding_model
-        )
         self.chunker = MarkdownChunker()
 
         # Track indexing status
@@ -69,9 +65,9 @@ class KnowledgeMCPServer:
                 Tool(
                     name="search_knowledge",
                     description="Semantic search through the knowledge base. "
-                                "Uses embeddings to find relevant content based on meaning, "
+                    "Uses embeddings to find relevant content based on meaning, "
-                                "not just keywords. Best for answering questions or finding "
+                    "not just keywords. Best for answering questions or finding "
-                                "related concepts.",
+                    "related concepts.",
                     inputSchema={
                         "type": "object",
                         "properties": {
@@ -91,8 +87,8 @@ class KnowledgeMCPServer:
                 Tool(
                     name="index_knowledge",
                     description="Index or re-index the knowledge base. "
-                                "Run this after adding new files to the vault. "
+                    "Run this after adding new files to the vault. "
-                                "Scans all markdown files and builds the search index.",
+                    "Scans all markdown files and builds the search index.",
                     inputSchema={
                         "type": "object",
                         "properties": {
@@ -115,9 +111,7 @@ class KnowledgeMCPServer:
             ]
 
         @self.server.call_tool()
-        async def call_tool(
+        async def call_tool(name: str, arguments: dict | None) -> list[TextContent]:
-            name: str, arguments: dict | None
-        ) -> list[TextContent]:
             """Handle tool calls."""
             if name == "search_knowledge":
                 return await self._search_knowledge(arguments or {})
@@ -128,9 +122,7 @@ class KnowledgeMCPServer:
             else:
                 raise ValueError(f"Unknown tool: {name}")
 
-    async def _search_knowledge(
+    async def _search_knowledge(self, arguments: dict[str, Any]) -> list[TextContent]:
-        self, arguments: dict[str, Any]
-    ) -> list[TextContent]:
         """Search the knowledge base semantically."""
         query = arguments.get("query", "")
         top_k = arguments.get("top_k", 5)
@@ -153,7 +145,7 @@ class KnowledgeMCPServer:
                 return [
                     TextContent(
                         type="text",
-                        text="No results found. Try indexing your knowledge base first."
+                        text="No results found. Try indexing your knowledge base first.",
                     )
                 ]
 
@@ -181,45 +173,70 @@ class KnowledgeMCPServer:
             logger.exception("Search error")
             return [TextContent(type="text", text=f"Search error: {str(e)}")]
 
-    async def _index_knowledge(
+    async def _index_knowledge(self, arguments: dict[str, Any]) -> list[TextContent]:
-        self, arguments: dict[str, Any]
-    ) -> list[TextContent]:
         """Index the knowledge base."""
         force = arguments.get("force", False)
 
         vault_path = Path(self.vault_path)
 
         if not vault_path.exists():
-            return [
+            return [TextContent(type="text", text=f"Vault path does not exist: {self.vault_path}")]
-                TextContent(
-                    type="text",
-                    text=f"Vault path does not exist: {self.vault_path}"
-                )
-            ]
 
         try:
             # Clear existing index if forced
             if force:
                 logger.info("Force re-indexing...")
                 self.vector_store.clear()
+                chunks = self.chunker.chunk_directory(str(vault_path))
+                new_chunks = chunks
             else:
-                logger.info("Indexing knowledge base...")
+                logger.info("Indexing knowledge base (incremental)...")
 
-            # Chunk all markdown files
+                # Chunk all markdown files
-            chunks = self.chunker.chunk_directory(str(vault_path))
+                all_chunks = self.chunker.chunk_directory(str(vault_path))
 
-            if not chunks:
+                if not all_chunks:
-                return [
+                    return [TextContent(type="text", text="No markdown files found in vault.")]
-                    TextContent(
-                        type="text",
-                        text="No markdown files found in vault."
-                    )
-                ]
 
-            logger.info(f"Created {len(chunks)} chunks, adding to vector store...")
+                # Get current sources from the vault
+                current_sources = set()
+                for chunk in all_chunks:
+                    source = chunk.metadata.get("source")
+                    if source:
+                        current_sources.add(source)
+
+                # Get indexed sources and detect deleted files
+                indexed_sources = self.vector_store.get_existing_sources()
+                deleted_sources = indexed_sources - current_sources
+
+                # Remove chunks from deleted files
+                if deleted_sources:
+                    logger.info(f"Removing chunks from deleted files: {deleted_sources}")
+                    for source in deleted_sources:
+                        self.vector_store.remove_chunks_by_source(source)
+
+                # Filter to only new/modified chunks
+                new_chunks = self.vector_store.filter_new_chunks(all_chunks)
+
+                if not new_chunks:
+                    # Check if we have any existing index
+                    stats = self.vector_store.get_stats()
+                    if stats["total_chunks"] > 0:
+                        return [
+                            TextContent(
+                                type="text",
+                                text=f"No new or modified files to index.\n"
+                                f"Total chunks in index: {stats['total_chunks']}",
+                            )
+                        ]
+                    # No existing index, fall through to index everything
+                    new_chunks = all_chunks
+
+            logger.info(f"Processing {len(new_chunks)} new/modified chunks...")
 
             # Add to vector store (this embeds them)
-            self.vector_store.add_nodes(chunks, embedding_model=self.embedding_model)
+            if new_chunks:
+                self.vector_store.add_nodes(new_chunks, embedding_model=self.embedding_model)
 
             self._indexed = True
 
@@ -227,8 +244,8 @@ class KnowledgeMCPServer:
             return [
                 TextContent(
                     type="text",
-                    text=f"Successfully indexed {len(chunks)} chunks from the knowledge base.\n"
+                    text=f"Successfully indexed {len(new_chunks)} chunks from the knowledge base.\n"
-                         f"Total chunks in index: {stats['total_chunks']}"
+                    f"Total chunks in index: {stats['total_chunks']}",
                 )
             ]
 
@@ -247,10 +264,10 @@ class KnowledgeMCPServer:
             TextContent(
                 type="text",
                 text=f"Knowledge Base Statistics:\n"
-                     f"- Vault path: {self.vault_path}\n"
+                f"- Vault path: {self.vault_path}\n"
-                     f"- Markdown files: {len(md_files)}\n"
+                f"- Markdown files: {len(md_files)}\n"
-                     f"- Indexed chunks: {stats['total_chunks']}\n"
+                f"- Indexed chunks: {stats['total_chunks']}\n"
-                     f"- Index status: {'Ready' if self._indexed else 'Not indexed'}"
+                f"- Index status: {'Ready' if self._indexed else 'Not indexed'}",
             )
         ]
 
@@ -279,4 +296,5 @@ async def main():
 
 if __name__ == "__main__":
     import asyncio
+
     asyncio.run(main())

src/knowledge_rag/vector_store.py

@@ -45,8 +45,7 @@ class KnowledgeVectorStore:
 
         # Get or create collection
         self._collection = self._client.get_or_create_collection(
-            name=collection_name,
+            name=collection_name, metadata={"description": "Knowledge base embeddings"}
-            metadata={"description": "Knowledge base embeddings"}
         )
 
         # Wrap in LlamaIndex vector store
@@ -64,7 +63,9 @@ class KnowledgeVectorStore:
         """Get the LlamaIndex ChromaVectorStore."""
         return self._vector_store
 
-    def add_nodes(self, nodes: List[TextNode], embedding_model: "BaseEmbedding | None" = None) -> None:
+    def add_nodes(
+        self, nodes: List[TextNode], embedding_model: "BaseEmbedding | None" = None
+    ) -> None:
         """Add nodes to the vector store."""
         from llama_index.core import VectorStoreIndex, StorageContext
 
@@ -127,8 +128,11 @@ class KnowledgeVectorStore:
         """Clear all embeddings from the store."""
         self._client.delete_collection(self._collection_name)
         self._collection = self._client.get_or_create_collection(
-            name=self._collection_name,
+            name=self._collection_name, metadata={"description": "Knowledge base embeddings"}
-            metadata={"description": "Knowledge base embeddings"}
+        )
+        # Recreate the ChromaVectorStore wrapper with the new collection
+        self._vector_store = ChromaVectorStore(
+            chroma_collection=self._collection,
         )
 
     def get_stats(self) -> dict[str, Any]:
@@ -137,3 +141,78 @@ class KnowledgeVectorStore:
             "total_chunks": self._collection.count(),
             "collection_name": self._collection_name,
         }
+
+    def get_indexed_files(self) -> dict[str, float]:
+        """Get all indexed files and their modification times.
+
+        Returns:
+            Dict mapping source path to file modification time
+        """
+        indexed_files = {}
+
+        # Get all items from the collection
+        items = self._collection.get()
+
+        if items and items.get("metadatas"):
+            for metadata in items["metadatas"]:
+                source = metadata.get("source")
+                file_mtime = metadata.get("file_mtime")
+                if source and file_mtime is not None:
+                    # Store the latest mtime for each source
+                    if source not in indexed_files or file_mtime > indexed_files[source]:
+                        indexed_files[source] = file_mtime
+
+        return indexed_files
+
+    def get_existing_sources(self) -> set[str]:
+        """Get set of all indexed source file paths."""
+        return set(self.get_indexed_files().keys())
+
+    def filter_new_chunks(self, nodes: List["TextNode"]) -> List["TextNode"]:
+        """Filter out chunks that are already indexed.
+
+        Compares source file path and modification time to skip unchanged files.
+
+        Args:
+            nodes: List of TextNode chunks to filter
+
+        Returns:
+            List of chunks that are new or modified
+        """
+        indexed_files = self.get_indexed_files()
+
+        new_chunks = []
+        for node in nodes:
+            source = node.metadata.get("source")
+            file_mtime = node.metadata.get("file_mtime")
+
+            if source is None:
+                # Include chunks without source (shouldn't happen)
+                new_chunks.append(node)
+                continue
+
+            # Check if this file has been indexed
+            indexed_mtime = indexed_files.get(source)
+            if indexed_mtime is None:
+                # New file, not in index
+                new_chunks.append(node)
+            elif file_mtime > indexed_mtime:
+                # File has been modified since last index
+                # First remove old chunks for this file
+                self._remove_chunks_by_source(source)
+                new_chunks.append(node)
+            # else: file unchanged, skip it
+
+        return new_chunks
+
+    def _remove_chunks_by_source(self, source: str) -> None:
+        """Remove all chunks from a specific source file."""
+        # Get IDs of chunks to delete
+        items = self._collection.get(where={"source": source})
+
+        if items and items.get("ids"):
+            self._collection.delete(ids=items["ids"])
+
+    def remove_chunks_by_source(self, source: str) -> None:
+        """Public method to remove all chunks from a specific source file."""
+        self._remove_chunks_by_source(source)