fix: prune orphaned service data when service is renamed in config.yaml (#75)

When a service is renamed or removed from config.yaml, the old service
name's points remain in both the code symbols and git commits Qdrant
collections, showing up in unfiltered searches.

Add a shared prune_orphaned_services() utility (via PrunableStore
protocol) that compares indexed service names against the configured
set and deletes orphaned data. Wire it into both IndexPipeline.index_all
and GitHistoryPipeline.index_all so it runs automatically on every
full reindex (POST /reindex and POST /reindex-history).

Author: GoodbyePlanet

.gitignore

@@ -3,7 +3,6 @@
 
 # AI
 .ai/
-.tokensave/
 
 # Python
 .venv/
@@ -32,4 +31,4 @@ config.yaml
 # Claude Code local settings
 .claude/settings.local.json
 
-memory/
+memory/

server/indexer/git_history.py

@@ -15,6 +15,7 @@
     fetch_commits_with_diffs,
     list_commits,
 )
+from server.indexer.cleanup import prune_orphaned_services
 from server.indexer.pipeline import ProgressEvent
 from server.store.commit_store import CommitStore
 
@@ -197,6 +198,13 @@ async def index_all(
         progress_callback: Callable[[ProgressEvent], Awaitable[None]] | None = None,
     ) -> dict[str, Any]:
         services = settings.load_services()
+        configured_names = {s.name for s in services}
+        orphaned = await prune_orphaned_services(
+            self._store, configured_names, label="git commits"
+        )
+        if orphaned:
+            logger.info("Pruned %d orphaned service(s): %s", len(orphaned), orphaned)
+
         results: dict[str, Any] = {}
         for svc in services:
             logger.info("Indexing git history for: %s", svc.name)

server/indexer/pipeline.py

@@ -14,6 +14,7 @@
 from server.embeddings.base import EmbeddingProvider
 from server.embeddings.bm25 import BM25SparseProvider, get_sparse_embedding_provider
 from server.embeddings import get_embedding_provider
+from server.indexer.cleanup import prune_orphaned_services
 from server.indexer.github_source import fetch_blob_content, list_github_files
 from server.parser.base import CodeSymbol, ParseError
 from server.parser.registry import parse_file
@@ -281,6 +282,13 @@ async def index_all(
         progress_callback: Callable[[ProgressEvent], Awaitable[None]] | None = None,
     ) -> dict[str, Any]:
         services = settings.load_services()
+        configured_names = {s.name for s in services}
+        orphaned = await prune_orphaned_services(
+            self._store, configured_names, label="code symbols"
+        )
+        if orphaned:
+            logger.info("Pruned %d orphaned service(s): %s", len(orphaned), orphaned)
+
         results: dict[str, Any] = {}
         for svc in services:
             logger.info("Indexing service: %s", svc.name)

server/store/commit_store.py

@@ -227,5 +227,33 @@ async def _update_one(p: dict[str, Any]) -> None:
 
         await asyncio.gather(*(_update_one(p) for p in payloads))
 
+    async def get_indexed_services(self) -> list[str]:
+        """Return distinct service names that have indexed commits."""
+        services: set[str] = set()
+        offset = None
+        while True:
+            results, offset = await self._client.scroll(
+                collection_name=self._collection,
+                limit=1000,
+                offset=offset,
+                with_payload=["service"],
+                with_vectors=False,
+            )
+            for point in results:
+                svc = point.payload.get("service")
+                if svc:
+                    services.add(svc)
+            if offset is None:
+                break
+        return sorted(services)
+
+    async def delete_by_service(self, service: str) -> None:
+        await self._client.delete(
+            collection_name=self._collection,
+            points_selector=Filter(
+                must=[FieldCondition(key="service", match=MatchValue(value=service))]
+            ),
+        )
+
     async def close(self) -> None:
         await self._client.close()

server/store/qdrant.py

@@ -309,6 +309,11 @@ async def get_service_stats(self) -> list[dict[str, Any]]:
             )
         return result
 
+    async def get_indexed_services(self) -> list[str]:
+        """Return distinct service names that have indexed code symbols."""
+        stats = await self.get_service_stats()
+        return sorted(s["service"] for s in stats)
+
     async def collection_info(self) -> dict[str, Any]:
         info = await self._client.get_collection(self._collection)
         return {