fix: prune orphaned service data on rename/removal (#75)

[GoodbyePlanet]

Summary

Fixes #75 — when a service is renamed or removed from config.yaml, its old points remain orphaned in both the code symbols and git commits Qdrant collections, showing up in unfiltered searches.

Changes

• New: server/indexer/cleanup.py — Defines a PrunableStore protocol and a shared prune_orphaned_services() function that compares indexed service names against the configured set and deletes orphaned data.
• server/store/commit_store.py — Added get_indexed_services() (scrolls commits, collects distinct service names) and delete_by_service() (deletes all commit points for a service).
• server/store/qdrant.py — Added get_indexed_services() (delegates to existing get_service_stats(), filtering out the internal "unknown" placeholder so it can never be treated as an orphaned service name).
• server/indexer/pipeline.py — Calls ensure_collection() then prune_orphaned_services() at the start of IndexPipeline.index_all().
• server/indexer/git_history.py — Calls ensure_collection() then prune_orphaned_services() at the start of GitHistoryPipeline.index_all().

Safety fix (post-review)

Code review flagged that an empty configured-services set (e.g. config.yaml with services: [], or the key missing) would previously cause prune_orphaned_services() to treat every indexed service as orphaned and wipe the entire store. Fixed: the function now refuses to prune and logs a warning when the configured set is empty, since that's far more likely to be a config error than an intentional wipe-everything request.

Behavior

Call	Prunes orphans?
POST /reindex (no service)	Yes
POST /reindex-history (no service)	Yes
POST /reindex with "service": "foo"	No — single-service reindex
reindex() MCP tool (no service arg)	Yes
reindex(service="foo") MCP tool	No
config.yaml has no configured services (empty/missing)	No — prune is skipped to avoid wiping the store

Testing

• All 264 tests pass (uv run pytest), including 10 new tests added in this update:
  • tests/test_cleanup.py (new) — orphan deletion, configured-service protection, empty-config guard, no-op on empty store, sorted multi-orphan output
  • tests/test_pipeline.py / tests/test_git_history.py — index_all() prunes orphans before indexing, and skips pruning when no services are configured
  • tests/test_store.py — QdrantStore.get_indexed_services() excludes the "unknown" placeholder
• ruff check and ruff format --check pass clean