What

Adds a sanctioned, additive write-back path for external metadata so a downstream tool — an LLM enrichment pass, an analysis stage, an editor extension — can attach its own metadata to existing graph nodes without re-indexing and without racing the sharded in-memory store.

Today there is no safe way for a caller holding a graph.Store (rather than a concrete *Graph) to mutate Node.Meta: the shard lock the in-memory backend takes is private, so reaching into GetNode(id).Meta directly races the sharded map and panics on a live daemon. This PR closes that gap.

How

• graph.Store.MergeNodeMeta(id, kv) (changed, found) — the only sanctioned Node.Meta mutation path for a Store holder. Additive and idempotent (deep-equal delta via the pure metaDelta helper), taken under the node's shard write lock, and it never touches structural fields (id / kind / name / path / lines). Implemented for both the in-memory and SQLite backends and covered by a shared store-conformance case so the two behave identically.
• annotate_nodes MCP tool (also served at POST /v1/tools/annotate_nodes through the shared registry — no separate HTTP code): merges a free-form per-node meta map under a caller-chosen namespace (default ext). Every key is stored as <namespace>_<key>, so an annotation can never shadow an indexer-owned Meta key. Optionally adds idempotent semantically_related edges between node pairs. Returns {annotated, unchanged, not_found, edges_added}.

The merge is deliberately scoped: never deletes keys, never mutates structural data, non-fatal per item (an unknown id is recorded in not_found, the batch continues).

Tests

• Pure metaDelta unit (delta/idempotency/nil-handling).
• In-memory + SQLite conformance (MergeNodeMeta): additive merge, deep-equal idempotency, found semantics for an unknown id, lazy Meta init, structural fields untouched.
• MCP handler: round-trip, idempotent re-run, namespace prefixing (incl. no double-prefix), semantically_related edge add + dedup, default score, bad input, and a registration guard.

All green; go build ./..., go vet, and gofmt clean on the changed files.

Notes / scope

• Cross-restart durability of annotations is intentionally out of scope for this v1: the merge mutates in-memory state and rides the gob+gzip shutdown snapshot (the SQLite backend re-persists the node). Happy to follow up with explicit per-call persistence if you'd prefer.

🤖 Generated with Claude Code