Bug: multi-index search drops index provenance (hits become indistinguishable / id collisions)

[kapral18]

Problem

When querying multiple indices in Elasticsearch (e.g. index: kibana,elasticsearch), each hit has an _index field.

This MCP currently drops that provenance when mapping hits into tool responses (e.g. semantic_code_search returns only { id, score, type, language, kind, content, locations }).

That makes multi-index results indistinguishable to the caller and also creates a correctness hazard:

• _id values are only unique per index, not globally. Two different indices can return the same _id, but this MCP treats id as globally unique.

Impact

• Users cannot tell which repo/index a hit came from.
• Follow-up operations that rely on a single id can be ambiguous or wrong if _id collisions occur across indices.

Code pointers

• src/mcp_server/tools/semantic_code_search.ts: hit._id is used but hit._index is not exposed.
• Other tools also key results purely by filePath (which can also collide across repos/indices).

Expected

• Include index provenance in responses (e.g. index or sourceIndex per hit), and ensure downstream joins/reads can disambiguate using (index, id).
• If multi-index is not supported, fail fast with a clear error instead of returning blended/untraceable results.