feat(mcp): expose index freshness and relationship provenance

[vvenegasv]

What does this PR do?

This PR adds machine-readable freshness and provenance evidence to MCP responses, helping clients determine whether results come from a current index, a stale or partial index, direct source resolution, or heuristic inference.

Changes include:

• Persisting the indexed Git HEAD and file coverage metrics for each project.
• Extending index_status with additive evidence about indexed/current revisions, working tree state, freshness, coverage, and known limitations.
• Returning edge_evidence from trace_path and trace_call_path when relationship provenance is available.
• Preserving backward compatibility by returning unknown or unavailable values when older indexes do not contain the new metadata.

Why is this needed?

Consumers of the MCP need factual and inspectable signals to decide whether a result can be trusted as-is, whether the repository should be re-indexed, or whether the result should be verified directly against source code.

Rather than exposing an opaque reliability score, this change provides the underlying evidence needed for clients to make that decision.

Checklist

• Every commit is signed off (git commit -s)
• Tests pass locally (make -f Makefile.cbm test)
• Lint passes (make -f Makefile.cbm lint-ci)
• New behavior is covered by a test