Keep query and status indexed-HEAD stamps consistent

[Widthdom]

Summary

After a --changed-between refresh, query envelopes keep the old full-scan indexed_at_head_sha while status reports the latest indexed HEAD. The same DB therefore presents two incompatible freshness stamps.

Audit ID: O-21. Reproduced on v1.40.3.

Existing issue relationship

Residual/regression related to closed #1509, #1527, and #4313, which established HEAD/freshness/status contracts.

Expected behavior

Each stamp must have one stable meaning. All commands reading the same DB should expose the current indexed checkout, or explicitly separate latest-delta HEAD from full-scan baseline.

PR scope

Keep this to persisted HEAD provenance and response naming/compatibility.

Implementation guide for Codex 5.6 sol xhigh

• Define and document indexed_at_head_sha semantics across full, files, commits, and changed-between updates.
• Update the stamp transactionally with the committed index delta.
• If the legacy field meant full-scan baseline, add an explicit field and compatibility mapping rather than silently changing old DB reads.
• Add branch-switch/delta/full-scan fixtures and compare status/query/MCP envelopes.
• Run full tests and add a bilingual changelog fragment referencing the prior issues.

Acceptance criteria

• Status and queries agree after every refresh mode.
• The latest stamp never advances on a failed/rolled-back update.
• Any full-scan baseline is separately named and documented.

[Widthdom]

Work started on branch fix-issue4854.