Fix branch-switch index convergence

[Widthdom]

Summary

• Reconcile current-HEAD Git-scoped refreshes from the persisted whole-workspace baseline, including paths touched by earlier scoped writes when a later commit range has no net diff.
• Separate latest-write provenance, whole-workspace verification, and the legacy full-scan baseline across status, map, query/inspect, and MCP responses.
• Publish verification only after successful full or baseline-reconciled scoped runs; partial, cancelled, sparse, unresolvable, or incomplete pending-path coverage stays fail-closed.
• Read status, map, and symbol-analysis provenance with their response bodies from one SQLite snapshot, and expose the same analyze provenance in MCP default, compact, and count formats.
• Preserve project-local workspace metadata for explicit --db <project>/.cdidx/codeindex.db inspect queries while retaining the one-snapshot provenance contract.

Validation

• Merged latest origin/main at af83296abef48ccbf1e2569a6244c1d066c99b26.
• dotnet build CodeIndex.sln -c Release --no-restore — passed with 0 warnings and 0 errors.
• Focused Recompute trust and completeness metadata for filtered portable archives #5053/Make branch-switch refresh converge and keep indexed HEAD provenance consistent #5054 integration matrix — 32 passed on net8.0 and 32 passed on net9.0.
• Focused workspace-metadata and explicit-DB inspect matrix — 16 passed on net8.0 and 16 passed on net9.0.
• The previously failing CI test RunInspect_WithJsonUsesProjectLocalCdidxPathForExplicitProjectDb passes locally.
• Focused Issue Make branch-switch refresh converge and keep indexed HEAD provenance consistent #5054 and map snapshot matrix — 24 passed on net8.0 and 24 passed on net9.0.
• dotnet format CodeIndex.sln --verify-no-changes --no-restore — passed.
• Changelog fragment validation — validated all 4 current fragments.
• Debug-binary dogfood full index — 1,276 files, 47,609 symbols, 477,917 references, 0 warnings/errors.
• Debug-binary current-HEAD scoped refresh — passed with 0 warnings/errors; final status --check --json reports index_matches_workspace: true, complete reference graph, and a clean worktree.
• An exploratory full-solution run exposed a map projectRoot snapshot regression; the run was stopped after diagnosis, the root cause was fixed, and the targeted matrix above passed on both TFMs.

Adversarial review

Two Codex adversarial-review rounds were completed, which is the workflow maximum. All actionable findings were addressed, including net-zero Git ranges after scoped writes, one-snapshot analysis provenance, consistent MCP analyze formats, sparse/full-scan fail-closed behavior, and map project-root snapshot consistency.

Documentation and changelog

• Updated the bilingual README, User Guide, Developer Guide, Testing Guide, and AGENT_GUIDE.md.
• Added/updated changelog.d/unreleased/5054.fixed.md.
• AGENTS.md, AGENT.md, and CLAUDE.md were not changed.

Related regressions

• Preserves the scoped-refresh and indexed-HEAD compatibility established by cdidx dot-command does not refresh full-scan HEAD stamp #2809 and Keep query and status indexed-HEAD stamps consistent #4854; those issues are referenced for context and are not closed by this PR.

Follow-up candidates

• None.

Fixes #5054