Skip checkpoints for completed no-op backfills

[Widthdom]

Summary

• Preflight pending rows, persisted folded values, readiness metadata, graph refresh state, and extractor versions under the index lock; skip the automatic checkpoint only for a verified completed no-op.
• Add explicit --checkpoint, preserve --no-checkpoint, and report stable checkpoint_skipped / checkpoint_skipped_reason output in JSON and human-readable modes.
• Preserve checkpoint protection for real mutations and add coverage for no-op, forced, dry-run, stale metadata, value drift, graph refresh, lock contention, WAL/SHM, validation failure, and legacy-schema cases.

Root cause

backfill-fold created its automatic checkpoint before it determined whether any row or readiness mutation was required. Moving only the pending-row count was insufficient because non-NULL folded values can still be stale, so the preflight also validates persisted values before returning already_complete.

Validation

• dotnet restore CodeIndex.sln
• dotnet build CodeIndex.sln -c Release -p:UseSharedCompilation=false
• dotnet test CodeIndex.sln -c Release --no-build -p:UseSharedCompilation=false
  • net9.0: 10,413 passed, 420 skipped, 0 failed
  • net8.0: 10,886 passed, 7 skipped; one transient performance-budget failure (21.8s versus 20s), whose isolated rerun passed in about 4s
• Final targeted backfill suite on net8.0 and net9.0: 20 passed, 1 published/trimmed skip, 0 failed per target framework
• dotnet format CodeIndex.sln --verify-no-changes --no-restore
• dotnet run --project tools/CodeIndex.Changelog -- check
• Codex adversarial review: initial persisted-value validation finding fixed; post-fix review found no blocking/actionable issue
• Local index status --check --json: fresh and matched

Documentation and changelog

• Updated the English and Japanese sections of DEVELOPER_GUIDE.md and TESTING_GUIDE.md.
• Added changelog.d/unreleased/4889.fixed.md.
• Did not modify AGENTS.md, CLAUDE.md, AGENT_GUIDE.md, or CHANGELOG.md.

Follow-up candidates

• None.

Fixes #4889