[codex] Fix SQLite diagnostics and query hardening

[Widthdom]

Summary

• Added configurable SQLite busy timeout status reporting and prepared command cache diagnostics.
• Centralized SQLite dynamic SQL parameter builders and ready-bit user_version stamping.
• Surfaced planner statistics maintenance failures as best-effort last_index_run diagnostics without failing successful index runs.
• Hardened database diff and cross-database dependency reads with quoted PRAGMA identifiers, explicit diff comparison budgets, read-only attach fallback, and segment-aware test-path filtering.
• Added regression coverage for bounded DbDebug query-plan diagnostics.

Scope Notes

• No requested issue was excluded; no pre-existing work-start comments were found before posting work-start comments.
• No additional follow-up issues were opened.

Documentation and Changelog

• Updated status contract documentation in README.md, DEVELOPER_GUIDE.md, and AGENT_GUIDE.md.
• Added changelog fragments:
  • changelog.d/unreleased/3702.fixed.md
  • changelog.d/unreleased/3716.fixed.md
  • changelog.d/unreleased/3718.fixed.md
  • changelog.d/unreleased/3739.fixed.md
  • changelog.d/unreleased/3767.fixed.md
  • changelog.d/unreleased/3795.fixed.md
  • changelog.d/unreleased/3834.fixed.md

Validation

• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~SqliteDynamicSqlTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~DiffCommandRunnerTests|FullyQualifiedName~QueryCommandRunnerTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~Issue3718"
• dotnet build CodeIndex.sln
• dotnet run --project tools/CodeIndex.Changelog -- check
• git diff --check origin/main..HEAD
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll index /Users/widthdom/Projects/mine/cdidx/CodeIndex3rd
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll status --check --json
• Codex adversarial review: No blocking/actionable issues found.

Fixes #3834
Fixes #3702
Fixes #3795
Fixes #3767
Fixes #3739
Fixes #3718
Fixes #3716