Align repository dogfood index topology

[Widthdom]

Summary

• Align the checked-in workspace manifest with the canonical repository-wide root index by using index_strategy: single.
• Pin repository dogfood index, query, MCP, LSP, and maintenance operations to .cdidx/codeindex.db, including repository audit examples.
• Add drift coverage that rejects unpinned local dogfood commands and keeps the manifest and guidance synchronized.

Root cause

The manifest required per-member databases while the authoritative workflow built and queried a root database. In addition, commands that relied on the current directory could still select another database when CDIDX_DATA_DIR or active-workspace configuration was present.

Validation

• dotnet build CodeIndex.sln -c Debug -p:UseSharedCompilation=false
• dotnet build CodeIndex.sln -c Release -p:UseSharedCompilation=false
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --no-restore --filter "FullyQualifiedName~DocumentationDriftTests" on net8.0 and net9.0
• make lint
• dotnet run --project tools/CodeIndex.Changelog -- check
• bash .codex/scripts/check-workflow-links.sh
• Root and workspace status checks with an overriding CDIDX_DATA_DIR; both members are ready through one shared database.
• Representative search, definition, references, MCP, LSP, and optimize dry-run checks against the explicit root database.
• codex review --base origin/main in two rounds; both actionable P2 findings were addressed.

Documentation and changelog

Updated AGENT_GUIDE.md, SELF_IMPROVEMENT.md, DEVELOPER_GUIDE.md, TESTING_GUIDE.md, .codex/README.md, .codex/workflows/issue-fix.md, and repository audit documents.

Added changelog.d/unreleased/5062.fixed.md.

Fixes #5062

Follow-up candidates

None.