cdidx dot-command does not refresh full-scan HEAD stamp

[Widthdom]

Summary

dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll . --json is documented and recommended in agent guidance as the full-scan fallback, but in the observed branch-switch case it behaved as an incremental run and did not refresh the full-scan HEAD stamp.

Observed

After --changed-between left status --check stale, I ran:

dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll . --json

The command scanned 379 files but reported:

• mode:"incremental"
• files_scanned:379
• files_skipped:379
• head_changed:true
• prior_indexed_head_commit:"04314618..."
• current_head_commit:"b9ac272..."
• head_change_notice recommending cdidx index <path> --rebuild

status --check remained stale until I ran cdidx index . --rebuild --yes --json.

Expected

Either:

• cdidx . --json should perform the documented full-refresh behavior and update the relevant full-scan HEAD stamp; or
• the documentation and agent guide should stop presenting cdidx . --json as the full-scan fallback and point directly at index . --rebuild --yes where required.

Impact

The self-improvement workflow currently tells agents to use a command that can leave the index stale, causing confusing recovery steps and extra rebuild attempts.

[Widthdom]

Work started on branch fix-issue2809.