chore: reconcile Bootstrap manifest contract

[jmcte]

Summary

• Reconcile the project manifest with the current Bootstrap schema and safety contract.
• Declare the repository's CodeQL language/build targets, canonical class migration, or managed-path dependencies as applicable.

Governing Issue

No governing issue is linked; this is a scheduled Bootstrap fleet reconciliation.

Validation

• The repaired Bootstrap control plane produced a plan for this manifest without schema or ownership-validation errors.
• The change is limited to project.bootstrap.yaml.

Bootstrap Governance

• No real secrets, runtime auth, or machine-local environment files are committed.
• Existing local worktrees were preserved; this PR was created from refreshed origin/main.

Merge Automation

Auto-merge is not available until a maintainer reviews and enables it for this scheduled reconciliation PR; fallback merge-readiness applies.

Notes

• This PR is intentionally manifest-only. Bootstrap-managed generated files should be applied only after this manifest contract is reviewed and merged.

[athena-omt]

Blocking: the required Bootstrap Drift check fails on this head. The pinned Bootstrap control plane (35eb9a9) reports a non-empty managed-file plan for project.bootstrap.yaml. Its manifest schema does not define either repo.classMigration or ci.codeqlLanguages, so normalization drops these additions and regeneration changes the manifest. Please either remove the unsupported fields and regenerate with the pinned CLI, or update the pinned Bootstrap control plane to a version that defines and preserves both fields; then rerun CI. Other current checks pass, but the CI gate remains blocked.