fix: resolve CodeQL false positives in retrieval changes

[suguanYang]

Summary

• Mark Alembic migration metadata as explicit module exports so CodeQL does not report required revision, down_revision, branch_labels, and depends_on globals as unused.
• Replace the mixed module import in the large-snapshot contract test.
• Remove redundant route-local initialization.
• Narrow namespace/manifest snapshot lookup fallback handling to SQLAlchemyError and log the fallback context.
• Add the missing rollback() implementation to the counting session test double.

Why

Alembic consumes migration metadata by convention, so deleting those globals would break migration discovery. Exporting them via __all__ is a narrow, repository-local way to communicate that contract to CodeQL while preserving the check elsewhere.

Verification

• uv run ruff check ...
• uv run pyright ...
• pytest apps/api/tests/contract/test_retrieval_serving_manifest_contract.py apps/api/tests/contract/test_retrieval_manifest_cache_contract.py
• Python compilation and git diff --check

The separate classic-route scoring and serving-index projection findings require behavior-level design/contract changes and are intentionally not mixed into this tooling/fallback cleanup PR.