fix(check-manifest): track root freshness inputs

[eitsupi]

Summary

• include root dbt_project.yml in manifest freshness checks
• include vars.yml when it exists
• share one freshness-input collector between summary and check-manifest
• sort and deduplicate inputs when resource paths overlap the project root

Behavior

A root project input is reported stale only when its mtime is newer than manifest.json. The optional vars.yml file is ignored when absent and is not treated as a deleted manifest resource.

check-manifest remains a direct project/manifest validator and does not depend on the analyzed manifest cache.

Verification

• cargo test --workspace --all-targets --all-features
• cargo clippy --workspace --all-targets --all-features -- -D warnings
• cargo fmt --all
• portable integration coverage for newer, older, missing, and duplicate root inputs