Refactor Test run_check Helper to Builder Pattern

The run_check helper function has 5 parameters, making test calls verbose and harder to read:
run_check(Some("all"), Some(&repo_path), Some(&base_sha), Some(&sha1), None)

Start by locating the run_check helper and its test call sites, including the five-argument example in the issue. Replace the verbose parameter-based calls with a builder-pattern interface while preserving the existing check behavior, then run the relevant test suite to confirm the refactor.

Written by the indexing model from the issue text.