fix: avoid skipping pre commit when deleted files staged

[mrexox]

Closes #919

🔧 Summary

For pre-commit we use git diff --diff-filter=ACMR and this avoids checking for deleted files. But sometimes user wants a pre-commit hook to run on any change to the files (even when deleting files). For that cases (when {staged_files} template is not used) we should not force skipping the command/job.

• Implement special check for implicit pre-commit skip logic to also count deleted files
• Add a test