feat: speed up pushes by calling unshallow first

What does this merge request do and why?

Speeds up git push by undoing the shallow clone of the git repo. Based on this conversation.

This MR makes the change for the fix_pipeline and convert_to_gitlab_ci flows. If this works in prod, I will make the change for issue-to-mr in the next MR.

Relates to gitlab-org/gitlab#578660

How to set up and validate locally

1. Set up Duo Agent Platform
2. Run a Fix Pipeline Flow
3. Check your Flow Output in Automate > Agent sessions:

Example Langsmith

Merge request checklist

• Tests added for new functionality. If not, please raise an issue to follow up.
• Documentation added/updated, if needed.
• If this change requires executor implementation: verified that issues/MRs exist for both Go executor and Node executor or confirmed that changes are backward-compatible and don't break existing executor functionality.