Refactor git refresh system (small refactor)

[matentzn]

Resolves #ISSUE(s).

Overview

This PR:

• One
• Two
• Three

Pre-merge checklist

Documentation

Was the documentation added/updated under docs/?

• [ ] Yes
• [ ] No, updates to the docs were not necessary after careful consideration

QC

Was the full pipeline run before submitting this PR using sh run.sh make build-mondo-ingest on this branch (after docker pull obolibrary/odkfull:dev), and no errors occurred?

• [ ] Yes
• [ ] No, there are no functional (code-related) changes to the pipeline in the PR, so no re-run is necessary

New Packages

Were any new Python packages added?

• [ ] Yes, requirements.txt.full was updated and an ODK issue submitted
• [ ] No

Were any other non-Python packages added?

• [ ] Yes, Dockerfile updated and an ODK issue submitted
• [ ] No

PR Review and Conversations Resolved

Has the PR been sufficiently reviewed by at least 1 team member of the Mondo Technical team and all threads resolved?

• [ ] Yes

[matentzn]

Its a draft, this has not been tested yet :P will do it soon.

[twhetzel]

To confirm, Nico will run the feature branch build.

[matentzn]

Something is going very wrong this this PR and I cant look into it right now; grrrrrrrrr