Add transform input branch inference for git submodules

[lfleck]

Summary

After allowing .git files for submodules in PR56, this PR adds branch inference for transform inputs in git submodules.

Checklist

• [x] You agree with our CLA
• [x] Included tests (or is not applicable).
• [x] Updated documentation (or is not applicable).
• [x] Used pre-commit hooks to format and lint the code.