Re-enable debug logging of Git commands and output

What does this MR do?

Re-implement debug logging of Git commands executed via Git::Repository. It ended up not working after Runtime::Env.verbose? was replaced with Runtime::Env.debug?

Also use Runtime::Logger instead of warn for consistent logging.

Does this MR meet the acceptance criteria?

• Changelog entry added, if necessary
• Documentation created/updated
• Tests added for this feature/bug
• Conforms to the code review guidelines
• Conforms to the merge request performance guidelines
• Conforms to the style guides
• Conforms to the database guides
• Link to e2e tests MR added if this MR has Requires e2e tests label. See the Test Planning Process.