feat: added bare for cloning and updating

[ronantakizawa]

Description (e.g. "Related to ...", etc.)

Added --bare tags for repository cloning and updating to clone and update bare repositories. Resolves issue #413

Code review checklist (for code reviewer to complete)

• [ ] Pull request represents a single change (i.e. not fixing disparate/unrelated things in a single PR)
• [ ] Title summarizes what is changing
• [ ] Commit messages are meaningful (see this for details)
• [ ] Tests have been included and/or updated, as appropriate
• [ ] Docstrings have been included and/or updated, as appropriate
• [ ] Changelog has been updated, as needed (see CHANGELOG.md)

[renatav]

This update process is really complex, so I tried to explain a few important considerations. Let me know if providing more details would be helpful.