refactor: migrate checkout_files_at_commit, restore_all, and restore_from_branch_ref to git2 (#311)

## Summary

Port the following methods to git2:

- `checkout_files_at_commit`
- `restore_all`
- `restore_from_branch_ref`

I also verified that these are actually used, which is not something to take for granted. I had delayed taking these on because they rely on behavior of `git clean -fd` which doesn't have a direct analogue in git2, but now we have an implementation in the helper method `remove_untracked`.

I should point out that the previous CLI-based methods had some weird behavior which is _not_ replicated namely to reset the entire repo but only clean under the target dir, which I imagine is an artifact of when we were assuming that the "config dir" and the "repo dir" were always one and the same. I added tests to pin the new behavior which I think was intended by the API contract and the HEAD reset, namely, cleaning the entire repo when we simulate `-fd`. @czxtm let me know if you have any concerns about this.

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## Test Plan

Ran through several manual tests in addition to verifying that the several existing unit tests still pass, and added a number of new unit tests in the process.

- [ ] No test plan needed

## Docs

- [ ] Docs updated (companion PR in darkmatter/nixmac-web: #\___)
- [x] No docs update needed

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Author: scottmcmaster