Update git_root on refresh

[smatting]

Fixes #931 and fixes #442

This PR updates in_prepared_repo to a different scenario (called "Scenario 2"), namely that the user changes directory to a git repo after setup() has already been called. This makes 14 tests fail, also including the tests for hunk operations which explains the issue #931.

The second commit fixes all failing tests, by making sure repository.git_root and repository.git_path is updated on every refresh of the status. Also this commit removes the unused repository.cwd.

Maybe this PR could be extended so that in_prepared_repo would run each test for both scenarios:

1. Scenario 1: User runs setup() while already being in the right git repo (i.e. you start nvim inside the git repo).
2. Scenario 2: User changes directory after setup() has been called (i.e. you start nvim and then :cd into the git repo)

I was not able to fit both scenarios into in_prepared_repo because running Scenario 1 first would influence the outcome of running Scenario 2, so some critical cleanup was missing between running both scenarios. Maybe somebody can help me with this? With the bugfix included in this PR all tests pass when running them in either Scenario 1 and Scenario 2 separately. We could of course also duplicate all tests, but that would be ugly. What we really want is that that every test passes in either scenario, because that assert that neogit behaves the same.

[smatting]

I'm no longer sure this PR makes sense, now that I have read more of the codebase: it appears like everything related to cwds is much more complicated than it has to be. Wouldn't it be much simpler if all git commands would be executed with cwd = git.repo.git_root and this state would only be updated when you call neogit.open() and only then?

[CKolkey]

Hmm. Yeah, sounds reasonable to me. A lot of the CWD logic is from before I got involved with this project. If you think there's a better (simpler) way, I'd love to see what you have in mind :)

[smatting]

@CKolkey I manged to pull it off: #963