Fix handling of relative paths and running from non-Git-root #584
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Now Git calls work correctly even if the common root directory in which to run Git doesn't exist anymore.
- rename `cwd=` to `repo_root=` for clarity - transform paths: relative to cwd -> relative to `repo_root`
Add such test cases to tests for - `_git_exists_in_revision()` - `get_missing_at_revision()`
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Fixes #522