vimPlugins: update auto-commiting based on review

- Use git.Repo(ROOT, search_parent_directories=True) to find nixpkgs
repo.
- Don't commit overrides.nix.
- Remove "-a" short argument.
- Remove "--commit" flag and commit by default.
- Improve help/error messages.
- Favor closure pattern over classes.Use a closure to wrap the update
function with state rather than a callable class.
- break NixpkgsRepo class into functions
- Optional None-type arguments
- Remove repo checks from update.py. Git is too flexible and permits too
many workflows for my attempt to replace documentation with code to work.
My goal would be to separate the `--add` functionality from the update
functionality in the near term and then there will be no reason for this
usage to create commits anyway.

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