repo.index.add() method attempts to chmod files which it should not

[jrollins]

The behavior of the repo.index.add() method behaves differently than the CLI equivalent git add:

0$ git add *
0$ python3 -c 'import git; git.Repo.init().git.add("*")'
0$ python3 -c 'import git; git.Repo.init().index.add("*")'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/opt/conda/base/envs/cds/lib/python3.10/site-packages/git/index/base.py", line 885, in add
    entries_added.extend(self._entries_for_paths(paths, path_rewriter, fprogress, entries))
  File "/opt/conda/base/envs/cds/lib/python3.10/site-packages/git/util.py", line 176, in wrapper
    return func(self, *args, **kwargs)
  File "/opt/conda/base/envs/cds/lib/python3.10/site-packages/git/index/util.py", line 111, in set_git_working_dir
    return func(self, *args, **kwargs)
  File "/opt/conda/base/envs/cds/lib/python3.10/site-packages/git/index/base.py", line 745, in _entries_for_paths
    entries_added.append(self._store_path(filepath, fprogress))
  File "/opt/conda/base/envs/cds/lib/python3.10/site-packages/git/index/base.py", line 698, in _store_path
    istream = self.repo.odb.store(IStream(Blob.type, st.st_size, stream))
  File "/opt/conda/base/envs/cds/lib/python3.10/site-packages/gitdb/db/loose.py", line 233, in store
    chmod(obj_path, self.new_objects_mode)
PermissionError: [Errno 1] Operation not permitted: '/path/to/repo/.git/objects/02/60b9d2b53981a5ddbe20f3f0aae350b2806d22'
1$ 

I don't see any reason that the python-native methods should be doing anything different than what the CLI does.

[Byron]

I totally agree - this was from a time when GitPython strived to implement Git independently. In retrospect, this was totally ill-advised, but here we are.
It's probably not too difficult to make this works by doing bare git calls.