Make git-version-info.py compatiable with worktree

[GardevoirX]

When working with git worktree and running tox tests, one would encounter with the following error. This PR aims at passing a correct directory for running git update-index -q --really-refresh

(tox) qxu@cosmopc3:~/repos/metatomic-heat-flux$ tox -e torch-tests
torch-tests: commands[0] /home/qxu/repos/metatomic-heat-flux/python/metatomic_torch> pip install --no-deps --no-build-isolation --check-build-dependencies .
Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu
Processing ./.
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [50 lines of output]
      Traceback (most recent call last):
        File "/home/qxu/repos/metatomic-heat-flux/.tox/torch-tests/lib/python3.14/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
          main()
          ~~~~^^
        File "/home/qxu/repos/metatomic-heat-flux/.tox/torch-tests/lib/python3.14/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
          json_out["return_val"] = hook(**hook_input["kwargs"])
                                   ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
        File "/home/qxu/repos/metatomic-heat-flux/.tox/torch-tests/lib/python3.14/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 175, in prepare_metadata_for_build_wheel
          return hook(metadata_directory, config_settings)
        File "/home/qxu/repos/metatomic-heat-flux/.tox/torch-tests/lib/python3.14/site-packages/setuptools/build_meta.py", line 380, in prepare_metadata_for_build_wheel
          self.run_setup()
          ~~~~~~~~~~~~~~^^
        File "/home/qxu/repos/metatomic-heat-flux/.tox/torch-tests/lib/python3.14/site-packages/setuptools/build_meta.py", line 317, in run_setup
          exec(code, locals())
          ~~~~^^^^^^^^^^^^^^^^
        File "<string>", line 336, in <module>
        File "<string>", line 220, in create_version_number
        File "<string>", line 200, in git_version_info
      Exception: failed to get git version info.
      stdout: 44

      stderr: Traceback (most recent call last):
        File "/home/qxu/repos/metatomic-heat-flux/python/metatomic_torch/../../scripts/git-version-info.py", line 201, in <module>
          print(git_hash_all_code())
                ~~~~~~~~~~~~~~~~~^^
        File "/home/qxu/repos/metatomic-heat-flux/python/metatomic_torch/../../scripts/git-version-info.py", line 138, in git_hash_all_code
          update_git_index()
          ~~~~~~~~~~~~~~~~^^
        File "/home/qxu/repos/metatomic-heat-flux/python/metatomic_torch/../../scripts/git-version-info.py", line 109, in update_git_index
          run_subprocess(
          ~~~~~~~~~~~~~~^
              ["git", "update-index", "-q", "--really-refresh"],
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
              env=env,
              ^^^^^^^^
              cwd=gitdir.parent.absolute(),
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          )
          ^
        File "/home/qxu/repos/metatomic-heat-flux/python/metatomic_torch/../../scripts/git-version-info.py", line 37, in run_subprocess
          raise Exception(
          ...<3 lines>...
          )
      Exception: failed to run 'git update-index -q --really-refresh' (exit code 128)
      stdout:
      stderr: fatal: this operation must be run in a work tree




      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> from file:///home/qxu/repos/metatomic-heat-flux/python/metatomic_torch

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
torch-tests: exit 1 (1.43 seconds) /home/qxu/repos/metatomic-heat-flux/python/metatomic_torch> pip install --no-deps --no-build-isolation --check-build-dependencies . pid=3652321
  torch-tests: FAIL code 1 (1.46=setup[0.03]+cmd[1.43] seconds)
  evaluation failed :( (1.49 seconds)
(tox) qxu@cosmopc3:~/repos/metatomic-heat-flux$

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