Fix for bug where the all files in a repo are marked for delete after a pull.
Fix for bug where the all files in a repo are marked for delete after a pull.

Must use the configured version of git consistently.
Replace plain 'git' with git.Git.GIT_PYTHON_GIT_EXECUTABLE.

The versions used that showed the problem on macOS where:

Apple's git:

% /usr/bin/git --version
git version 2.24.3 (Apple Git-128)


Homebrew git:
% /usr/local/bin/git --version
git version 2.30.0
barry-scott/scm-workbench,barry-scott/scm-workbench,barry-scott/scm-workbench,barry-scott/git-workbench,barry-scott/git-workbench