Only run python lint against tracked files

What does this MR do?

This MR changes the two places we run flake for python linting to only analyze python files tracked by git instead of all python files under the project directory.

When using venv installed into a local directory, installing packages will result in *.py files being located under the project directory. The old method of using find to locate python files to analyze would include these package files, resulting in flake taking a very long time and reporting errors on files not under our control. Using git ls-files to find python files instead results in only files that are under our control being analyzed.