Various improvements to run.py

[jchorl]

I'd recommend reviewing commit-by-commit, I tried to keep them isolated and understandable. In order:

1. Switch from passing concatenated strings to subprocess.check_output to passing lists to subprocess.run. The reason is that "my_cool_app " + input_file will break if input_file contains a space or a myriad of other special chars. This can also enable vulnerabilities if e.g. a file is named || true; rm -rf /
2. Adopt pathlib.Path for cwd, it's easier to do path operations and seems to be a successor for os.path
3. Similarly, type args with Path and int and bool. Might as well rely on argparse to properly parse types.
4. Just removing an unnecessary comment
5. I ran the ruff linter and got it passing on run.py. I noticed mixing 2 vs. 4 space indentation, some unused vars, etc. The linter put the code in better shape.

I only got to run.py as some of the other files are bigger and more work. But hopefully this helps. Tested on python3.12.

[jchorl]

Note there are a couple breaking changes here:

• -k/--keep uses BooleanOptionalAction, so the flags become -k/--keep and --no-keep (as opposed to -k true or -k false)
• Same for -r/--repeats