fix: run external tools on git repo folder

[miki725]

• Followed the steps in the contributor's guide: https://crashoverride.com/docs/other/contributing#filing-the-pull-request
• PR title uses semantic commit messages
• Filled out the template to a useful degree
• Updated CHANGELOG.md if necessary

Issue

External tools would run against specific file being chalked.

Description

When running external tool for chalk insert it should run on a git repo, not on the path of the chalked artifact. For example:

chalk insert hello.py

Should run semgrep on the git repo, not hello.py.

Testing

➜ maketest test_plugins.py::test_semgrep[sample_1-True] --logs --pdb