Fix git-submodule running in wrong location

[zvecr]

Description

When config or environment variable point to an invalid location, normpath can return a directory that does not reflect the change of directory performed by the cli. We never want current directory paths, so the code has been updated to just use regular pathlib funcs.

Types of Changes

• Core
• Bugfix
• New feature
• Enhancement/optimization
• Keyboard (addition or update)
• Keymap/layout/userspace (addition or update)
• Documentation

Issues Fixed or Closed by This PR

• https://discord.com/channels/440868230475677696/473506116718952450/1206416039206719508

Checklist

• My code follows the code style of this project: C, Python
• I have read the PR Checklist document and have made the appropriate changes.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• I have tested the changes and verified that they work and don't break anything (as well as I can manage).