Add a comment to hint why we clean directories

[Nishnha]

What are you trying to accomplish?

Add a comment to hint why we clean the directories.
This serves as a code hint to anyone working on that section of code that they need to be careful about security implications.

Anything you want to highlight for special attention from reviewers?

Paths with ../.. are normalized in Core, so the Dependabot Core library cannot access directories outside of the project.

How will you know you've accomplished your goal?

The new code comment is present.

Checklist

• I have run the complete test suite to ensure all tests and linters pass.
• I have thoroughly tested my code changes to ensure they work as expected, including adding additional tests for new functionality.
• I have written clear and descriptive commit messages.
• I have provided a detailed description of the changes in the pull request, including the problem it addresses, how it fixes the problem, and any relevant details about the implementation.
• I have ensured that the code is well-documented and easy to understand.