◇ Could this help me?
Yes. This is an accurate map of the real configuration surface, and the distinction it draws between commands you invoke and skills the model selects for itself is the single most commonly confused point in this area. Treat the permissions file as a guardrail rather than a sandbox: it constrains what the assistant will normally do, and it is not a substitute for keeping secrets out of the working directory. This is a general practice.
Set up this repository's assistant configuration properly. Create a shared project instructions file covering architecture, structure, and conventions, and a git-ignored local file for personal paths and notes. Split any oversized instruction file into topic files under a rules folder. Then write a permissions configuration that allows running the test suite and reading source files, blocks reading or writing environment and secret files, and requires approval for anything that deletes files or touches version control history. Explain each permission you set and why.