[Documentation] Add docs for permissions and ENV vars

[bjrne]

Are there any env variables missing? Maybe someone with more knowledge of priorities when choosing values from .env files and bash contexts can add a paragraph about that.

[Baschdl]

@bjrne Did you leave the same sections on purpose in the README?

[bjrne]

For now, yes, as we still work with it. A new readme is part of an extra issue, #33. And also some paragraphs still contain helpful information for writing other parts of the documentation, so I thought I'd leave it in. Replacing the whole Readme in the end is easy enough :)