support updating multiple flake directories simultaneously

[DavHau]

Description

This is useful for monorepos containing multiple flakes. For example it might be desired for a nixpkgs update to happen on all sub-flakes at the same time.

Added a new option flake-dirs allowing to specify multiple flake directories to be updated simultaneously via a single PR.

Checklist

• [ ] Tested functionality against a test repository (see "How to test changes")
• [x] Added or updated relevant documentation (leave unchecked if not applicable)

I did not use the test repo, but this PRs revision is already in use on the dream2nix repo