pre-commit: use buildPythonPackage

Allows to build a python env with pre_commit module:

  python3.withPackages(p: [p.pre-commit])

pre-commit is already converted to an application in `git-and-tools/default.nix`:

  pre-commit = pkgs.python3Packages.toPythonApplication pkgs.python3Packages.pre-commit;

So that it can still be installed as a standalone application.