The global variables don't work for applying configuration, we need to
switch to using the 'setup' function. This also aligns the default
option values in tokyonight upstream.

This allows to pass overlays and other such modifications of nixpkgs.

This is useful to be able to take full advantage of the Nix module
system, with `imports` and `options`.

The following information were out of date or incomplete:

- The `build` function has be changed to the `makeNixvim` function.
- `makeNixvimWithModule` has been introduced in order to allow more
customization.
- Added a full example using nixvim in a standalone flake