Let's simplify things by defining all modules in `./plugins`, `./modules`
and `./wrappers/modules`.
Instead of currying `pkgs` into a bootstrapping module, we can require
`defaultPkgs` be provided as a special arg.
This refactor allows us to completely remove `flake-modules/modules.nix`!
To enable some features (like adding tree-sitter queries) we need to add
files to specific directories in the runtime path (queries/lang/file.scm
for tree-sitter queries for example).
This commit adds support for specifying such files. You must be careful
to not have any collisions between `files` and `extraFiles`.
