file_sys: Add factory class for RomFS file system.

Same as directory, file shouldn't expose Open either.

Open should not be an interface exposed by Directory because it is the Archive thats implement the methed to open the directory. The service API of 3DS also implies this - Open is not a function of directory service, but is of FS main service

and make the mode parameter a reference since it is a BitField union

This makes clang-format useful on those.

Also add a bunch of forgotten transitive includes, which otherwise
prevented compilation.

These operations are limited by the open flags specified while opening the file.

Buffer lengths should be size_t, and file offsets should be u64.

Fixed a few warnings and cleaned up the code