Make module dependency check recursive

[dustdfg]

Fixes #97812

The env.disabled_modules and methods.disable_module weren't used anywhere so the first one was repurposed and the second just deleted

[Repiteo]

The module logic in general could probably use a broad refactor; didn't realize just how messy it could get until I went to verify the changes

Nonetheless, the logic is sound and the changes work! Changing the container type should be fine, as I doubt anything is using that variable directly

[dustdfg]

The module logic in general could probably use a broad refactor; didn't realize just how messy it could get until I went to verify the changes

I would say it about half of the SCons itself.... Anyway, I don't know what messiness you noticed but I've noticed following:

1. Disabling/enabling one module leads to rebuild all the files (by feelings it is half of the engine) which directly/transitively depend on modules/modules_enabled.gen.h

2. module_check_dependencies is already used not as it was meant:

def module_check_dependencies(self, module):
    """
    ...
    Meant to be used in module `can_build` methods.
    ...
    """

It is used only inside main SConstruct so I assume there could be some other bugs

3. There is some module sorting logic. I assume it is about: if A depend on B so we should build B before A. That takes into account optional dependencies but lots of the modules don't declare their optional dependencies and we doesn't see sudden build errors. Examples of such modules: navigation optionally depends on csg and gridmap; text_server_fb optionally depends on freetype, svg and msdfgen. So one of three things:
   1. I misunderstand module sorting
   2. Sorting (and subsequently optional dependencies) is useless
   3. We have hole in the bottom of the boat but it surprisingly doesn't want to sink

[Repiteo]

Thanks!