Support scons custom_modules

[fire]

custom_modules is used a lot in my build system, I had to inline two python files to restore this and it made my code style worse.

Currently the SCons is told the location of the builtin_api.gen.json is custom_modules/builtin_api.gen.json I don't remember the exact error.

[Geequlim]

Never head of custom_nodule any documentation about this?

[fire]

https://docs.godotengine.org/en/stable/development/compiling/introduction_to_the_buildsystem.html#custom-modules

[fire]

I use git subrepo to merge so not necessary.