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I've seen this config repo which is really cool and easy to read and basically works this way: the init files does some preliminary stuff, then loads all the files in the /core and /config directory. I've seen that if i compile the byte code of the scripts in /config by themselves, there are some warnings of variables and functions not defined. The included files do not have explicit dependencies because everything is automatically included by the init file.
Have a look at Purcell’s (extremely popular) config: https://github.com/purcell/emacs.d
The System Crafters Rational Emacs distro takes the same approach too: https://github.com/SystemCrafters/rational-emacs/tree/master/modules