How does the build system know which directories to process Makefiles in?

[Alex]

Just curious as to how the build system knows which directories to process the 
Makefiles in them? I've seen some moz.build files reference them with 
CONFIGURE_SUBST_FILES += ['Makefile'], but then some directories such as the 
root SpiderMonkey directory (js/src) have Makefiles but with no reference to 
them from the moz.build file of said directory.
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