My story is similar, but using Laravel as the canonical example of how not to structure things. Even without Facades, the internals are an impenetrable maze of magic methods, with things like Macroable adding methods from dog-knows-where. Even adding phpdoc types doesn’t work when dealing with things like scopes.
It is the only framework I have read top to bottom.
Also the FreeBSD kernel, if you want to see a C code base that's quite beautiful (for C).