Ugh, this is exactly what I've been dealing with lately. Got stuck using PHP for some project for reasons beyond my control. When I realized there was this "autoloader" thing magically loading and "linking" code without me explicitly having requested it, I understandably threw up my hands in despair. How are you supposed to know, at a glance, which parts of the project are being referenced by a particular class/file? Can you predict whatOh, right, "You need to know your framework," they say. But it's the frameworks that are full of this shit!!!
I've settled on accepting autoload as it is, since there's really no sane way around it. Which is very typical PHP: pathological solutions to insane problems. Throwing in use statements for every class you use is about the best you can do. Even those are a bit... off, but it sure the hell beats writing Foo\Bar\baz->doStuff($x); all over the place. And the PSR-4 guidelines seems to have caused many package maintainers to come up with... interesting namespace layouts.
Sorry about the rant. I'm pretty sure it's part of the grieving process, and Anger, Bargaining, and Depression are all co-incident.