Scan preloaded stubs earlier

[weirdan]

This should prevent Psalm from sometimes marking user-defined classes as
built-in.

Fixes #5126
Fixes #5626

[orklah]

Would it also solve #5626 and #6203 ?

There's a couple repo that uses preloading:
https://github.com/lperamo/otra
https://github.com/nextcloud/notify_push

maybe we could try to see nothing breaks

Unfortunately I don't know those parts of the code so I'm not gonna be a big help here

[VincentLanglet]

Tried on my work project and my personal project, it seems to fixed both.
Big thanks.

Just, you sometimes run

$this->config->visitPreloadedStubFiles($this->codebase, $this->progress);
$this->visitAutoloadFiles();

and sometimes

$this->visitAutoloadFiles();
$this->config->visitPreloadedStubFiles($this->codebase, $this->progress);

don't know if it change something.

[weirdan]

don't know if it change something.

It shouldn't, but I'd better get them consistent, lest anyone get confused by this later (myself included).

[weirdan]

notify_push seems to be fine, otra looks broken (missing directories and files), but it's not related to the PR.

I don't think it'll solve #6203, but I'm pretty sure it'll fix #5626 (unfortunately it misses reproducer).