I have a project in PHPStorm, which contains a few libraries (Zend, Doctrine, ...) grouped under a library folder.
When running the code inspection, I <
If you need to completely exclude few files from any analyse (for example a compiled php file) like it not even exist, you can right click on file in source tree and select "Mark as Plain Text". This action totally remove any inspections on this file. With this I removed a lot of notifications about "source duplications" in Laravel 5.
If you need to activate it again - once more right click and "Mark as PHP".
This works nice for a few files. If you need to exclude whole directory with everything inside, use directory marking from settings or right click on directory and "Mark Directory As -> Excluded".