You can do partial scans. If you create a list of files and only feed it the ones you care about it can scan those. It will complain about missing classes, but you can ignore those with phan -i

Usually a middle ground works best. Run it once on just your files and look at the undeclared classes then add the files from the framework that define those so you get at least one level of checks of your calls into the framework. Or just feed it everything, but it can take some time to scan thousands of files and if you aren't using most of that code it gets annoying.