Modern PHP application development doesn't really use the "deploy PHP scripts to a folder" model any more.

The more likely scenario is that a framework with a front controller is used, which is invoked by php-fpm, proxied by nginx.

It's easy enough to do, though.

The bulk of what I do is still, essentially, 'deploy to a folder'. There's some build steps, and a symlink swap from old to new, but that's still what it's doing. And I can still go edit a single file in a folder some place if I need to test/debug something. That's rare, but there are times when production is the only place an issue shows up (or... the only place you can replicate it - usually you can figure out enough from that to replicate locally later).