Okay haha I figured it was something like that. Thanks lennaert! Also, it's probably not normally possible to run PHP with Node Webkit without some sort of modification to Node Webkit itself, is there?
I guess since this isn't working for me I'll just use Node Webkit. My plan was to use PHP for file system management, under the impression that it was as universal as Javascript. I had no clue how to use PHP, I go and learn a bit of it, and now it was a waste of time XD.
Still, thanks for the help on this subject! I'll definitely be needing to know these things when I set up my own game server.