How can I completely remove PHPStorm, and all associated files on Ubuntu 13.04?

Please remove the main folder and ~/.PhpStorm* folders. That should be enough.

sudo rm -R ~/.PhpStorm*

You usually can't uninstall files installed without your package manager by just deleting the directory you extracted, though this often is actually true of Java based archives.

I don't know phpstorm specifically, but I can give you some generic instructions.

The very first thing I'd recommend you do is check if phpstorm itself includes some kind of uninstall script. I'd guess you already did, though.

Failing that, you should open a terminal and type whereis phpstorm - this should tell you where most of the files associated with it are located. You could then try deleting them manually. /etc and /usr/share are also some likely places to look.

You could also search through the hidden files in your home folder for one called .phpstorm or the like. This would probably contain most of the configuration and I don't think would show up with the "whereis" command.

That's all I can think of off the top of my head if the shortcuts and the like are already gone, but it might do the job. This is a messy and ugly way of doing things and may well leave something behind - try to install with your package manager whenever possible.

On Ubuntu, after moving back to netbeans I also found traces of phpstorm hiding under ~/.java/.userPrefs/prefs.xml