You made it a little difficult to review this because you mixed some refactoring in with the core change. I would greatly prefer two commits.

It seems like any program arguments other than file arguments results in no gui. That is pretty hard to confirm unless you make sure every option has gui = false. I would prefer a check like gui = filenameList.length == args.length.

I would be more comfortable with a g option to force a gui. I would expect nearly all scripts to use some arguments, but breaking existing any scripts people are using would leave a bad taste in my mouth. Is there a reason that an argument cannot be included for clicking files?

@TheThirdOne You're absolutely right - I've switched to only enabling the GUI if no arguments are passed (Current behavior) or if the g flag is passed, as well as split the changes into two commits.