Enable the Rubocop DeprecatedClassMethods cop

This reports uses of File.exists? and Dir.exists?, which were both deprecated in Ruby and will eventually be removed in favor of .exist?. Also fixes all existing uses of the deprecated methods.

LGTM.

@rspeicher want to merge before conflicts occur?

Status changed to merged

mentioned in commit 4735a753

@connorshea Now go to EE and make sure nothing there will fail once this is merged.