Make the CommonJs functionality optional

The Common/Js functionality of the JS compiler is supported by default when the RequireJs functionality isn't required. This PR changes that so that Common/Js functionality has to be explicitly enabled given that it causes problems on Windows. This behaviour is also inline with the closure compiler where Common/Js handling has to be explicitly enabled.

The PR is aimed at 2.2.1 given that something has changed and js compilation is failing consistently on Windows. I'm personally unsure how it ever worked on Windows when used in conjunction with Common/Js.