Fix usage of the jQuery global in a few spots.

Fix usage of the jQuery global in a few spots.
- jQuery changed to $ in some files because there is a closure that creates a locally scoped $, but the jQuery var is globally scoped, meaning using jQuery instead of $ inside that closure could result in interacting with a different instance of jQuery than the uses of $ in that same closure.
- In mwExtension wrap the code inside a closure which it is missing. Also take this chance to fix the whitespace style `fn( arg )` instead of `fn(arg)` on the isArray I added.
This is partially a followup to r94331.

Note: The jquery plugins inside the jquery/ folder look fine for use of jQuery within closures, except for mockjax.