Ok so I'm lost here, frustrated and pulling my hair and out. Plus probably about to be fired or take a pay cut.
I moved Files from a development server to my local machine. The files are consistent (used diff tool), all the dependencies are there. It works for the most part. The problem is that the some of the javascript (not all) is just not working. We're using jquery and a lot of plugins for it. I've checked with the web developer plugin in firefox and all the js files are loading. I cleared the cache in both firefox and chrome multiple times to no avail. The development server is a windows server running wamp. My local machine is running ubuntu. Somebody tell me what I missed.