Okay, so I got lost here, was disappointed and pulled my hair. Plus, probably going to be fired or take a picture.
I moved the files from the development server to my local machine. Files are consistent (a comparison tool is used), all dependencies are. It works for the most part. The problem is that some of javascript (not all) just don't work. We use jquery and many plugins for this. I checked with the web developer plugin in firefox and all js files are uploaded. I cleared the cache in both Firefox and Chrome several times to no avail. A development server is a Windows server running wamp. Ubuntu is running on my local machine. Someone will tell me what I missed.
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