base.js will be automatically recreated, so you don't even have to delete it. It is just a minified combination of all the /js files.
For some reason when you combine the jquery v1.11 and jqueryui files it gives you virus failure (even though they pass when scanned individually, which is why I believe it is a false positive).
I updated the files to jquery v.1.12 and found the combined version no longer has issues.