RequireJS jQuery fixes

@jessmartin, this adds the `shim` settings to the optimizer configuration which should put jQuery back as a dependency for jQuery UI, jquery-encoder, and require-hammer. This cleans up cases where jQuery was included multiple times in some compiled modules and where some included modules were nulled out.

The changes from the first commit shouldn't be needed any longer, but they don't hurt anything.

I removed the jQuery dependencies from `configuration.js` and `object.js`, which may help the build time. The updated optimizer might actually be slower though. I haven't tested minified versions yet.