Respect fileExclusionRegExp in initial build directory copy

Currently the entire appDir or baseUrl directory is copied over initially. This is unnecessary, and if there are other directories or files in the appDir that are supposed to be ignored (per the fileExclusionRegExp option) there can be unwanted side-effects to having R.js muck with them.

I'm not sure if this change should be here as well: https://github.com/jrburke/r.js/blob/master/build/jslib/build.js#L274