support the concept of baseUrl

Currently a lot of AMD implementations depend on the require.js [baseUrl](http://requirejs.org/docs/api.html#config-baseUrl) config property to resolve modules properly. This implementation does not seem to support that concept, so a lot of work must be done to modify existing modules to follow a node-like directory structure.

I'd love it if this module automatically took care of that so we don't need to resort to any sort of mass file modification as we start to bring common.js modules into our codebase.

Start by reviewing how the transform currently resolves AMD modules and compare that behavior with require.js's baseUrl concept. Confirm the expected behavior against modules that use baseUrl and determine how CommonJS modules should resolve without mass file modification; done means those modules transform and resolve correctly with coverage for the new behavior.

Written by the indexing model from the issue text.