Fixed filepaths in included documents and fixed nested includes.

 - Changed how links were handled: Now transformMarkdown accepts a optional baseUrl parameter, which is appended to all links and images if they're relative to the document folder.
 - "transform" stage now creates an countDownLatch instead of a $.Deferred object. That allows loadExternalIncludes() to be recursive, only resolving the latch when all included files are ready, and to remain consistent.
 - loadExternalIncludes() now accepts an optional $dom parameter, a JQuery object containing the context in which included files must be resolved. If it's missing, loadExternalIncludes() resolves all includes in the global DOM.

From Issue #24