Normalize behavior of generated tracking.json file between different operating systems.

In OSX 10.7 ``options.files`` contains a list of paths relative to the project directory. In Windows and OSX 10.8 this path contains absolute paths. Systems that report absolute paths are unable to parse the tracking.json file and add absolute paths to the file causing it to be unusable to other developers.

This PR attempts to normalize the behavior between the files generated in different environments. The paths are made relative to ``config.watch.compiledDir``.