Added ability to specifiy root directory

This fixes issues when files are being required from a directory which is above ```__dirname```.

Resolving ```path.join(cacheDir, path.relative('.', filename))``` where  ```cacheDir = '../.coffee/'``` and ```filename = '../common/example.js'``` = ```../common/example.js``` 

where as we actually want ```../.coffee/common/example.js```