Fixes generated source maps root paths

This PR fixes the root path generated in the source map.

Assuming `cjsify manifest.js`, the following code which was generated :

    { ..., "sourceRoot" : "/home/arcanis/project/" }

Will become (with `--source-map-file project.map.js`)

    { ..., "sourceRoot" : "." }

Or, with `--source-map-file misc/project.map.js`

    { ..., "sourceRoot" : ".." }

**Note** : I have also fixed the Makefile since the last version of coffeescript does not seem to have the `--js` option. I assumed that it was the equivalent of `--print`, except that it reads from the file specified as the first argument instead of the standard input.