Fix module names for "register" implementation

When compiling with "register" implementation, we found that modules names only contains file names. Ex :

    src/common/filter.js -> System.register("filter")

In contrario, [karma's traceur preprocessor](karma-runner/karma-traceur-preprocessor) produce the expected result:

    src/common/filter.js -> System.register("src/common/filter")

This tiny pull request fix this, without changing the current behaviour of others implementaions ('amd', 'commonjs')
I don't want to special-case `register` unless you can come up with some Traceur docs/code showing it needs to be. And even then, it should probably be fixed in Traceur.

I'm however open to changing the default to `options.filename = file.relative;` which should give you your desired effect.