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')
And using src `cwd`, `base` & `cwdbase` options, it should be possible to have exactly what anyone wants in file.relative. This might be a good idea to switch to relative.