daffodil root jar is published but shouldn't be, and its contents are wrong

Two issues here:

1. running 'sbt publish' or 'sbt publishLocal' will publish a root jar, even though we gave it the 'nopub' setting.
2. the contents of the root jar are exactly the same as the daffodil-cli jar (which is missing the 'nopub' setting).

The root jar shouldn't be published, and even if it were published, it should not contain CLI classes.

We might want to look into upgrading to sbt 1.0 to resolve this problem and switch to the newer sbt syntax. The current stuff is being deprecated if not already removed in 1.0.