Address or suppress warnings.

Add `-deprecation` to `scalacOptions`, and `-Xlint:unchecked` to `javacOptions`, so we see details of warnings.

For *Classpaths.publishConfig* is deprecated*, set `overwrite = true`.

For *unchecked cast*, add `@SuppressWarnings("unchecked")`.

For *Possible heap pollution from parameterized vararg type T*, add `@SafeVarargs`.
Is this the same scalacOptions as in plugins.sbt? I wonder if the shared settings aren't getting copied properly.