Enable ScalaDoc groups, ignore chisel3.internal

This adds the `-groups` option to `scalacOptions`. This makes ScalaDoc
build with group support such that developers can group methods using the
`@group <groupName>` tag.

This also adds the `-skip-packages chisel3.internal` option. This makes
ScalaDoc build while ignoring everything in the chisel3.internal package.

Signed-off-by: Schuyler Eldridge <schuyler.eldridge@ibm.com>