Add layers for colored probe types or enablelayer (#3984)

Fix a bug where a layer definition would only be added to Builder state if
it was used in a layer block.  Also add these layers to the Builder state
if they are used by a layer-colored probe type or by a module's enable
layer.

Fixes #3983.

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