Respect silent mode in custom rules

Follow the instructions in the automake documentation to properly silence
commands in custom rules when silent mode is enabled.
Remove the only sub-Makefile.am.inc

We have more than one top-level directory in the project so it does not
make sense to only recurse into one to find Makefile.am.inc files.  Get
rid of the lonely instance of this instead of sharding the already-simple
top-level Makefile.am.