Fix packaging to include sub-command dir for debian derivatives

Previously I hadn't included libexec_dir in the packaging, since we now ship
the sub-commands in this directory all sub-command based commands were failing
(especially puppetdb ssl-setup).

This also corrects a couple of documentation changes that were missed.

Signed-off-by: Ken Barber <ken@bob.sh>
Fix other legacy uses of puppetdb-ssl-setup to use the sub-command

While the old command still works, we should be eventually deprecating it so
this patch removes many more cases of its usage.

This also will remove any warnings from package installation.

Signed-off-by: Ken Barber <ken@bob.sh>