(PUP-586) Deprecate Instrumentation System

The instrumentation system is being removed in Puppet 4.0.

This commit is for adding a deprecation message on the subcommands for
users to migrate off of it before it is finally deleted.
Merge pull request #2998 from demophoon/deprecation/master/deprecate-instrumentation-system

(PUP-586) Deprecate Instrumentation System