PDB-354 Deprecate old versions of commands

This patch drops a warning whenever an old version of the commands API is used
and updates the documentation to warn the user these old commands are
deprecated.

Signed-off-by: Ken Barber <ken@bob.sh>
Merge pull request #869 from kbarber/ticket/master/PDB-354-deprecate-old-commands

PDB-354 Deprecate old versions of commands