PTFM-5911 Don't consider applets outside of dest dir to conflict.
PTFM-5911 Don't recurse when looking for apps to delete!
Write error message to stderr, not stdout.
Additional flags for disabling compile or upload steps.

Also add a flag to allow (or suppress) output of the JSON describe of
the final output object (app or applet).
Merge branch 'master' into PTFM-5906-cmake-fixes