change usage of deprecated SshMachineLocation.run, and misc deprecation fixes
log and be more forgiving when user is mis-specified (set as config but not picked up as flag);
encountered due to mistakes in ibm cloud resolver, which are fixed there, but these warnigns would have helped a lot!
ensure config keys passed in location spec are applied to flags (this was the underlying cause of ibm setup failures)
Merge pull request #925 from ahgittin/fix/sshmachine-deprecation

Fix/sshmachine deprecation