Un-optional the non-optional commands.
Merge pull request #146 from daenney/mv-optional-commands

Un-optional the non-optional commands.
Update specs and fix FM-1361

- Add install.rb for pre-suite
- Add catches for failures/changes to manifest application
- Correct root ssh key copying
- Add sleeps for killing processes releasing ports
- Fix FM-1361
Merge pull request #145 from hunner/fix_beaker_tests

Update specs and fix FM-1361