remove set -e, some tests were causing the script to exit silently, upda...

Minor updates, and removing set -e. The script was exiting silently when testing for existence of files/commands.
The set -e is intentional. We want the script to fail if any of the commands fail. You can run the test command in a subshell which shouldn't inherit the set -e. If you want to remove the set -e, can you add better test conditions with error messages? The idea is that this script can be run multiple times (as it often fails as systems diverge, it was last tested on a Mavericks machine) but it shouldn't be re-running commands it has already run. Happy to work with you on this :)