added new flag, user_commands, and passing it to the AppController to exec
reading user_commands from appscalefile and passing it to run-instances
running commands specified by the user at the head node
added user_commands info to template files
added note in templates that stdout or stderr cannot be redirected in user commands
Merge pull request #341 from shatterednirvana/bootstrap-commands

Letting users specify commands to run on each node