Uniform bootstrap.sh with OCD variables.

This also gives more flexibility, since tools and appscale can not be on
different braches.
Added defaults branches for appscale and tools.
Fixed typo.
Typo and check that we restore missing confiles.
Added checks upon upgrade.

If appscale is running, it will need to be terminated. If we have a
straying monit process, terminating it.
Added --force-upgrade flag to bypass check.
Merge pull request #1531 from obino/use-botstrap

Uniform bootstrap.sh with OCD variables.