Illuminati: Fix reset of tree status and update Gemfile

After a commit, we would return before resetting @treechanged causing
all subsequent commits to happen regardless of there actually being a
change. This did not cause any corruption but would result in pointless,
empty commits.

Additionally, the net-ssh Gem has been updated with our fix for the
maximum packet size, so we have switched back from our own git repo to
the official one.