re-add indentation semantics to Gemfile

during a previous commit
(SHA 10e7b5b003bea9aea3286b9170f5e04b8a9e3735)
we removed indentation of gems, but this indentation
had semantic significance for us: any gem which was
not required by canvas but was required by another
gem required by canvas was indented. This allowed us
to clarify that canvas didn't actually use the gems
while still locking into specific versions of each

Also added a comment explaining this to Gemfile

Change-Id: I0f476e1bed6156f2f5969e54d56d44ded5442a0f
Reviewed-on: https://gerrit.instructure.com/32588
Tested-by: Jenkins <jenkins@instructure.com>
Reviewed-by: Simon Williams <simon@instructure.com>
Product-Review: Anthus Williams <awilliams@instructure.com>
QA-Review: Anthus Williams <awilliams@instructure.com>