Fix bundler on Railsify

#65 almost but didn't quite fix #64 for me.  It got through the bundle install step, but failed to find bin/knife on the next line.  I believe this is because it finds the binstub, but not the knife gem.

It works if I widen the Bundler.with_clean_env block so that it covers all the commands using the generated bundle.

P.s.: This diff is much clearer with git diff --ignore-all-space (aka -w) since most of the change is just indenting a block.