Stop deleting Gemfile in plugin dev environment.

The change in pull request #4861 causes `Gemfile` to be deleted whenever a `bundle exec vagrant` command is run, preventing any more `bundle` commands before a `git checkout Gemfile`, making development extremely difficult.

This pull request simply reverts the merge commit 00e388a8977f519f077dda44aff2ddc4c1b9b05a.