If my ruby script already has a require "bundler/setup", whenever I call a shell command (I've tested with `` and IO.popen) to execute a bundle install, it will use my project's current Gemfile instead of the Gemfile residing in the shell environment directory.

This bug seems a regression, because it worked fine back in version 0.9.

Steps to reproduce:

1. Clone the repository: git://github.com/diogob/bundler_test.git
2. Install the bundle with bundle install
3. Run ruby test.rb
4. It will print bundle install's output, which will install the json gem. It should install the git gem, which is in the current directory's Gemfile when the script calls bundle install.