reinstate standalone flag and remove .bundle in vendor task

the "standalone" flag during rake bootstrap is needed to generate the bundler setup.rb flag.
However, that generates a "tools/.bundle/config" file that sets the BUNDLE_PATH and will later mess with `rake plugin:install-defaults`, forcing all plugins to be installed in "vendor/bundle" instead of "vendor/plugins".

Setting "--path" in `rake plugin:install-defaults` isn't an option because then gems from "vendor/bundle" will not be reused, generating many duplication and some installation errors.

The only option I could find was to remove the ".bundle" dir after running `rake vendor`'s "bundle install"

Closes #2183 
+1 on improving how we invoke bundler later.