Chris, the files and directories that I would tag for source control
- app (directory)
- framework (directory)
- build.yml (file)
Keep in mind that the directory content can contain changes you make i.e. public may have added images, and different build versions may also affect it. You should also make note of the build version you use as the gem's are tied to it.
Hope this helps
Gemfile.new is a tempfile created by the rhoconnect update command. Once you have modified your Gemfile as the command instructs, you can throw away this file. Gemfile.lock should always be checked into source control for an application (hence why it is not in the .gitignore).