Updating Eclipse from Juno to Kepler in 5 simple steps. My PDT(PHP), Ruby, EGit, and SVN plugins all work after the update.
1. Click Help > Install New Software.
2. Click the add button and add this location: http://download.eclipse.org/releases/kepler/
3. After a short wait, the location has been added, click Cancel.
4. Click Help > Check for Updates.
5. I updated all plugins so I clicked OK whenever it asked and I accepted license agreements.
This will run for a while as it downloads and installs, once it is done it will ask to restart Eclipse. After Eclipse restarts you should be on Kepler.