Encountered this exact problem myself and determined the cause for the "setting classpath containers" action taking a very long time (or appear to just hang) is a that there is a large amount of content in your build output folder (for maven projects, that is normally the folder/directory at {project_root}/target) and it is causing eclipse (for some reason) get stuck on the "setting classpath containers" action.

Try to following to resolve the problem:

1. Close eclipse (you might have to kill pr end task eclipse to get it to close).
2. To avoid deleting anything important, do a review your
   {project_root}/target folder and its contents to make sure there
   isn't anything in that folder that you placed there yourself (aka
   anything you know for sure you need to keep around and should not
   delete - would be a special case scenario).
3. Open your favorite shell and remove everything under the {project_root}/target folder (excluding, of course, anything that you identified in step #2 that needs to remain).
4. Re-launch eclipse and hopefully that problem is resolved.