I'm working since a half year with Egit and Github, and it works quite well. My workflow works with many different Branches, where every new feature or Bugfix is a new branch which will be merged into the master branch when finished. My question is, is it possible to apply the changes in the master branch to all other active branches. Thanks.
Have you tried:
1) Switching to the branch in your local eclipse (right click project name -> Team -> switch to -> your branch)
2) Then doing a fetch from upstream (Team -> Fetch from upstream)
3) Then doing a merge from master (Team -> Merge -> click origin/ master)
This will merge all changes from master into your current checked out branch. Then you can just commit and push. Ultimately you can also replace steps 2 & 3 with a pull (Team -> Pull) as well if it is configured. I am not sure if there is an easier way, but you would do this for each branch you want updated.