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On the CDT project, I display the repository in the History view and the graph shows the origin/master and origin/cdt_7_0 lines as a single line. I originally thought someone had merged the two branches together! But when I looked at the parent/child ids of commits, which are correct, I realized it was only the graph that was wrong. Note that gitk does not have this problem. This may be a duplicate of Bug 335818.
Rendering history is/was fixed with http://egit.eclipse.org/r/#change,4744 and http://egit.eclipse.org/r/#change,4735. I checked it with CDT and the mentionend branches and it looks good now. When http://egit.eclipse.org/r/#change,4744 is accepted I'll close this bug unless you find some problems with the proposal.
This has been fixed with commit 251bc02840a2e722a6cf660e4adde0e63d3d2de1
What is the Target Milestone for this fix?
This should go into EGit 1.2 which currently beeing prepared.