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The underlying issue is that the PlotRefComparator does only look at the commit time. If there are symbolic references, however, the commit time will not differ. Probably the comparator must take additional information into account when the times are the same. Ideally, the sorting should also be by type (tags, heads, remote). Alternatively, the AbstractPlotReneder could re-sort the array before drawing the labels. The symptom in the EGit UI is that if you hit refresh on the History View, sometimes the sequence of the branch and tag labels (and the HEAD label) changes. Also, tags, branches, and remote branches are wildly mixed.
Fixed by change Ifc3863461654df7f34fdecbd2abe1f4b5d2ffb8e http://egit.eclipse.org/r/2032