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The context menu of a Git Repository contains an entry "Merge". This does not make sense and consequently does not work.
The menu entry does in fact make sense (it is "Merge...", not just "Merge") as it should bring up the same merge dialog as in Team>Merge on a project. Code review at http://egit.eclipse.org/r/#change,1464
Merged as 85597d526874d982748a106b75181016e26d2aaa