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I've found that when EMF Compare opens in Merge Tool during EGit merge/rebase conflict resolution, there is no options to move changes from one model to another. I makes EMF Compare only capable of showing differences, but not capable to merge. initial forum thread: http://www.eclipse.org/forums/index.php/mv/msg/262814/759184/#msg_759184
Created attachment 225812 [details] Repository to easily reproduce This bug is due to EGit using its own CompareEditorInput, and EMF Compare not being able to infer all necessary information from there. It will not be fixed for 1.3. For 2.1, This bug is even worse as an NPE is thrown right at the opening of the merge tool. Attached is a zipped git repository which only includes a single project "sandbox" and two branches : master and conflictual. Simply import "sandbox" into a workspace, checkout "conflictual" and try to rebase on "master". This will trigger the detection of a conflict on "sandbox/My.ecore". Trying to open the merge tool (right-click on conflictual file > Team > Merge Tool) on that ecore will trigger an NPE from EMF Compare.
fixed in 1294c59f24d8450799661d58918fc82bc724fd11