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Currently, after resolving a conflict with the merge tool, I have to stage the resolution myself in the staging view. This is a bit cumbersome, especially during an interactive rebase where I have to switch to and from the staging view all the time. The workflow of commandline git mergetool is nicer in that it will 1. stage the resolution if the mergetool changed the conflicting file 2. ask what to do if the mergetool returns without changing the file EGit should do something similar. But since it's not so obvious how one can accept the local version only, I'd suggest for 2. to ask if a) the incoming change should be discarded (or the local version accepted for resolution, not sure which is clearer) or b) if the merge has failed. For a) reset/stage as appropriate, for b) keep the conflict state