EGit
The recursive merge strategy needed for this is the default since EGit 3.0 (see bug 380314).
In case you are using an older version, see the download page for upgrading.
Workarounds
Alternatively, try resetting to your last local commit before you made the last merge, and then merge with origin/master
. Then if you made more changes on top of the original merge, cherry-pick these.
Another possibility would be to do the merge using C git (on the console), it can handle that situation.
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