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When a Cherry Pick leads to conflicts the Merge tool is not enabled. The repository state is "SAFE" in this case. This leads to subsequent problems with commit (I'll open a separate bug for this).
The only indication that a cherry-pick failed in Git is that there is a .git/MERGE_MSG file and the index has unmerged paths. Repository.getRepositoryState has to be changed to test for this and CherryPickCommand needs to write MERGE_MSG on conflicting state. Will come up with a patch as soon as I get to it.
Pushed JGit change http://egit.eclipse.org/r/2996 and EGit change http://egit.eclipse.org/r/2997 for this.
JGit changes merged into master.
EGit changes were also merged.
egit change merged as d9dcc70255dacea97d1681c4b785c63b5b17ddde