Looking at a file in the three way diff it is not clear which commit is which
Answered
I think that the left panel is the branch being merged to, the right panel is the branch being merged from and the middle panel is the result. However, it is not easy to tell since there is no human identifiable information -- the version number hash are not "readable." It would be nice to have the branch names and other identifying information available above the panels, Maybe via a roll over.
Stuart
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Check the latest 2018.2 EAP - 3-way merge shows branch names there.
Also, vote on if you want to see more details https://youtrack.jetbrains.com/issue/IDEA-102522