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Same here on Ubuntu 15.10. Tried Unity versions 5.3.2, 5.3.3, 5.4.0. Devs, any news on this issue? It has been a month since first reported.
UnityYAMLMerge doesn't work for me on Ubuntu 15.10. Here is the output I get: $ git mergetool --tool=unityyamlmerge Merging: myGame/Assets/Game.cs...