I am obviously overlooking something very simple here, but I am not seeing it. The command
webstorm diff ~/test.txt ~/test2.txt
runs the J
I just had the same problem. My git diftool configuration has been set up in my ~/.gitconfig and has been working fine, but today weirdly git difftool worked in one repo but ran git diff in another.
Fix: I updated from git 2.11.0 to git 2.11.1 and the problem seems to have gone away.
The git 2.11.1 release notes mention fixing a difftool-related regression. The described problem isn't what I was seeing, but maybe the fix fixed it anyway.