Update: it seems from the comments below that the questionnaire needs a later version of git -gui / msysGit. However, there are several other problems that I experienced when trying to reproduce the problem described below.
I think I was able to reproduce this: the problem is that I have the "Use TextConv for Differences and Benefits" checkbox selected in the Git Gui Edit > Options... dialog box. When I turned off this option, it worked fine - counterintuitively, in my opinion, although it is also described on the TextConv page on the Git wiki wiki .
Another problem I ran into was that the converter I tested with (lines) was not in my path, so I had to put the full path in my .gitconfig:
[diff "stringify"] textconv = c:/cygwin/bin/strings.exe
However, if this was a problem for you, I don’t think you would even see the message “Binary files A and B differ”, so I suspect this is the first problem.
Mark Longair Jan 16 2018-11-16T00: 00Z
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