How can I make WinMerge my git mergetool?

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You are talking about merge tool, yet you (and some other people with answers) are configuring it as a diff tool.

To configure a merge tool, you’d need to use merge.tool and mergetool configurations instead of diff.tool and difftool, like this:

git config --global merge.tool winmerge
git config --replace --global mergetool.winmerge.cmd "\"C:\Program Files (x86)\WinMerge\WinMergeU.exe\" -e -u -dl \"Base\" -dr \"Mine\" \"$LOCAL\" \"$REMOTE\" \"$MERGED\""
git config --global mergetool.prompt false

And then you can use

git mergetool

which will open you the two files to edit.

Kudos for @dvdvck mentioning in the comments that in command line parameters you can specify a third file for the result file for winmerge (outputpath parameter).

For completeness, I’ll mention that there is also this gist aimed at full configuration of winmerge for both as diff and merge tool.

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