If you've installed TortoiseGit, you can use the right click options to work with files. When inside Cygwin, you have the ability to call other programs too.
Edit your ~/.gitconfig with the following (adjust path if necessary):
[merge] tool = tortoise [mergetool "tortoise"] cmd = \"c:/Progra~1/TortoiseGit/bin/TortoiseMerge.exe\" /base:\"$BASE\" /theirs:\"$REMOTE\" /mine:\"$LOCAL\" /merged:\"$MERGED\"
Now when you need to resolve merge conflicts, type this:
git mergetool
Each conflict will open in TortoiseMerge
You can run git diff in an external editor, and/or use git difftool to run the external editor:
.gitconfig
[diff] tool = winmerge #this runs git diff in external tool #external = /cygdrive/h/git-diff-wrapper.sh [difftool "winmerge"] cmd = /cygdrive/h/git-difftool-wrapper.sh \"$LOCAL\" \"$REMOTE\"
git-diff-wrapper.sh
#!/bin/sh "C:/Program Files/WinMerge/WinMergeU.exe" -e -ub `cygpath -w $2` `cygpath -w $5` | cat
git-difftool-wrapper.sh
#!/bin/sh "C:/Program Files/WinMerge/WinMergeU.exe" -e -ub `cygpath -w $1` `cygpath -w $2` | cat