Success!
OK, it seems this is a problem with MSys or MSysGit mangling the Windows paths. Our local Git guru, with background input from Git support and my tests, helped me write a shell script to do two things: 1) Return the Windows absolute paths. 2) Convert the forward slashes to back slashes. Here are the details on _LVCompareWrapper.sh: File location: On my machine, this file is in the C:UsersPaulAppDataLocalProgramsGitbin directory. The actual filename does not matter, as long as the configuration item in the .gitconfig file points to it. The file contents are presently: #!/bin/bash # Method to determine absolute path # The -W parameter on the pwd command is necessary to return the Windows version of the path. # Not using the -W parameter will result in a conversion of temp directory to a 'tmp' path meaningful only in the Linux # environment. # Piping the result through tr '/' '' translates the forward slashes to backslashes. # Windows understands forward slashes, but LVCompare.exe does not. abspath () { ( DIR=$(dirname "$1") FN=$(basename "$1") cd "$DIR" printf "%s/%s" "$(pwd -W)" "$FN" | tr '/' '' ) } lvcompare="C:Program Files (x86)National InstrumentsSharedLabVIEW CompareLVCompare.exe" local=$(abspath "$1") remote=$(abspath "$2") exec "$lvcompare" -nobdpos -nofppos "$local" "$remote" # For the options, see http://zone.ni.com/reference/en-XX/help/371361H-01/lvhowto/configlvcomp_thirdparty/. Of course we need to modify the global .gitconfig file, too. Here are the details: This is the global .gitconfig file. On my machine this resides in the C:UsersPaul directory. The relevant part of the file (set up to work with SourceTree, but it is possible to use another tool or to use the wrapper tool via the git difftool command) presently is: [diff] tool = "sourcetree" [difftool "sourcetree"] cmd = ''C:/Users/Paul/AppData/Local/Programs/Git/bin/_LVCompareWrapper.sh'' "$REMOTE" "$LOCAL" # Note that the parameters are actually passed in reverse order to the wrapper. The parameter reversal does seem to me to be a bug in SourceTree. Paul