[diff]
    tool = intellij
    guitool = intellij
[difftool "intellij"]
    path = D:/Program Files (x86)/JetBrains/IntelliJ IDEA 2016.2/bin/idea.bat
    cmd = cmd \\"/C D:\\\\workspace\\\\tools\\\\symlink\\\\idea\\\\bin\\\\idea.bat diff $(cd $(dirname "$LOCAL") && pwd)/$(basename "$LOCAL") $(cd $(dirname "$REMOTE") && pwd)/$(basename "$REMOTE")\\"

The one gotcha here is that this cmd property does not accept any weird characters in the path. If your IDE’s install location has weird characters in it (e.g. it’s installed in Program Files (x86), you’ll have to create a symlink