Karabiner quit working in Sierra. How do I map my menu/application key to be Command?
Found the solution here https://github.com/tekezo/Karabiner-Elements/tree/master/usage

Uninstalled existing Karabiner
Installed Karabiner-Elements according to instructions in the link.
Created ~/.karabiner.d/configuration/karabiner.json
With the following JSON inside

{
    "profiles": [
        {
            "name": "Default profile",
            "selected": true,
            "simple_modifications": {
                "application" : "right_command"
            }
        }
    ]
}