Okay I think I figured it out.
In file, notify_functions.sh in the scripts folder of the EggTimer workflow, the $notification variable isn't set. I think this is because the plist info.plist file doesn't carry over to Alfred 3 perfectly.
I just hard coded
notification=NC
at the top of the file, just below function definition.
Here's my whole notify_functions.sh file:
notify () {
notification=NC
#What is the chosen notification method?
prefs=$(cat info.plist | tr -d '\n\t') #Load workflow's settings info
if [[ "$prefs" = *'<key>output</key><integer>0</integer>'* ]]; then
notification=default
fi
if [[ "$prefs" = *'<key>output</key><integer>1</integer>'* ]]; then
notification=NC
fi
if [[ "$prefs" = *'<key>output</key><integer>2</integer>'* ]]; then
notification=growl
fi
if [ $notification = default ]; then
notpref=$(cat ../../preferences/notifications/prefs.plist | tr -d '\n\t')
if [[ "$notpref" = *'<key>defaultoutput</key><integer>1</integer>'* ]]; then
notification=growl
else
notification=NC
fi
fi
if [ "$5" = alarm ]; then
growl_icon="$PWD/resources/icon_alarm.png"
nc_icon="$PWD/resources/icon_alarm.icns"
dummy_app="EggTimer Alarm"
else
growl_icon="$PWD/icon.png"
nc_icon="$PWD/resources/icon.icns"
dummy_app="EggTimer"
fi
if [ $notification = growl ]; then
osascript <<EOD
set imgfd to open for access POSIX file "$growl_icon"
set img to read imgfd as "TIFF"
close access imgfd
tell application id "com.Growl.GrowlHelperApp"
notify with name "$1" title "$2" description "$3\n$4" application name "EggTimer for Alfred" sticky "true" image img
end tell
EOD
fi
if [ $notification = NC ]; then
./MountainNotifier/MountainNotifier "$dummy_app" "$2" "$3" "$4" "$nc_icon"
fi
}
Hope that helps!