I'm having problems getting the warnings feature to work. I just installed ver 136 (I have plus). I opened an existing project and told embedxcode to upgrade when asked. I went into the Makefile and noticed the upgrade process did not add WARNING_OPTIONS. So I added:
WARNING_OPTIONS = unused-variable unused-function unused-label unused-value
You're right: the main makefile isn't updated because it contains specific settings to be kept, as the list of the libraries.
I took the option not to update the makefile to save the settings.
I put it right after the #SERIAL_BAUDRATE = 19200 line.
I created some variables that are not used and ran Build, but I didn't get any warnings.
Were the variables you created global or local?
Keep in mind compilation has optimisation options to remove unused portions of the code. Those optimisation options may interfere with the warning messages. Please refer to the Using the GNU Compiler Collection Manual.