CMD3 is just for sdk v2.1 and up. Previous sdks must be processed with the old sdk tools v2.
So you will have to either upgrade your app to sdk v2.1 or stick with sdk tools v2.
In CMD3 the command to upgrade is from the app folder 'sencha app upgrade ..\sdkfolder'. However upgrading may not work automatically as a lot of things have changed. Make sure you have a copy of your project before trying!! In case it fails you will have to do it 'manually'.