Hi had something similar on my todo list for a while, every since having read about a feature like this in Spring Roo.
Suggestion (similar in Roo): check for .MyClassName or ~.subpkg.AnotherClassName and replace '' with the default app package name. This allows something like this:
grails create-app MyApp -base-package=com.example.greatapp
grails create-controller ~.web.MyController
grails create-domain-class ~.core.Person
grails create-taglib ~.web.support.MyTagLib
Of course the '-base-package' part would have to be stored somewhere. I'd suggest application.properties, as this can be modified programmatically, e.g. by creating a script 'grails set-base-package com.example.greatapp'.