We came across the same issue where files changed in the grails directory were not seen when we did a create-app. We came to the realization that what we really wanted was a way to quickly create an application with our customizations. Not that we need grails to create that app. Our solution was to create a skeleton application with the desired customizations and jar up the application directory. When we want to create a new app,
grails create-app foo
cp /custom-grails-app.jar .
jar xf custom-grails-app.jar
vi application.properties
And now we have an application with the desired structure. Not the most elegant approach. But it works! ;)