When I use template from 
- to template-cleanup put files which should overwrite the default. For example my gradle propeties has group and name fields.
It will be rewritten by this part of code
GROUP="com.companyname.$SAFE_NAME"
and moved to root by this
cp -R app/src/main/java/com/companyname/template/* app/src/main/java/${GROUP//.//}/