added a comment - - edited
I'm using Grails 1.3.7. I have customised scaffolding view templates. If I run "grails generate-views my.DomainClass", I get asked for confirmation to overwrite view GSPs even if no views have been generated before.
The problem seems to be in the org.codehaus.groovy.grails.scaffolding.DefaultGrailsTemplateGenerator class. The generateViews method generates a view for each template file retrieved by getTemplateNames, but getTemplateNames looks in different locations for template files and does not remove templates with duplicate file names (disregarding the directory path). My guess is that it returns the default templates from $GRAILS_HOME/src/grails/templates/scaffolding/*.gsp and then the customised templates from <app>/src/grails/templates/scaffolding/*.gsp and then generateViews generates GSP files with the same names as the template files, even if there are several template files with the same name. It is just fortunate that the customised templates happen to be generated last. This would explain the confirmation messages and double generation.
The problem will be absent if no customised templates are present, so that might have been a barrier to reproducing this bug. Just run "grails generate-templates" first and then watch "grails generate-views" ask for confirmation to overwrite files that never existed before.
If this is fixed by removing template files with duplicate names, the documentation will need to make it clear which template locations take precedence over others. The code seems to look for templates in about six different places, though some are mutually exclusive.