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1. Create web application with JSF framework. 2. Rightclick web application's root node and choose "New > JSF Managed Bean". 3. Leave default bean name and add "my.test.stuff" for package. 4. Click "Files" tab, expand "src" node until added bean, rightclick "stuff" folder and choose "Refactor > Safely Delete" and delete this folder. Result: Folder is deleted with managed bean, but faces-config.xml still contain record for it. When I did preview, I didn't see faces-config.xml in the tree, but it should be there.
This is somehow an intended behavior. While users working on 'Files', the IDE usually not considers it as a 'project point of view' action. And hence it won't modify the other files because it's risky. We are currently only supporting Safe Delete for Projects logical view related to the faces-config.xml contents. This is most users do for their projects. *** This issue has been marked as a duplicate of 137476 ***