Include folders are set on the Project tab of the project's configuration. Include folders can and may contain subfolders. Documents inside the Include folder, include documents, cannot be renamed and no model can be created from them. They cannot be renamed because they are included in other documents by name. It is impossible to create a model from them because they should be designed to be included and as such they are incomplete model documents. Consult the ITP documentation about the role of include documents.
Note
You may need to compute the dependencies in a project for the ITP/MDK Repository to know which documents are included in other documents. This means that not in all cases the ITP/MDK Repository will stop a rename of an included file. The best way to avoid this situation is to compute the dependencies after an import and after the creation of an include document. Refer to Compute dependencies for more information on how to compute dependencies.