When the writer is launched from rules or Java code, you can set options to tweak the writer's behavior.
Map options = new HashMap();
options.put("ignoreStereotypeApplications", Boolean.TRUE);
Model umlModel =...
umlModel.write("XMI 2.1", "c:\\path.xmi", options);
The model writer can be configured using many options. Here is a list of the options:
ignoreStereotypeApplications
falsediagramInterchange
falseseparateProfileFiles
falseseparateDiagramInterchangeFile
falseincludeOMGProfiles
false