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With a tiny project: $ ls FXMLDocument.fxml* FXMLDocumentController.java* SvgWebview.java* To reproduce: - Only have FXMLDocumentController.java open in the editor. - In the project view, right click on FXMLDocument.fxml, and choose "Open". This brings up the "Scene Builder" - Add a new fx:id to something in the scene with scene builder - save in scene builder (use external editor to verify .fxml file changed) - In the project view, right click on FXMLDocument.fxml, and choose "Make Controller" Observe in the open FXMLDocumentController.java that the newly added fx:id is not put into the file by the "Make Controller" action. Note that if I open the .fxml file and then perform the steps, it works as expected.
That last sentence should say "edit" not "open". More clearly read: ... if I edit the .fxml file with the IDE editor ...
There has been already filed an issue for this. Simple workaround is to select Source > Scan for External Changes to make IDE aware of the external changes. Then Make Controller action will work. *** This bug has been marked as a duplicate of bug 240037 ***