To reproduce create a DFS with two registers pg0/r0 and r0 (the same name, but one inside a page, the other on the top level). Select Tools->STG->Generate STG. The following exception is thrown:
Exception in thread "AWT-EventQueue-0" org.workcraft.exceptions.ArgumentException: The name "M_r0_0" is already taken. Please choose another name.
at org.workcraft.dom.references.UniqueNameManager.setName(UniqueNameManager.java:77)
at org.workcraft.plugins.stg.STGNameManager.setName(STGNameManager.java:305)
at org.workcraft.plugins.stg.STGReferenceManager.setName(STGReferenceManager.java:62)
at org.workcraft.plugins.stg.STG.setName(STG.java:285)
at org.workcraft.plugins.stg.STG.setName(STG.java:281)
at org.workcraft.plugins.stg.STG.createPlace(STG.java:89)
at org.workcraft.plugins.stg.VisualSTG.createPlace(VisualSTG.java:211)
at org.workcraft.plugins.dfs.stg.StgGenerator.generateRegisterSTG(StgGenerator.java:314)
at org.workcraft.plugins.dfs.stg.StgGenerator.<init>(StgGenerator.java:85)
at org.workcraft.plugins.dfs.tools.StgGeneratorTool.run(StgGeneratorTool.java:39)
at org.workcraft.util.Tools.run(Tools.java:38)
at org.workcraft.gui.MainWindow.runTool(MainWindow.java:1062)
at org.workcraft.gui.MainMenu$ToolAction.run(MainMenu.java:68)
at org.workcraft.gui.MainWindow$1.actionPerformed(MainWindow.java:108)
at org.workcraft.gui.actions.ActionMenuItem.fireActionPerformed(ActionMenuItem.java:58)
at org.workcraft.gui.actions.ActionMenuItem.access$0(ActionMenuItem.java:55)
at org.workcraft.gui.actions.ActionMenuItem$ActionForwarder.actionPerformed(ActionMenuItem.java:34)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
at java.awt.Component.processMouseEvent(Component.java:6505)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3312)
at java.awt.Component.processEvent(Component.java:6270)
at java.awt.Container.processEvent(Container.java:2229)
at java.awt.Component.dispatchEventImpl(Component.java:4861)
at java.awt.Container.dispatchEventImpl(Container.java:2287)
at java.awt.Component.dispatchEvent(Component.java:4687)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
at java.awt.Container.dispatchEventImpl(Container.java:2273)
at java.awt.Window.dispatchEventImpl(Window.java:2719)
at java.awt.Component.dispatchEvent(Component.java:4687)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:729)
at java.awt.EventQueue.access$200(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:688)
at java.awt.EventQueue$3.run(EventQueue.java:686)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
at java.awt.EventQueue$4.run(EventQueue.java:702)
at java.awt.EventQueue$4.run(EventQueue.java:700)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:699)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
A temporary solution is to disable the Pages support in DFS plugin.