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I had closed the iphone simulator after running my app. monodevelop didn't seem to register that the app had stopped running (it has definitely stopped running, according to ps...)
I tried re-running the app and MD popped up a dialog that said "the app is presently running, would you like to stop it?" I clicked yes, but no change (and no app started.)
I hit Cmd-q at that point, and MD asked if I wanted to close the project, to which I clicked Close Project. All pads went away and I'm left with an empty monodevelop window.
I hit Cmd-q again and got an exception dialog (the app is still running):
Error while executing command: Quit.
System.Exception: There is no logger registered with the name 'MonoDevelop.Ide.Gui.Pads.InternalLogPad'
at MonoDevelop.Core.LoggingService.RemoveLogger (System.String name) [0x0002f] in /private/tmp/source/monodevelop/main/src/core/MonoDevelop.Core/MonoDevelop.Core/LoggingService.cs:127
at MonoDevelop.Ide.Gui.Pads.InternalLogPad.Dispose () [0x00000] in /private/tmp/source/monodevelop/main/src/core/MonoDevelop.Ide/MonoDevelop.Ide.Gui.Pads/InternalLogPad.cs:295
at MonoDevelop.Ide.Gui.DefaultWorkbench.OnClosed (System.EventArgs e) [0x0009f] in /private/tmp/source/monodevelop/main/src/core/MonoDevelop.Ide/MonoDevelop.Ide.Gui/DefaultWorkbench.cs:651
at MonoDevelop.Ide.Gui.DefaultWorkbench.Close () [0x000b3] in /private/tmp/source/monodevelop/main/src/core/MonoDevelop.Ide/MonoDevelop.Ide.Gui/DefaultWorkbench.cs:686
at MonoDevelop.Ide.Gui.Workbench.Close () [0x00000] in /private/tmp/source/monodevelop/main/src/core/MonoDevelop.Ide/MonoDevelop.Ide.Gui/Workbench.cs:128
at MonoDevelop.Ide.IdeApp.Exit () [0x00000] in /private/tmp/source/monodevelop/main/src/core/MonoDevelop.Ide/MonoDevelop.Ide/Ide.cs:393
at MonoDevelop.Ide.Commands.ExitHandler.Run () [0x00000] in /private/tmp/source/monodevelop/main/src/core/MonoDevelop.Ide/MonoDevelop.Ide.Commands/FileCommands.cs:372
at MonoDevelop.Components.Commands.CommandHandler.Run (System.Object dataItem) [0x00000] in /private/tmp/source/monodevelop/main/src/core/MonoDevelop.Ide/MonoDevelop.Components.Commands/CommandHandler.cs:61
at MonoDevelop.Components.Commands.CommandHandler.InternalRun (System.Object dataItem) [0x00000] in /private/tmp/source/monodevelop/main/src/core/MonoDevelop.Ide/MonoDevelop.Components.Commands/CommandHandler.cs:42
at MonoDevelop.Components.Commands.CommandManager.DefaultDispatchCommand (MonoDevelop.Components.Commands.ActionCommand cmd, MonoDevelop.Components.Commands.CommandInfo info, System.Object dataItem, System.Object target, CommandSource source) [0x00076] in /private/tmp/source/monodevelop/main/src/core/MonoDevelop.Ide/MonoDevelop.Components.Commands/CommandManager.cs:649
at MonoDevelop.Components.Commands.CommandManager.DispatchCommand (System.Object commandId, System.Object dataItem, System.Object initialTarget, CommandSource source) [0x002d1] in /private/tmp/source/monodevelop/main/src/core/MonoDevelop.Ide/MonoDevelop.Components.Commands/CommandManager.cs:619
*** This bug has been marked as a duplicate of bug 5647 ***