Plugin fixes jul2014

+Fix on closing plugin windows: plugin really stopped.
+Added settings to documenting with Doxygen (file "Doxyfile"). Started some documenting on EmulationCore/Propeller.cs, GUI/Emulator.cs, GUI/PluginEditor.cs, etc.
Ahh, OK. I'll take care of it, because I only added the 'public' modifier and I didn't see the indentation.
In the next edition I'll change it. Thanks.