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I was verify some changes I made by self-hosting (launched using debug). Much to my surprise, the expected new behavior did not appear. It did appear yesterday but not today. When I tried to debug, it was obvious that the source code in the debugger did not match the code it was running. There were no errors on launch, nothing in the log and the laucnh configuration appear to have the proper plugins selected. A rebuild of all projects did not fix the problem. Now I'm stuck. I have F3 fixes I would like to verify before submitting but I can't because Eclipse won't run the code!
I managed to fix the problem. I deleted all my launch configurations. This didn't fix the problem. Then I stated with a fresh workspace. This fixed the problem. Why would my workspace contents effect how PDE works?
It was not the workspace content, it was the .metadata. You probably had some plug-ins selected in the list of external plug-ins (in the preferences) or in the launch configuration. PDE was simply passing the plug-ins to the run-time instance even though there were duplicates. I added the code to warn about duplicates. A warning dialog will show up. After the dialog, PDE will resolve duplications by picking the workspace versions. Therefore, this will allow you to run the 'right' code and also be warned to fix your configuration to avoid the dialog altogether.