Class not found exception
I am assuming we are looking at a normal Java application. Eclipse creates Run Configurations for normal execution and Debug Configurations for debug launches. And there is usually no significant difference between Run and Debug configuration for the same class.
The easiest way is to start cleaning: go to "Run Configs ..." and delete all Java Application configurations. Then do the same for "Debug Configuration". Then run the application once in normal mode and once in debug mode.
Alternative: go to a new workspace (File -> Switch Workspace), import the project (File -> Import ..., be sure to copy the content) and run / debug the app.
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Check your startup / startup settings. You probably have a different configuration to debug and run. Most likely the debugger does not point to the main class of your program.
Just check the debug ... option (pull down the debug menu, don't click the button, then click "Debug ...") and the first page should have a "Main Class" field. Use the same main class as in your run parameter ...
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