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If I debug both Java and C/C++, once I've started the C/C++ debugger I can no longer set toggle breakpoints in Java files. Note that there are other problems intermixing Java and C/C++. I'm making this a P3 because this is only one of many and won't resolve the real issue of being able to debug both languages at once (althouth it does improve the situation, slightly).
Added call to GdbEngineProvider.getDestructor().killEngine() in GdbDebuggerImpl.finish(). That properly kills the engine and the session terminates properly.