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In bug 344408 comment #1, Toni mentions that: "project-less debugging does not work natively on Windows, because the binary is not recognized as an executable by the default binary parser (which is always the ElfParser)."
I stumbled over the same problem: I choose a binary (compiled with MinGW) on my disk and try to debug it using Eclipse. According to the CDT-FAQ this should be possible in Indigo: When I run this debug configuration, I always get the error message "Program is not a recognized executable." To verify this, I created the simple "Hello World ANSI C Project" example which is integrated in the CDT plugin. I could compile and debug the "hello.exe" example and it works like a charm. If I close the Hello World project and create a project-less configuration like it is described in the FAQ, than I always get the error "Program is not a recognized executable" when i try to execute the same "hello.exe" example. My system: Win XP, Eclipse Indigo + CDT 8, MinGW, GDB 7.3.1
Maybe a way to fix this is to use what Marc-Andre used to get the JUnit tests to run on Windows. See Bug 378834 comment 2
This works now that bug 382462 is fixed.