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I accidently named a header file that I had added into the header section of the Workplace Explorer with a '.c' extension. I used the inbuilt right-click->rename function to rename the extension to '.h'.
However when attempting to build, the error
.\CortexM3\ARM_GCC_441\Release\CapSenseCommon.o: file not recognized: File format not recognized
was produced (the changed file was called CapSenseCommon.h).
To fix this (and it was not immediately obvious) I had to remove the file from the project and then add it back in, this fixed the bug. It was with a PSoC 5 device (and hence using the Code Soucery GCC compiler).