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Makefile and IDE build produce different target

I have written a parser to extract the amake dependencies from the final output file. I then use it with nmake to build the same source presumably in the same order since the same .lnp file is passed to the linker in the make file as is generated by the ide. The makefile build works but the target output file is different. Are there any optimizations or other issues which may be bypassed when the IDE is not used for the build?

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