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user .cmd problem

ccs4.1.2, dsp/bios 5.41

in spru423h, section 5.1.3, the documentation says "You should then create your own linker command file that begins by including the linker command file created by running the configuration script".  But when I do this I get errors becasue the bios generated cmd file is still being included in the linker command line.  In other words, the bios cmd file is being included twice.

now I am not sure haow this is supposed to work.  (an example would be nice... :)