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Linker .cmd files

I'm trying to build a project for the C6678 having configured for using some SYS/BIOS task, semafore etc. and some basic NDK functions included by using the graphic .cfg editor.

Everything compiles, but I am not able to link the project. I have made my own linker command file, I want to control which section is loaded where in memory, but somehow the linker gets additional input from a file ./configPkg/linker.cmd file, so my memory definitions clash with definitions in that file. This linker.cmd file have a header:

/*
 * Do not modify this file; it is automatically generated from the template
 * linkcmd.xdt in the ti.targets.elf package and will be overwritten.
 */

so I'd better not edit this file.

So my problem is, how to get rid of usage of this file, or how can I control the content of this file?

Odd Trandem