Hi Stefano,
Normally an application would have its own linker file but since the FSLMQX is a huge software package supporting many processors and demo's, the linker files have been consolidated to the following path:
\Freescale MQX 3.5\mqx\source\bsp
with specific path for M52259EVB of:
\Freescale MQX 3.5\mqx\source\bsp\m52259evb\cw\intflash.lcf
When you compile the build_libs.mcp, it linker scripts are copied from the above path into the following path:
\Freescale MQX 3.5\lib\m52259evb.cw\mqx
You application or the demo (and \mqx\examples) reference the linker files in the \lib path.
So if you want to modify the "real" linker script it is the \mqx\source\bsp path.
Alternatively you can copy any of the linker scripts into your application path and load it into your project and use.
Regards,
David