e2 6.1 kpit gnu project migration

We have a e2 studio 5.4 project with KPIT Gnu 14.01 (RX62N CPU) running since a certain time. As we now want to migrate the project into the new e2 6.1 we are facing a problem that we cannot add additional input files to the linker, this section is disabled in the linker settings as the costum linkage order is.