Modifing the Makefile

This kind of thing is best achieved by using the linker script rather than relying on command line ordering, since this can be (and is) overridden by the ordering of the linker sections.

To place a particular function or variable into a given section, you should use either the section attribute or .section directives. Examples of how to use these can be found in the section "Advanced Placement Options" in the Nios II Software Developers Handbook.

You may need to create a new linker section to hold your code to ensure it gets placed in the correct relative location. In which case you should create a custom linker script based on the default generated.x. You can direct the IDE to use your new linker script from the system library properties page.

Documentation on how to write linker scripts can be found in the GNU ld manual, although you should hopefully be able to figure out how to define a new section using the examples given in generated.x.