I guess i am missing something.
Based on the documentation i understand that linked resources are added to the makefile automatically.
Makefiles and the Nios II SBT for Eclipse
The Nios II SBT for Eclipse creates and manages the makefiles for Nios II software projects. When you
create a project, the Nios II SBT creates a makefile based on the source content you specify and the
parameters and settings you select. When you modify the project in Eclipse, the Nios II SBT updates the
makefile to match.
When you add a linked resource (file or folder) to your project, the SBT for Eclipse adds the file or folder
to your makefile with an absolute path name. You might use a linked resource to refer to common source
files in a fixed location. In this situation, you can move the project to a different directory without
disturbing the common source file references.
A linked resource appears with a modified icon (green dot) in the Project Explorer, to distinguish it from
source files and folders that are part of the project. You can use the Eclipse debugger to step into a linked
source file, exactly as if it were part of the project.