Hi,
Thanks for your help. It was the linker script import bug indeed. I also had to change the directory under C/C++ General to what you mentioned. Some of the .d files under the Debug folder had the same spurious paths though, so I had to manually change them to my workspace path (I did this step before fixing the linker script import bug, so I wonder if I had to do it at all had I fixed the import bug before).
I was able to build successfully, and program the zedboard as well.