Timothy,
I have no linked files in my workspace/projects.
I found a workaround for the problem. Fortunately, before I upgraded the compiler, I archived my project to source control, and checkpointed it. The solution was to restore the main project's .cproject and .ccsproject from the archive. I was then able to rebuild my project. Now I can uninstall 5.1.1 and continue development under 5.0.6.
From the TI CCS road map, 5.5 was originally scheduled for August. Good thing it's late. Hopefully they can get this fixed in there. Silver lining and all that.
Gerry Belanger