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ccs5 project changes not remembered

I am changing the layout of C and H files under my project folder. This requires changing the Include Options.  After changing the Include Options I successfully rebuilt the project. 

But, after closing and reopening ccs5 my changes are not there, the old paths are still in the Include Options. All of the files are read-only under source control.  One time ccs5 locked up but has never displayed an error. 

After trying various combinations of checking out .??project files I found that the .cproject file was changed after changing the Build Options.

Is that right?  Do I need to check out the .cproject? (in ccs4 it was the .project file) Maybe ccs5 should give a warning that .cproject is read-only when I try to change Build Options?