So I have managed a work around by specifying ${PWD} before the LinkDef file. Which gives it a specific one. But I think rootcint should check the pwd for a LinkDef file before searching the include directories. I am not sure what caused this problem, especially since I have not see it on any other systems. I do have ‘-I./’ before all the other -I{Dir} flags. Perhaps its attempting to parse ALL the LinkDef files? In which case I do not see why it should do that.
As for renaming each LinkDef file. Thats beyond my control. I dont write the software. And this has never been a problem before.
–Jon