the plugins "project file patterns" are there to define where you tag parse for symbols I presume, not really anything to do with searching.
Nope, they are used for searching alright when you select "Project" in the "Find in Files" dialog. But these patterns are used to define which files/directories to search in (such as *.c) and not which files/directories NOT to search in (such as .git) which is what @van-de-bugger suggests.