Answering this question because I couldn't believe that hard-coding paths comparisons was the only solution, and indeed, there is a clang_Location_isFromMainFile function that does exactly what you want, so that you can filter unwanted results in the visitor, like this :
if (clang_Location_isFromMainFile (clang_getCursorLocation (cursor)) == 0) {
return CXChildVisit_Continue;
}