Comment 9 for bug 1432882

I could spot the difference between the two versions. It can be seen by running:
./refgen test.cpp -std=c++11 -v

With the ubuntu libclang, the output I get is (stripped to the essential bits):
Selected GCC installation: /usr/lib/gcc/x86_64-linux-gnu/4.8
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../include/c++/4.8/x86_64-linux-gnu"
ignoring nonexistent directory "../lib/clang/3.4/include"
ignoring nonexistent directory "/include"
#include "..." search starts here:
#include <...> search starts here:
 /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../include/c++/4.8
 /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../include/c++/4.8/backward
 /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../include/x86_64-linux-gnu/c++/4.8
 /usr/local/include
 /usr/lib/gcc/x86_64-linux-gnu/4.8/include
 /usr/include/x86_64-linux-gnu
 /usr/include
End of search list.

However, with the PPA libclang, the output is:
Selected GCC installation: /usr/lib/gcc/x86_64-linux-gnu/4.8
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../include/c++/4.8/x86_64-linux-gnu"
ignoring nonexistent directory "../lib/clang/3.4.2/include"
ignoring nonexistent directory "/include"
#include "..." search starts here:
#include <...> search starts here:
 /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../include/c++/4.8
 /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../include/c++/4.8/backward
 /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../include/x86_64-linux-gnu/c++/4.8
 /usr/include/clang/3.4.2/include
 /usr/local/include
 /usr/lib/gcc/x86_64-linux-gnu/4.8/include
 /usr/include/x86_64-linux-gnu
 /usr/include
End of search list.

It is essentially identical, except that the PPA version has one additional line that makes it all work:
 /usr/include/clang/3.4.2/include

Now where this line came from, or why was it removed in the official ubuntu version, I have no clue... I will contact the author of the PPA to see if he could help.