CompilationDatabaseProjectManager: Clang Code Model lost "BuiltIn" header paths, stdlib headers can't be found [4.9 beta1 regression]

Loading a compile_commands.json / CompilationDatabaseProjectManager project in 4.9-beta1 (2857, or current git master) lacks the system paths provided by the compiler, meaning STL headers like vector won't be found.

Loading that project in 4.8.1 works, and loading a simple GenericProject with 4.9-beta1 also works, i.e. it has the corrects paths.

To reproduce with test.cpp and these two project types:

echo '#include <vector>' > test.cpp
clang++ -c test.cpp -o test.o -MJ test.json -I/includepath -isystem/includepath2
{ echo '['; cat test.json; echo ']'; } > compile_commands.json

touch gp.creator gp.includes gp.config 
echo test.cpp > gp.files

Tools -> C++ -> Inspect C++ Code Model (or Ctrl-Shift-F12) -> "Header Paths" Tab shows that only includepath and includepath2 are present when the compile_commands.json is loaded.