External xcode build system - Shell Script Call error

I am creating a makefile project in xcode5 that works fine for the most part. This is an autoconf project with many subdirectories - it doesn't matter.

However, I have a problem with Problem Navigator. When I have an error in one of the files somewhere in my project, xcode correctly detects the problem and spits out the error in the Navigator Navigator - however, it seems that xcode cannot associate the error with the file in the Project Navigator.

In the example below, I inserted a garbage line into one of the hello methods, which the compiler clearly does not like. Unfortunately, the .cpp file was not found, even if it is in the project

Screenshot from Issue Navigator

I suspect that xcode does this best by analyzing the output of makefile / clang ++ and trying to determine where the problem is, but obviously does not work.

Log Navigator

/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-recursive
Making all in src
make[2]: Nothing to be done for `all'.
Making all in src/pops
make[2]: Nothing to be done for `all'.
Making all in src/jops
make[2]: Nothing to be done for `all'.
Making all in src/jops/tops
/bin/sh ../../../libtool  --tag=CXX   --mode=compile clang++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../..    -I /usr/include/openssl -I../../../src/ -g -O2 -MT test.lo -MD -MP -MF .deps/test.Tpo -c -o test.lo test.cpp
libtool: compile:  clang++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../.. -I /usr/include/openssl -I../../../src/ -g -O2 -MT test.lo -MD -MP -MF .deps/test.Tpo -c test.cpp  -fno-common -DPIC -o .libs/test.o
test.cpp:8:9: error: use of undeclared identifier 'hello'
        hello
        ^
1 error generated.
make[2]: *** [test.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

- xcode ? IDE xcode, .

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