include <header> path and starting point

Question

I have a problem similar to this Including header files recursively for syntastic except my directory structure is a lot more complex so I'm not sure where to place the config file.

the .cpp file I'm editing (let's name it myfile.cpp) looks like this

#include <path/to/fileA.h>
#include <path/to/another/fileB.h>
...

and my the directory structure looks something like this:

program
|-include
  |-path
    |-to
      |-fileA.h
      |-another
        |-fileB.h
|-modules
  |-module1
    |-myfile.cpp
|-src

Moreover the make command is run from a directory on the same level as program (program-out) but I guess this has nothing to do with it.

So the question is: where should I put my config file containing the -I flag? which directory should I pass as parameter? Also considering that my include directives make use of <> and not ""

//EDIT Currently my config file contains the following

-Iinclude
-I../include
-I../../include
-I../../../include

and I placed a copy in program, program/src, program/modules/module1 and also in a few folder inside program-out prepending program to include

But it still doesn't work