In SCons manual:

=================
In order to inform the C compiler about the repositories,  SCons will
add appropriate -I flags to the compilation commands for each directory
in the $CPPPATH list. So if we add the current directory to the
construction environment $CPPPATH like so:

    env = Environment(CPPPATH = ['.'])
    env.Program('hello.c')
    Repository('/usr/repository1')

Then re-executing SCons yields:

    % scons -Q
    cc -o hello.o -c -I. -I/usr/repository1 hello.c
    cc -o hello hello.o
=================

The additional include directory is definitely not what we want. Just
remove the additional Repository line.