aoflagger

The include paths for foo/bar.cpp contained ../../ breaking out of the
source tree. This can pick up files in other directories. This should be
fixed by not using .. in include paths. That's however not the scope of
this patch series.

This ../../ worked due to aocommon's global include path. The next patch
makes aocommon an submodule, which breaks the build due to this
artifact. Hence fix the paths before making aocommon a submodule.