Re-organise the sources, add a top level "src" and "include" dir and move relevant files.
Disable autotools automated includes and define them manually. This fixes problems with collision of header names with system headers.
Include the autoconf config.h in the default includes and remove it where it's explicitely included. Remove _GNU_SOURCE defines since it's detected at configure for platforms that requires it and added to the config.h.
Signed-off-by: Michael Jeanson <mjeanson@efficios.com> Signed-off-by: Mathieu Desnoyers <mathieu.desnoyers@efficios.com>