Cleanup: Re-organise source dir

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>