Adds automake subdir-objects option

As of Automake 1.4, it starts to warning about the lack of utilization
of `subdir-objects' option, which will be default in the further
releases. Avoiding break stuff we are patching ModSecurity to support
such option when it still an option (Issue #760).
Automake: Using ../ instead of $(top_srcdir)

After enable `subdir-objects', the variable $(top_srcdir) was not being
resolved, a directory labeled "$(top_srcdir)" was created instead.
Adds doxygen configuration files