Fixed #21662 -- Kept parent reference in prepared geometry

Thanks Robert Scott for the report.
Dropped support for GEOS < 3.1
Added more spatial predicates for prepared geometries

GEOS 3.3 added crosses, disjoint, overlaps, touches and within
predicates on prepared geometries.
Documented the Apps and AppConfig APIs.
Updated a few doc paragraphs following the app-loading refactor.