Get rid of mod_spatialite dependency

[wonder-sk]

We load mod_spatialite module to sqlite3 because we need some basic ST_* functions like ST_IsEmpty() which are used in triggers of tables of geopackages.

Maybe we can somehow use libgpkg implementations from geodiff?

[wonder-sk]

For geometry-based filtering, we are using more functions from spatialite:

• ST_Intersects
• ST_GeomFromText
• GeomFromGPB

(could be replaced by reading data and then doing intersection tests with shapely)