Refactor whole pbf_file_reader file into a module

[RaczeQ]

Split one big file into a more manageable and testable module.

• Add tests per smaller steps
• Enable the option to change geometry calculation (centroid, bbox, convex hull, full reconstruction) - blocker for Add option to simplify data extraction by returning only centroid / bounding box as a geometry of the object #229
• Move OSM element type-specific functions into separate files (node / way / relation)