Fix the bugs of generating topojson with complicated geojson

[natsuapo]

I did the test again with proper path and debug the code.

This time there are three fails in all test:
Two fails are related to test_extract in the assertion of intermediate dict structure. I think these fails are inevitable since I changed the process structure of feature and geometry collections.

One fail is related to test_topology_to_geojson_nested_geometrycollection in test_topology. This is also an assertion fail as in my process, I changed the geojson structure of nested geometrycollection, so it cannot be reverted to the same geojson after it is converted to topojson. But as far as I read the generated geojson, I think they can refer to the original geojson with the same geometry.

I am sorry that I cannot solve the remaining fails since they are much related to other data structures. But I think at least this adaption can be utilized for generating topojson from geojson with attributes. I am not sure whether to merge it or not, so I leave the decision to the maintainers.

[mattijn]

Thank you for pushing! Last evening I tried to solve the issue as well and the changes were near identical to yours, but I've to check once again when I find some time.

I'm not really font of the (nested) geometrycollections within the geojson dataformat.

I also still had some failing tests elsewhere, but that might be indeed because of changes regarding improved serialization.

Thanks again!

[mattijn]

Merged and update the remaining tests. Thanks for the PR👍