WIP: Fix deferred vertex deletion, add unit test.

GeometryKernel::collect_garbage used to first perform the TopologyKernel garbage collection, usually shrinking its vertex_deleted_ member, then accesses it using is_deleted() with the old vertex indices.

This causes out-of-bounds memory access (made visible by cmake -DSTL_VECTOR_CHECKS=ON) and wrong results, the remaining vertices will have the wrong coordinates.