In a few places, nodes were added without updating the Identifiers and
vector. In other places nodes we removed without removing from and
rebuilding the vector. This is solved in a few ways. First I exposed
a function to rebuild the vector from scratch, and added unique ID
finding to a few places.
The changes to node group building and separating are more involved,
mostly because it was hard to see the correct behavior without some
refactoring. Now `VectorSet` is used to store nodes involved in the
operation. Some things are handled more simply with the topology
cache and by passing a span of nodes.
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