Fix: Various mishandling of node identifiers and vector

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.

source/blender/nodes/shader/node_shader_tree.cc

@@ -446,10 +446,12 @@ static void flatten_group_do(bNodeTree *ntree, bNode *gnode)
     /* migrate node */
     BLI_remlink(&ngroup->nodes, node);
     BLI_addtail(&ntree->nodes, node);
+    nodeUniqueID(ntree, node);
     /* ensure unique node name in the node tree */
     /* This is very slow and it has no use for GPU nodetree. (see T70609) */
     // nodeUniqueName(ntree, node);
   }
+  ngroup->runtime->nodes_by_id.clear();
 
   /* Save first and last link to iterate over flattened group links. */
   bNodeLink *glinks_first = static_cast<bNodeLink *>(ntree->links.last);