Refactor variable graph to use weak references

Right now, the VariableGraph uses the Variable objects as nodes. I think this means that networkx holds a reference to the object, and so Variables can never be garbage collected. This could lead to very large graphs if someone did a lot of operations on Variables, e.g., in a loop or something.

We should change the way the graph works so that it uses the ID of the variable as the node name, then hold a weakref to the object keyed on the ID. Any DependentVariables should hold references to their dependencies internally to keep them alive. When we evaluate on the graph, we can add a garbage collection step that prunes out dead variables before traversal.

Start by locating VariableGraph and its evaluation or traversal entry point, then inspect how Variable and DependentVariable objects are retained. Confirm how graph nodes and dependencies are currently represented. Done means graph nodes use variable IDs, objects are weakly referenced, dependent variables retain their dependencies, and dead variables are pruned before traversal.