Change names in C++ to be Yellowstone consistent

[maxitg]

Changes

• Changes names in the C++ code to be Yellowstone consistent and allow generalization to other systems, e.g., expression -> token, Set -> HypergraphSubstitutionSystem, etc.
• Renames Expression. and Event. to AtomsIndex. and TokenEventGraph., as they better describe what's in those files.
• Moves some definitions from hypergraph-specific files to IDTypes.hpp and TokenEventGraph.hpp.

Comments

• There are no functionality/logic changes, just renaming and reorganizing.

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