Improve node indexing in tree

[MischaPanch]

At the current state, the node indices are not really use (only for visualization and debugging). In principle they could be used to associate prototypes to the nodes, but this is not possible now because of the way the index is created. Only internal nodes are associated to a prototype, but leaves don't have a higher index than internal nodes.

Generally, the tree structure might benefit from further refactoring. Maybe we can use the binarytree library.

[Clifford-appliedAI-GmbH]

This is partially resolved as of #33 (note: not just that PR, also due to earlier commits), but there's still some redundant indexing remaining.