refactor: further refactoring of graph analysing

[jnussbaum]

• make docstrings better understandable
• make variable names better understandable
• make_graph(): 4th return element can be deduced from the other ones --> don't return it
• _remove_leaf_nodes(): make a clear distinction between node_indices and remaining_node_indices

[BalduinLandolt]

Some detail remarks

[jnussbaum]

This PR aims to improve readability, understandability, and maintainability of the graph analyzing. This comes with a small performance cost: With the big SGV XML file, the duration of the stashing deteriorated from ca. 1:20 min to ca. 1:45 min. But the stashing happens only once per xmlupload, so this is unproblematic.