Multi-issue: TO DO dump

[conormckenzie]

TODO:

• Move each of these TODOs to an individual issue

• Move Index class outside of IndexManager since it's a structural spec, effectively (similar to Node and Edge classes)

• Review duplication in IndexManager (Change Nodedata class in IndexManager to not duplicate the structure of a Node)

• (Requires answer to question 1 below) Track new nodes and edges; track changed nodes and edges

• Append new nodes & edges to files rather than overwrite entire file each time

• Make method to print all nodes, edges to console

Theoretical considerations which need to be answered:

1. Does using a certain method of tracking new & changed nodes & edges, for example as 4 independent lists, introduce limitations on how the graph can be updated?
2. Are there problematic limits to the scalability of the file/directory scheme used to store the nodes and edges to disk?

[conormckenzie]

Assigning to myself the task of splitting these TODOs into individual issues