Remove O(N^2) operation from NumberedObjectCollection

[MicahGale]

Is your feature request related to a problem? Please describe.

I was analyzing some data from parsing times and found that we have O(N^2) scaling despite fixing #510. After some investigation I found the culprit is in NumberedObjectCollections.append. This runs through all of self.numbers every time which is a generator over the entire list.... O(N^2).

So this should be eliminated.

Describe the solution you'd like

A few solutions.

1. Remove this operation from read_input and do a bulk add that is optimized
2. Make NumberedObjectCollection a lot more like dicts, and rely on __num_cache a lot more. Through the number property we guarantee that numbers are always update for objects tied to problem. So maybe we use this O(n^2) operation only as a last resot.