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The Innovation numbers seem to explode during addNodeMutation() and addConnectionMutation(). I believe passing in the global connection and node lists from the Evaluator class to the aforementioned methods will allow for checking if a connection exists globally (in which case innovation is not incremented and the connection is assigned the appropriate innovation number).

Please see paragraph 5 of pg.108 in Stanely:

A possible problem is that the same structural innovation will receive different innovation
numbers in the same generation if it occurs by chance more than once. However,
by keeping a list of the innovations that occurred in the current generation, it
is possible to ensure that when the same structure arises more than once through independent
mutations in the same generation, each identical mutation is assigned the
same innovation number. Thus, there is no resultant explosion of innovation numbers.