Built color selection infrastructure and assigned stage-specific colors (WIP).

Added 2 plots to methods (WIP).

main.log

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 \OT1/cmr/m/n/12 the sub-se-quent lo-cal in-terneu-rons ([]; [])
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 []\OT1/cmr/bx/n/17.28 Two mech-a-nisms driv-ing the emer-gence of intensity-
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