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Colour Explanation.
The gray colour is a perk automatically gained upon becoming the class. It/they do not count towards a perk choice.
The red options are only select-able once per class. Once selected they cannot be chosen again.
The blue options work much the same way as red only they are skills instead of perks.
The orange perks work like the gray ones but only last for that class since they're titles.
The purple options are perks that can be selected multiple times.
The dark red ones are skills that can be selected multiple times.
The pale green options can only be chosen once. They are Pokemon Ability Upgrades.
The bright green options can only be selected once. They are trainer abilities.