The ability tree shows all abilities in the game and how they depend on each other.
It would be very helpful to make a similiar list/tree of all tools in the game and what ability they belong to, or somehow include complete tool infos in the ability tree.
Although it's less crucial, it would also be nice to have green and blue fragment lists and infos about what code bits they consist of (since it's really hard to get confused with the red frags).