Design of systems/structures for the thanatos mmo project

questions

should a skill gem contain the ids of compatable skills, or skills have the id of compatable skillgems?

how to implement modifications as there is no consistant structure to them.

how to implement buffs/debuffs as every property of a player / entity could be attempted to be modified?

posion / burn / damage over time impl details.

should there be a unique ID for each instance of item / for every item in the server?