Fix manual mode for item/fluid filter covers and conveyors/pumps

[programmer3481]

What

tries to fix many of manual io bugs
see: https://discord.com/channels/701354865217110096/1089296351906504835/1442285824074055731

Outcome

• all cases of items being pushed/pulled through item filter/conveyor covers from external sources have been fixed for all manual io modes
• this includes item voiding bug due to filter cover's extract method not handling simulate parameter correctly
• attempt to fix auto output + manual io mode bugs, with limitations; for example, auto output + conveyor with filter doesn't respect manual io

Additional Information

many of these probably needs a bigger code refactor that i'm not knowledgable enough to do such as

• conveyors inheriting filter cover behavior somehow, so handling for both's filters isn't duplicated and missing in places
  - MetaMachine.getItemCapFilter's io parameter should probably be changed, it doesn't really make sense with IO.BOTH/NONE, it only is used with IO.IN/OUT anyway
• refactor other duplicate code probably, like getItemcCapFilter is used everywhere in similar ways, bunch of similar exportToNearby methods, etc

Potential Compatibility Issues / Implementation Details

should be no compat issues, tried to not modify current code structure as much as possible
although a bigger cleanup is probably needed later, see above