AA flight, confused, please help!?

As has been already implied, the exception doesn't say what you think it does. What it says that if you are flying on an AA ticket whose flights are operated by another carrier (that is not AA, Eagle, or American Connection), then you won't have to pay the baggage fees to AA. A codeshare is a marketing agreement between airlines, in which Airline A is allowed to sell tickets on Airline B's flights with Airline A's flight numbers. The flight is actually operated by Airline B, and you'd check in with that airline and be subject to their rules. The arrangement between American and American Eagle is not a codeshare agreement in this sense, because, for the purposes of marketing their flights, they are treated as the same airline.

The "operating carrier baggage allowance and charges will apply" part means that if the other carrier you're flying with has their own charges for baggage, you will have to pay their fee if required.

Unless you meet one of their other exceptions (e.g. this flight is part of an eligible international itinerary or you have elite status with AAdvantage), you will be required to pay the baggage fee on your Eagle flight.

A codeshare flight is a commercial flight which is operated by one airline, but marketed by others. If your plane is part of the American Eagle carrier then that exception does not apply.

j

Airlines sometimes codeshare with each other on certain routes/flights. This means that you booked with AA but I booked with, say, Delta, and the flight is operated by Delta. It has two flight numbers. In this case, the Delta rules re baggage costs will apply as it is their aircraft.

well they are co operated airlines