Here are some notes on the New York Jets new reporting structure, this definitely clarifies the relationship between the new coach and GM.
1. Mike Maccagnan (GM) and the new head coach (yet to be named) both report directly to Woody Johnson. So the head coach will not report to the GM.
2. Mike Maccagnan (GM) will have final say on the final roster.
3. The head coach decides who plays on game day. He has final say on that.
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