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Agent does not interact with SQL Server at all. Always on does not have any impact on the agent. You install the agent as usual.
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I suppose the key concern is to submit job to the active node of Always-On Availability Group.
AAG is a Windows cluster without shared storage. Install agent to each of the nodes and select local rather than cluster. Add the agents using CCM as usual. Add the AAG network name as an "Network Load Balancer Router" at CCM (see screenshot below). Before doing so, set EM parameter "EnableLoadBalancerRouter" to true (default false) and restart CCM.
Network Load Balancer Router will discover the active agent name behind the alias name and submit job to the physical agent. Note that all agents participating in AAG must be identical in terms of s/w version, agent protocol version, listening port.
Thank you George. Yes, I should have been more clear, but you anticipated my concern precisely!