The manifest defines what an AI agent is allowed to do over its entire deployed lifetime. That's too coarse for most real deployments. You want the agent to be able to read customer data when it's responding to a customer query — but not when it's running a batch analytics task. You want different agents deployed with the same manifest to have different effective permissions depending on what task they're executing.
Capability tokens solve this. They are signed credentials — issued per session or per task — that scope the agent's permissions to a subset of its manifest-defined capabilities, for a specific time window, with a maximum action count.