feat(cli): migrate plugin + daemon commands to control protocol (C6 o… #2092

Job	Run time
cargo-check (orchestrator-web-server)	1m 28s
cargo-check (orchestrator-cli)	1m 47s
cargo-check (protocol)	34s
cargo-check (orchestrator-core)	34s
rustfmt	22s
cargo-check (orchestrator-web-api)	1m 15s
cargo-check (orchestrator-web-contracts)	26s
clippy	1m 0s
cargo-check (llm-cli-wrapper)	24s
cargo-check (agent-runner)	25s
smoke-help	1m 18s
	9m 33s

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