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You should be able to pass a file to --token-file that is read for the token value.
This has been added in v0.2.0-rc3
ubuntu@k3s-node2:~$ sudo ./k3s agent --server https://192.168.0.3:6443 --token-file token.txt
INFO[2019-03-08T06:28:29.341790729Z] Starting k3s agent v0.2.0-rc6 (2771ae1)
INFO[2019-03-08T06:28:29.455829097Z] Logging containerd to /var/lib/rancher/k3s/agent/containerd/containerd.log
root@k3s-node1:~# /home/ubuntu/k3s kubectl get nodes
NAME STATUS ROLES AGE VERSION
k3s-node1 Ready <none> 111m v1.13.4-k3s.1
k3s-node2 Ready <none> 9s v1.13.4-k3s.1