install key using ssh-copy-id through forwarded ssh-agent

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So I'm using ssh-agent on my host and we use vagrant, virtualbox and other normal tools to setup our environment. At one point, we need to provision new machines (we build appliances) and push our key into that appliance. So far, we had been unprotecting our keys and just copying our id_rsa(.pub)? on the virtual machine. It suited us!

Recently, I started using ssh-agent on my main machine to host my keys with a password (much better obviously) but from time to time, I seem to have problems running ssh-copy-id to copy my id towards the appliance.

Most of the time, I have to just copy my protected key files to the vm and then it works but I'm sure i was able at one point to leave the virtual machine clean from any ssh keys and still use ssh-copy-id to copy my ssh-agent provided identity through the vm. It doesn't seem to be working half of the time.

Am I crazy? What could be the root cause of this? How to I solve this problem to ensure that my SSH protected id is forwarded only from my local agent into the vm and into any other appliance properly?

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