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I am a unix/linux guy. I have setup a server installation for our racked machines and our cloud VMs to configure sshd to trust signed user certificates, those signed by the trusted CA.

Everything is working fine using ssh-add and ssh-agent on linux and on macosx.

One guy has a windows client, using mobaxterm. From the documentation, it has some support for ssh-agent and pageant.

I can get a public key from him, and sign it just fine. But, where does the resulting certificate go?

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MobaXterm has a virtual mapping, usually in %Documents%\MobaXterm\home. Alternatively, you can go to Settings>Configuration>General and see where the persistent home directory is set. You can create a folder .ssh here, then put your private key, public key, and signed certificate in this folder.

If you do not want to store your keys here, you can create a file at /home/.ssh/config, and specify an Identity, including a mapping to the path of all three of those files. The drives of the computer will be mounted under /drives/%drive_letter% so you will need to convert your Windows path.

C:\Documents and Settings becomes /drives/c/Documents\ and\ Settings

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