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I'm using 12.10 with gnome-shell 3.6.

I have multiple ssh keypairs (created with ssh-keygen). They're stored in ~/.ssh/ids/hostname/id_rsa and I have a file ~/.ssh/config which says which key to use with which host.

Whenever I connect to one of the hosts, it always prompts me for the id_rsa password. I want the keys to be unlocked whenever I'm logged in.

I tried to import the keys into seahorse (aka Passwords and Keys), but I ran against this bug

I then tried to use ssh-add. This gave me the proper behavior, but it didn't persist across sessions/reboots.

Before I created different keys for different hosts, gnome-shell would give me a popup asking for my login password, and after I entered it, the keys would be unlocked for the rest of the session. How can I get this to work again?

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check out this link, make sure you correctly transfered the public key to the server… – Sam Nov 24 '12 at 23:52
I did correctly transfer them. As I mentioned, when I used ssh-add to unlock the private keys, I could log in to the various hosts with no problem (and no password, either from my account on that host and from the keyfile). – hnasarat Nov 25 '12 at 0:13

Seahorse will automatically detect the ssh keyfiles if they're in the top-level ~/.ssh directory. My work-around solution was to change how I organized my keyfiles. As such, seahorse detects them, and gnome-shell detects them only asks for my login password once per keyfile.

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