Ssh-add -D doesn’t erase stored keys from the ssh-agent

Turns out this one was incredibly simple. Instead of using that script, I simply removed the "--agents" option from my old keychain launch script (guide here).

This causes the Keychain program to seek out both ssh-agent AND gpg-agent files. Now my encryption system does work quite seamlessly, even while relying on both types of agents.

The SSH agent handles signing of authentication data for you. When authenticating to a server, you are required to sign some data using your private key, to prove that you are, well, you.

As a security measure, most people sensibly protect their private keys with a passphrase, so any authentication attempt would require you to enter this passphrase. This can be undesirable, so the ssh-agent caches the key for you and you only need to enter the password once, when the agent wants to decrypt it (and often not even that, as the ssh-agent can be integrated with pam, which many distros do).

The SSH agent never hands these keys to client programs, but merely presents a socket over which clients can send it data and over which it responds with signed data. A side benefit of this is that you can use your private key even with programs you don't fully trust.

Another benefit of the SSH agent is that it can be forwarded over SSH. So when you ssh to host A, while forwarding your agent, you can then ssh from A to another host B without needing your key present (not even in encrypted form) on host A.