The culprit is gpg-keyring-daemon.  It subverts the normal operation of
ssh-agent, mostly just so that it can pop up a pretty box into which you
can type the passphrase for an encrypted ssh key.  And it paws through
your .ssh directory, and automatically adds any keys it finds to your
agent.  And it won't let you delete those keys.  How do we hate this?
Let's not count the ways -- life's too short.

The failure is compounded because newer ssh clients automatically try
all the keys in your ssh-agent when connecting to a host.  If there are
too many, the server will reject the connection.  And since gnome-
keyring-daemon has decided for itself how many keys you want your ssh-
agent to have, and has autoloaded them, AND WON'T LET YOU DELETE THEM,
you're toast.

What you really want to do is to turn off gpg-keyring-daemon altogether.
Go to System --> Preferences --> Startup Applications, and unselect the
"SSH Key Agent (Gnome Keyring SSH Agent)" box -- you'll need to scroll
down to find it.

You'll still get an ssh-agent, only now it will behave sanely:  no keys
autoloaded, you run ssh-add to add them, and if you want to delete keys,
you can.  Imagine that.

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Server Team, which is subscribed to openssh in Ubuntu.
https://bugs.launchpad.net/bugs/505278

Title:
  ssh-add -D deleting all identities does not work. Also, why are all
  identities auto-added?

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