Sorry about the delay, got really busy.

I gave up on gnupg-agent. I got it to work out of the bix, except that it just wouldn't see the pinentry program and kept failing. In the end I just removed them.

I was trying it to get pass working on the n900. From version 1.5 it doesn't need gnupg-agent, so I just used it as is without the agent.

The only issue there is now it wants a newer version of tree, but only for a limited subset of functionality that I don't use.