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Hello!
I'm using OSX 10.9 and have installed gpg (and gpg2, if it matters) through
homebrew and git-annex through cabal.

Whenever I'm trying to add an encrypted remote through the web ui I get a
lot of "You need a passphrase to unlock the secret key for user:" on stdout
and, obviously, I can't enter my passphrase (If this was the case I wouldn't
make this post to begin with :))
Is this behavior normal? What should I do to avoid it?

Yes, I am using gpg-agent. When other applications ask for my passphrase I get
the "enter passphrase" dialog from GPGTools, but this isn't the case with git-annex.