git-annex bundles gpg on OSX, but this bundled one is not integrated with gpg-agent. So, if gpg is installed system-wide, it's probably better to use that one (barring any versioning issues).

A solution might be to move the gpg binary to a different directory and put it at the end of PATH, not the front. So system one is used if available.

This should also be considered for the linux standalone builds.

done for both OSX and linux. --Joey