Whew, I got the finishing touches on the import tree feature, and it's merged into master! Still work to do on that, particularly supporting more interesting special remotes than directory. It may be two or three weeks until I get back to working on it.

Even with only directory special remotes, some nice things can be done with this. Like bi-directional syncing between a removable drive with no git-annex repository on it, and a subdirectory of the git-annex repository:

$ git config remote.drive.annex-tracking-branch master:subdir
$ date > /mnt/new-from-drive
$ date > subdir/new-from-repo
$ git annex add
add subdir/new-from-repo ok
$ git annex sync --content
commit
 1 file changed, 1 insertion(+)
 create mode 120000 subdir/new-from-repo
ok
list drive ok
import drive new-from-drive ok
update refs/remotes/drive/master ok

Merge made by the 'recursive' strategy.
 subdir/new-from-drive | 1 +
 1 file changed, 1 insertion(+)
 create mode 120000 subdir/new-from-drive
export drive new-from-repo ok