Quoting Avery Pennarun [off-list ref]
Yup. This is basically a bug in "git merge -s subtree": it guesses
which subtree to merge into, rather than actually taking a prefix
parameter. I've been meaning to either submit a patch for this, or
find a way to work around it.
Probably you can save time by using what was already done
http://thread.gmane.org/gmane.comp.version-control.git/76650/focus=89021
--
Nanako Shiraishi
http://ivory.ap.teacup.com/nanako3/