Quoting Oliver Kullmann [off-list ref]
it seems no reply yet (if I understand that web-email-interface
properly); has nobody any idea here, or is it a Git bug,
or my fault?
Because you don't specify where in your current directory hierarchy the root level of the tree you are merging goes when you run "git merge -s subtree", the merge mechanism has to find the most similar directory by itself, and if you have more than one similar directories, it can't guess correctly.
It sounds similar to
http://thread.gmane.org/gmane.comp.version-control.git/135009/focus=135033
--
Nanako Shiraishi
http://ivory.ap.teacup.com/nanako3/