In shared-mime-info 0.17 the alias x-directory/normal for inode/directory was added. This breaks the associations for the directory type in nautilus 2.14.0. Previously with shared-mime-info 0.16 you could associate directories with applications and open them using the "Open With" menu. Removing this alias from freedesktop.xml reenables this.
I don't quite understand what you mean here. Could you be a bit more precise in your description?
In nautilus you can associate file types with applications in directories, e.g. by adding MimeType=x-directory/normal; to a desktop file of an application. The alias x-directory/normal for inode/directory breaks this behaviour and the applications won't appear in nautilus' "open with" menu anymore.
Reopening as the required information was given...
This looks like a nautilus bug to me, where it would special case x-directory/normal. Please bring this up with the Nautilus developers.
Just for reference, this was reported to the GNOME guys: http://bugzilla.gnome.org/show_bug.cgi?id=335161
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