I have a $HOME/Mail folder from where cleaned up the mbox folder, so it should be maildir only. I tried to add it as a maildir resource to akonadi, and although in the settings dialog it shown that it is a valid maildir folder, nothing appeared under the resource.
After a long time I realized it needs a .Mail.directory folder as well. So a symlink from Mail to .Mail.directory fixed the issue, although this is not nice as:
- usually the toplevel Mail folder doesn't have the corresponding .directory
- there was no warning/error that the folder I pointed to is not usable in this form and how can this be fixed

The mixedmaildir resource recognized the folder without the .Mail.directory