When a file library's "Access to Sub-directories" option was enabled, any auto-created directories would have their data dir initialized as "blank" (empty), so their data files (e.g. <code>.dat, <code>.ixb) would be created in the ctrl directory.

I guess nobody used this feature? It is pretty cool, but not really documented. If you were using it before this commit, you'll need to move your sub-directories data files to data/dirs or re-add the files (recreate the database files). And you can remove the old cruft from the ctrl dir.