First, shouldn't we be saying directories can "only" contain mail folders and other directories? Or do we leave the format of directories open for additions such as indexes?

The directories mentioned here are only the BikINI versions of directories, not the file-system version, thus it should say "only". - dave

Also, the sentence, "Otherwise, implementation becomes very difficult if the implementor chooses to use mbox files or such for mail folders," does not make much sense at first glance. Does this mean it would be difficult to represent Directories with mbox files if they contain mail folders, directories, and messages? If so, then make sure it is clear that directories must not contain messages.

There is no reason to include that sentence so long as we specify "only". - dave

Issue done.