The maildir format specification
(see http://cr.yp.to/proto/maildir.html) is clear that files named with leading dots should be ignore:
Unless you're writing messages to a maildir, the format of a unique
name is none of your business. A unique name can be anything that
doesn't contain a colon (or slash) and doesn't start with a dot. Do not
try to extract information from unique names.
Test case:
liw@havelock$ find Maildir -ls
8921206 4 drwxrwxr-x 5 liw liw 4096 Apr 26 23:03 Maildir
8921207 4 drwxrwxr-x 2 liw liw 4096 Apr 26 23:03 Maildir/cur
8921209 4 drwxrwxr-x 2 liw liw 4096 Apr 26 23:03 Maildir/tmp
8921208 4 drwxrwxr-x 2 liw liw 4096 Apr 26 23:03 Maildir/new
8913523 0 -rw-rw-r-- 1 liw liw 0 Apr 26 23:03 Maildir/new/.foo
liw@havelock$ python -c 'import mailbox
maildir = mailbox.Maildir("Maildir")
print maildir.keys()
'
['.foo']
liw@havelock$
The correct output would be the empty list.
"mutt -f Maildir" correctly shows now messages in that folder.