A slight misconfiguration had SpamAssassin dropping spam into ~/Maildir/.spam/ while Dovecot was looking for mbox files in ~/mail/. From my initial bit of Googling, I was expecting to have to download some program to do the heavy lifting. Luckily, I came across a very simple blog post with a very simple answer that worked like a charm.
Need to generate an mbox out of a Maildir mailbox? Formail helps:
cd $MAILDIR/cur for i in * ; do cat $i | formail -c >> $MBOXFILE ; done