-a already implies -r/-R, so no need for both.
FreeBSD's cp complains:
cp: the -R and -r options may not be specified together
# Prepare a snapshot of the updated maildir. The gdb script will
# update the database in this snapshot as it goes.
- cp -ra $MAIL_DIR $MAIL_DIR.snap
+ cp -a $MAIL_DIR $MAIL_DIR.snap
cp ${NOTMUCH_CONFIG} ${NOTMUCH_CONFIG}.snap
NOTMUCH_CONFIG=${NOTMUCH_CONFIG}.snap notmuch config set database.path $MAIL_DIR.snap