I think this will be obsolete pretty soon when the equivalent is
built-in to notmuch, but in the mean time, here is a script that
somebody might find useful: retag a whole directory (recursively). I
don't claim it is nice in any way, but it seems usable for me, taking
about 5 seconds to retag a directory containing 1000 messages.

I use it like 

  tagdir Maildir/.list.debian-devel -inbox +debian +devel