OK, so I've got the server starting and I can browse the databases with PhpMySQL. None of the tables actually exist however. Server.err gives messages like this:
131013 16:17:31 [ERROR] Cannot find or open table websitewp/wp_options from
the internal data dictionary of InnoDB though the .frm file for the
table exists. Maybe you have deleted and recreated InnoDB data
files but have forgotten to delete the corresponding .frm files
of InnoDB tables, or you have moved .frm files to another database?
or, the table contains indexes that this version of the engine
doesn't support.
See
http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting.html
how you can resolve the problem.
BTW, when I ran the installer and tried to upgrade from 5.5 to 5.6 (which is where this all started) it instead gave me a new instance of 5.6 running in parallel with the existing 5.5 install. It was not obvious to me how to use it to actually upgrade an existing database. :-(