I was meaning to add an updates folder to the PEQ CVS for instances like this when the user tables change. If you do a full install, then you're set, but obviously those who don't wish to lose their toons need to manually update their DB.
For the new tables, all you need to do is look at the tables on the PEQ CVS, and compare them to your current db. Any that you are missing, source (that's why the user tables are split up on CVS - so you can source in individual ones if you wish) Yes, new additions to commands, variables, and rule_values are tacked on the end of those files.
For the changed tables (character_ for example was changed) check out the utils/sql/09252008.sql file on the source SVN first and look for the ALTER table queries. If it effects a table that has a file on PEQ CVS, then you need to source it. (As an example, the character_ alters need to be done, but the spawngroup one does not as that is included in the system part of the DB already) Once that is done, go through the changelog and look for alter queries that aren't in that big change file that you might have missed along the way.
I'm going to add an updates folder to PEQ CVS to help ease this in the future now.
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