The binaries are just copied into your c:\eqemu\ folder and are supported by the peq database. The spells files aren't needed for manual update anymore. If you have a recent peq database you have everything you need for the database to have the bots working.
The thing to remember is that when updating the database, first run the cvs file bot_npcs.bat to save your created bots. Then you can update the database and then source in the bots from the sql file created by bot_npcs.bat back into the database. The other bot related tables do not get deleted when updating the database... unless you completely start from scratch and blow everything away.
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