I don't add customizations to the database and then try and get them out, I create the custom sql file manually, and at the same time as I add the changes to the database. Then after a database update I can just source in the custom sql and I'm back to where I was.
The bot issue can be several things. Are you using 1129 or the SVN version? With 1129 you need to add EQBOTS to the Zone pre-processor in Visual Studio, if SVN then the Configuation Manager has a separate bot setting you can choose for debug or release binaries. If you are compiling in linux, search the eqoffline thread for linux answers.
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