In SVN as well as the download archives (.zip .tar.gz) the blank Bot.conf and MySQL.conf should be moved to an examples/ or doc/ directory so that bot upgrades do not clobber the customized configurations.

To me it's not a huge deal as I have nightly backups, but n00bs might not like clobbering their configuration files as the probably lost their MySQL login info a few minutes after they set it up.

Leave an empty conf directory in svn and the archives.

Edit:
Also, php.ini seems to belong with the PHP bundle, not the bot files.