The /usr/local permissions are set by your linux distribution and not changed by ispconfig. So you should not change them.
Regarding vmail: The mail system uses maildrop that runs as user vmail and maildrop invokes external commands, so it needs a shell. See also:
http://markmail.org/message/w25epboj...+state:results
libuuid is not from ISPConfig, so I dont know if you can change it or not.
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Does mysql need to be listening on every interface if we are not planning a multiserver setup?
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No. But then your customers are also not able to use tools like the mysql windows gui tools to manage their databases.
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What do you think about security tools like tiger, logwatch, Samhain, Aide? Do you use any of them yourself?
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I use logwatch on my servers.