Here is the first part of my question.
Should I set up two user accounts; one for the database and another for the web server? Or is it better to have one root user for all purposes?
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Typically you keep one user per daemon. So, you might have a mysqld user that is severely restricted to just being able to run mysqld, right? Then you add users inside your database using MySQL.
You would also perhaps have a www or apache user that only runs the web server. You then have code which the apache user can read, but it uses a MySQL command to connect to the MySQLd port and authenticate you by using those users you added in the previous step. Does that make sense?
It's your dev environment though...If you don't believe you're a target, well...