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If you wish to use mysql you will have to run the server once, open server.properties and set data-source to mysql.
Run it again, it'll error out. Don't worry. There should be a mysql.properties file now. Edit to your server, username, password, and db.
Don't forget to execute the included minecraft.sql file on your database.
After that, you would likely need to create a database through the MySQL client for Minecraft to use, along with a user for it. For instance, the window when doing this might look like:
# mysql -p
Enter password: (enter your MySQL root password)
mysql> create database minecraft;
mysql> grant all privileges on minecraft.* to 'minecraft'@'localhost' identified by 'somepassword';
After this, it would be able to connect to the "minecraft" database at "localhost" with username "minecraft" and password "somepassword".
Getting the whole LAMP stack on there is a little more complicated and something that I haven't done on CentOS personally. But, it looks like the basic part of it would be to install Apache and a special version of PHP that supports MySQL:
Could help me better if I switched to Gentoo? I'm just worried about installing minecraft and those two mods cause I've only found guides for CentOS for those.
With Gentoo, I would be able to provide a bit more assistance, but it's also been awhile since I've set up a basic single-user install (we use something much more complicated here for our shared hosting).
What did it respond when you issued the commands to install the MySQL-enabled PHP and Apache that I mentioned above?