Bukkit

To Use MySQL in your plugins just change this values in your plugin/config.yml.
Make sure your server is offline/stopped when you change this values or you must use "/<Pluginname> reload".

database:
  saveType: MYSQL
  saveOnShutdown: true
  MYSQL:
    connection:
      host: yourhosthere
      #default: localhost
      port: '3306'
      dbname: yourdatabasenamehere
      #default: Crazy
      user: yourusernamehere
      #default: root
      password: yourpasswordhere
      #default: '' (empty)
    tableName: yourtablenamehere
    cached: true
    columns:
      column1: name
      column2: column2
      ...
      columnx: columnx

The server automatically adds every missing entry using the dafult values when started.
Or use "/<Pluginname> mode saveType MYSQL" once, to generate all missing entries.

Changing Database Savetype
When you want to change your saveType but to keep your old databaseentries.
You have to change the saveType ingame "/<Pluginname> mode saveType <MYSQL/FLAT/CONFIG>"
If the new database type couldn't be accessed the old one will be used.

If you want to transfer your data from one mysql database to another, temporarily change saveType to FLAT and stop the server.
After that you can edit MySQL connection data and restart the server the change saveType to MySQL.

Notice
USE BACKUPS
When the server doesn't save/move your datas, make sure you used "/stop" to shutdown the server or type "/<Pluginname> save"