Merged "application" and "system" into the new "core" folder.

It will maybe confuse users what this directory's are, and I don't want them modifying the files in these.
Delete "plugins.php" config file, which is not used.

I think I forgot to remove it.
Changed all old plain-text database-queries to use the "Active Record Class"

This enables the ability to (theoretically) use an other database engine than "MySQL", and now everybody can define a table prefix in the config.