Remove automatic enablement of application and core modules

This PR makes it so the application module and core module must be explicitly enabled in bootstrap.php alongside other modules. This gives the user total control and flexibility when enabling modules.
Yes, I did remove it in my previous PR but I thought there was too much going on making it hard to understand, so I decided to split it up. If this PR gets merged then the replacement of $_paths with $_modules would be the next PR.