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I've been developing complex Drupal applications for years and I appreciate elefant's the simple and effective architecture. I see a lot of potential!
One suggestion would be separating out the core apps form the custom/contributed apps.
Placing the core apps under a /core directory and keeping the custom under /apps. This would help with upgrading and customizing.
Then you could use an override model in the handler discovery. First look in the apps folder then to the core folder. This would allow for overriding of individual handler and not entire apps.
For example, If I wanted to override add handler for blog I could just place the custom handler in /apps/blog/handlers/add.php