refactor(cli)!: hard-cut legacy scripts and standardize console runtime

- remove legacy bin/module-*.php and bin/doctor.php entry scripts

- move module/doctor execution into class-based runners under lib/Console

- add stable JSON output for doctor and module:sync

- introduce bin/dev for init/up/down/logs/console/qa workflow

- update DI wiring, phpstan scan config, tests, and docs to new CLI contract

lib/App/Module/Contracts/ModuleDeactivationHandler.php

@@ -7,7 +7,7 @@ use MintyPHP\App\AppContainer;
 /**
  * Handles cleanup when a module is deactivated.
  *
- * Invoked by `bin/module-deactivate.php` after a module has been removed
+ * Invoked by `php bin/console module:deactivate` after a module has been removed
  * from the enabled list. The handler receives the full app container and
  * can perform cleanup tasks like removing orphaned data or revoking permissions.
  */