### Godot version

master

### System information

Ubuntu

### Issue description

I think one of the recent changes wrapped the project converter in `#ifndef DISABLE_DEPRECATED` but missed the coresponding code in `main.cpp` (and potentially other places).
```
main/main.cpp: In static member function 'static bool Main::start()':
main/main.cpp:2551:33: error: 'ProjectConverter3To4' was not declared in this scope
 2551 |                 int exit_code = ProjectConverter3To4(converter_max_kb_file, converter_max_line_length).convert();
      |                                 ^~~~~~~~~~~~~~~~~~~~
main/main.cpp:2556:33: error: 'ProjectConverter3To4' was not declared in this scope
 2556 |                 int exit_code = ProjectConverter3To4(converter_max_kb_file, converter_max_line_length).validate_conversion();
```

### Steps to reproduce

for instance, try to compile with `deprecated = "no"` in your `custom.py`.

### Minimal reproduction project

n/a
PhysicsServer3D::get_singleton()->end_sync();
			PhysicsServer2D::get_singleton()->end_sync();
			exit = true;
			break;
		}
		uint64_t navigation_begin = OS::get_singleton()->get_ticks_usec();
		NavigationServer3D::get_singleton()->process(physics_step * time_scale);
		navigation_process_ticks = MAX(navigation_process_ticks, OS::get_singleton()->get_ticks_usec() - navigation_begin); /
		navigation_process_max = MAX(OS::get_singleton()->get_ticks_usec() - navigation_begin, navigation_process_max);
		message_queue->flush();
		PhysicsServer3D::get_singleton()->end_sync();
		PhysicsServer3D::get_singleton()->step(physics_step * time_scale);
		PhysicsServer2D::get_singleton()->end_sync();
		PhysicsServer2D::get_singleton()->step(physics_step * time_scale);
		message_queue->flush();
		physics_process_ticks = MAX(physics_process_ticks, OS::get_singleton()->get_ticks_usec() - physics_begin); /
		physics_process_max = MAX(OS::get_singleton()->get_ticks_usec() - physics_begin, physics_process_max);
		Engine::get_singleton()->_physics_frames++;
		Engine::get_singleton()->_in_physics = false;
	}
	if (Input::get_singleton()->is_using_input_buffering() && agile_input_event_flushing) {
		Input::get_singleton()->flush_buffered_events();
	}
	uint64_t process_begin = OS::get_singleton()->get_ticks_usec();
	if (OS::get_singleton()->get_main_loop()->process(process_step * time_scale)) {
		exit = true;
	}
	message_queue->flush();
	RenderingServer::get_singleton()->sync(); /
	if (DisplayServer::get_singleton()->can_any_window_draw() &&