refactor(app): reorganize application structure and update includes

- Moved core components such as `Controller` and `Window` from `src/app/core/` to `src/app/` and `src/app/platform/`, respectively, to improve modularity and clarity.
- Updated include paths across the codebase to reflect the new locations of these components.
- Introduced a new foundational core library in `src/core/` for project management and ROM patching logic, enhancing the separation of concerns.
- Adjusted CMake configurations to ensure proper compilation of the new core library and updated dependencies in various modules.

Benefits:
- Streamlines the application structure, making it easier to navigate and maintain.
- Enhances code organization by clearly delineating core functionalities from application-specific logic.
- Improves overall architecture by promoting a clearer separation of concerns between different components.

src/app/gui/app/feature_flags_menu.h

@@ -1,7 +1,7 @@
 #ifndef YAZE_APP_GUI_FEATURE_FLAGS_MENU_H
 #define YAZE_APP_GUI_FEATURE_FLAGS_MENU_H
 
-#include "app/core/features.h"
+#include "core/features.h"
 #include "imgui/imgui.h"
 
 namespace yaze {

src/app/gui/core/background_renderer.cc

@@ -3,7 +3,7 @@
 #include <algorithm>
 #include <cmath>
 
-#include "app/core/timing.h"
+#include "app/platform/timing.h"
 #include "app/gui/core/theme_manager.h"
 #include "imgui/imgui.h"
 
@@ -24,7 +24,7 @@ void BackgroundRenderer::RenderDockingBackground(ImDrawList* draw_list, const Im
                                                const ImVec2& window_size, const Color& theme_color) {
   if (!draw_list) return;
   
-  UpdateAnimation(core::TimingManager::Get().GetDeltaTime());
+  UpdateAnimation(TimingManager::Get().GetDeltaTime());
   
   // Get current theme colors
   auto& theme_manager = ThemeManager::Get();

src/app/gui/widgets/dungeon_object_emulator_preview.cc

@@ -4,7 +4,7 @@
 #include "zelda3/dungeon/room.h"
 #include "zelda3/dungeon/room_object.h"
 #include "app/gui/automation/widget_auto_register.h"
-#include "app/core/window.h"
+#include "app/platform/window.h"
 #include <cstdio>
 
 namespace yaze {