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/editor/agent/agent_chat_widget.cc

@@ -18,7 +18,7 @@
 #include "absl/strings/str_join.h"
 #include "absl/time/clock.h"
 #include "absl/time/time.h"
-#include "app/core/project.h"
+#include "core/project.h"
 #include "app/editor/agent/agent_chat_history_codec.h"
 #include "app/editor/agent/agent_ui_theme.h"
 #include "app/editor/agent/agent_chat_history_popup.h"
@@ -136,7 +136,7 @@ void AgentChatWidget::SetRomContext(Rom* rom) {
 
   // Only initialize labels ONCE per ROM instance
   if (rom && rom->is_loaded() && rom->resource_label() && last_rom_initialized != rom) {
-    core::YazeProject project;
+    project::YazeProject project;
     project.use_embedded_labels = true;
 
     auto labels_status = project.InitializeEmbeddedLabels();
@@ -2757,7 +2757,7 @@ void AgentChatWidget::CreateNewFileInEditor(const std::string& filename) {
 }
 
 void AgentChatWidget::LoadAgentSettingsFromProject(
-    const core::YazeProject& project) {
+    const project::YazeProject& project) {
   // Load AI provider settings from project
   agent_config_.ai_provider = project.agent_settings.ai_provider;
   agent_config_.ai_model = project.agent_settings.ai_model;
@@ -2816,7 +2816,7 @@ void AgentChatWidget::LoadAgentSettingsFromProject(
   }
 }
 
-void AgentChatWidget::SaveAgentSettingsToProject(core::YazeProject& project) {
+void AgentChatWidget::SaveAgentSettingsToProject(project::YazeProject& project) {
   // Save AI provider settings to project
   project.agent_settings.ai_provider = agent_config_.ai_provider;
   project.agent_settings.ai_model = agent_config_.ai_model;

src/app/editor/agent/agent_chat_widget.h

@@ -15,7 +15,7 @@
 #include "cli/service/agent/advanced_routing.h"
 #include "cli/service/agent/agent_pretraining.h"
 #include "cli/service/agent/prompt_manager.h"
-#include "app/core/project.h"
+#include "core/project.h"
 
 namespace yaze {
 
@@ -254,8 +254,8 @@ public:
   void UpdateAgentConfig(const AgentConfigState& config);
   
   // Load agent settings from project
-  void LoadAgentSettingsFromProject(const core::YazeProject& project);
-  void SaveAgentSettingsToProject(core::YazeProject& project);
+  void LoadAgentSettingsFromProject(const project::YazeProject& project);
+  void SaveAgentSettingsToProject(project::YazeProject& project);
 
   // Collaboration history management (public so EditorManager can call them)
   void SwitchToSharedHistory(const std::string& session_id);

src/app/editor/code/project_file_editor.cc

@@ -6,6 +6,7 @@
 #include "absl/strings/match.h"
 #include "absl/strings/str_format.h"
 #include "absl/strings/str_split.h"
+#include "core/project.h"
 #include "util/file_util.h"
 #include "app/editor/system/toast_manager.h"
 #include "app/gui/core/icons.h"
@@ -170,7 +171,7 @@ absl::Status ProjectFileEditor::SaveFileAs(const std::string& filepath) {
   modified_ = false;
   
   // Add to recent files
-  auto& recent_mgr = core::RecentFilesManager::GetInstance();
+  auto& recent_mgr = project::RecentFilesManager::GetInstance();
   recent_mgr.AddFile(filepath_);
   recent_mgr.Save();
   

src/app/editor/code/project_file_editor.h

@@ -4,7 +4,7 @@
 #include <string>
 
 #include "absl/status/status.h"
-#include "app/core/project.h"
+#include "core/project.h"
 #include "app/gui/widgets/text_editor.h"
 
 namespace yaze {
@@ -20,7 +20,7 @@ class ToastManager;
  * - Syntax highlighting for INI-style format
  * - Real-time validation
  * - Auto-save capability
- * - Integration with core::YazeProject
+ * - Integration with project::YazeProject
  */
 class ProjectFileEditor {
  public:

src/app/editor/dungeon/dungeon_object_selector.cc

@@ -4,7 +4,7 @@
 #include <iterator>
 #include <cstring>
 
-#include "app/core/window.h"
+#include "app/platform/window.h"
 #include "app/gfx/resource/arena.h"
 #include "app/gfx/types/snes_palette.h"
 #include "app/gui/canvas/canvas.h"

src/app/editor/editor_library.cmake

@@ -83,7 +83,7 @@ endif()
 # - System editors (settings, commands, extensions)
 # - Testing infrastructure
 #
-# Dependencies: yaze_core_lib, yaze_gfx, yaze_gui, yaze_zelda3, ImGui
+# Dependencies: yaze_app_core_lib, yaze_gfx, yaze_gui, yaze_zelda3, ImGui
 # ==============================================================================
 
 add_library(yaze_editor STATIC ${YAZE_APP_EDITOR_SRC})
@@ -103,7 +103,7 @@ target_include_directories(yaze_editor PUBLIC
 )
 
 target_link_libraries(yaze_editor PUBLIC
-  yaze_core_lib
+  yaze_app_core_lib
   yaze_gfx
   yaze_gui
   yaze_zelda3

src/app/editor/editor_manager.cc

@@ -16,9 +16,9 @@
 #include "absl/strings/match.h"
 #include "absl/strings/str_cat.h"
 #include "absl/strings/str_format.h"
-#include "app/core/features.h"
-#include "app/core/project.h"
-#include "app/core/timing.h"
+#include "core/features.h"
+#include "core/project.h"
+#include "app/platform/timing.h"
 #include "app/editor/session_types.h"
 #include "app/editor/code/assembly_editor.h"
 #include "app/editor/dungeon/dungeon_editor_v2.h"
@@ -65,7 +65,7 @@
 #include "app/gfx/debug/performance/performance_dashboard.h"
 
 #ifdef YAZE_WITH_GRPC
-#include "app/core/service/screenshot_utils.h"
+#include "app/service/screenshot_utils.h"
 #include "app/editor/agent/agent_chat_widget.h"
 #include "app/test/z3ed_test_suite.h"
 #include "cli/service/agent/agent_control_server.h"
@@ -650,7 +650,7 @@ absl::Status EditorManager::Update() {
 
   // Update timing manager for accurate delta time across the application
   // This fixes animation timing issues that occur when mouse isn't moving
-  core::TimingManager::Get().Update();
+  TimingManager::Get().Update();
 
   // Delegate to PopupManager for modal dialog rendering
   popup_manager_->DrawPopups();
@@ -1131,7 +1131,7 @@ absl::Status EditorManager::LoadRom() {
   test::TestManager::Get().SetCurrentRom(GetCurrentRom());
 #endif
 
-  auto& manager = core::RecentFilesManager::GetInstance();
+  auto& manager = project::RecentFilesManager::GetInstance();
   manager.AddFile(file_name);
   manager.Save();
 
@@ -1257,7 +1257,7 @@ absl::Status EditorManager::SaveRomAs(const std::string& filename) {
       sessions_[current_session_idx].filepath = filename;
     }
 
-    auto& manager = core::RecentFilesManager::GetInstance();
+    auto& manager = project::RecentFilesManager::GetInstance();
     manager.AddFile(filename);
     manager.Save();
   }
@@ -1327,7 +1327,7 @@ absl::Status EditorManager::OpenProject() {
     return absl::OkStatus();
   }
 
-  core::YazeProject new_project;
+  project::YazeProject new_project;
   RETURN_IF_ERROR(new_project.Open(file_path));
 
   // Validate project
@@ -1391,7 +1391,7 @@ absl::Status EditorManager::OpenProject() {
   ImGui::GetIO().FontGlobalScale = user_settings_.prefs().font_global_scale;
 
   // Add to recent files
-  auto& manager = core::RecentFilesManager::GetInstance();
+  auto& manager = project::RecentFilesManager::GetInstance();
   manager.AddFile(current_project_.filepath);
   manager.Save();
 
@@ -1422,7 +1422,7 @@ absl::Status EditorManager::SaveProject() {
         user_settings_.prefs().autosave_interval;
 
     // Save recent files
-    auto& manager = core::RecentFilesManager::GetInstance();
+    auto& manager = project::RecentFilesManager::GetInstance();
     current_project_.workspace_settings.recent_files.clear();
     for (const auto& file : manager.GetRecentFiles()) {
       current_project_.workspace_settings.recent_files.push_back(file);
@@ -1456,7 +1456,7 @@ absl::Status EditorManager::SaveProjectAs() {
   auto save_status = current_project_.Save();
   if (save_status.ok()) {
     // Add to recent files
-    auto& manager = core::RecentFilesManager::GetInstance();
+    auto& manager = project::RecentFilesManager::GetInstance();
     manager.AddFile(file_path);
     manager.Save();
 
@@ -1474,7 +1474,7 @@ absl::Status EditorManager::SaveProjectAs() {
 }
 
 absl::Status EditorManager::ImportProject(const std::string& project_path) {
-  core::YazeProject imported_project;
+  project::YazeProject imported_project;
 
   if (project_path.ends_with(".zsproj")) {
     RETURN_IF_ERROR(imported_project.ImportZScreamProject(project_path));

src/app/editor/editor_manager.h

@@ -16,7 +16,7 @@
 #include <string>
 
 #include "absl/status/status.h"
-#include "app/core/project.h"
+#include "core/project.h"
 #include "app/editor/agent/agent_chat_history_popup.h"
 #include "app/editor/code/project_file_editor.h"
 #include "app/editor/system/editor_card_registry.h"
@@ -302,7 +302,7 @@ class EditorManager {
 
   gfx::IRenderer* renderer_ = nullptr;
 
-  core::YazeProject current_project_;
+  project::YazeProject current_project_;
   EditorDependencies::SharedClipboard shared_clipboard_;
   std::unique_ptr<PopupManager> popup_manager_;
   ToastManager toast_manager_;

src/app/editor/graphics/graphics_editor.cc

@@ -8,7 +8,7 @@
 #include "absl/strings/str_cat.h"
 #include "app/gui/core/ui_helpers.h"
 #include "util/file_util.h"
-#include "app/core/window.h"
+#include "app/platform/window.h"
 #include "app/gfx/resource/arena.h"
 #include "app/gfx/core/bitmap.h"
 #include "app/gfx/util/compression.h"

src/app/editor/overworld/overworld_editor.cc

@@ -15,7 +15,7 @@
 #include "absl/status/status.h"
 #include "absl/strings/str_format.h"
 #include "core/asar_wrapper.h"
-#include "app/core/features.h"
+#include "core/features.h"
 #include "app/editor/overworld/map_properties.h"
 #include "app/editor/overworld/entity.h"
 #include "app/editor/overworld/tile16_editor.h"

src/app/editor/overworld/overworld_entity_renderer.cc

@@ -1,7 +1,7 @@
 #include "overworld_entity_renderer.h"
 
 #include "absl/strings/str_format.h"
-#include "app/core/features.h"
+#include "core/features.h"
 #include "app/editor/overworld/entity.h"
 #include "app/gui/canvas/canvas.h"
 #include "zelda3/common.h"

src/app/editor/overworld/scratch_space.cc

@@ -12,7 +12,7 @@
 #include "absl/strings/str_format.h"
 #include "core/asar_wrapper.h"
 #include "app/gfx/debug/performance/performance_profiler.h"
-#include "app/core/window.h"
+#include "app/platform/window.h"
 #include "app/editor/overworld/entity.h"
 #include "app/editor/overworld/map_properties.h"
 #include "app/editor/overworld/tile16_editor.h"

src/app/editor/session_types.h

@@ -1,7 +1,7 @@
 #ifndef YAZE_APP_EDITOR_SESSION_TYPES_H_
 #define YAZE_APP_EDITOR_SESSION_TYPES_H_
 
-#include "app/core/features.h"
+#include "core/features.h"
 #include "app/editor/code/assembly_editor.h"
 #include "app/editor/code/memory_editor.h"
 #include "app/editor/dungeon/dungeon_editor_v2.h"

src/app/editor/system/menu_orchestrator.cc

@@ -1,7 +1,7 @@
 #include "menu_orchestrator.h"
 
 #include "absl/strings/str_format.h"
-#include "app/core/features.h"
+#include "core/features.h"
 #include "app/editor/editor.h"
 #include "app/editor/editor_manager.h"
 #include "app/editor/system/editor_registry.h"

src/app/editor/system/project_manager.cc

@@ -5,7 +5,7 @@
 
 #include "absl/strings/str_format.h"
 #include "app/editor/system/toast_manager.h"
-#include "app/core/project.h"
+#include "core/project.h"
 
 namespace yaze {
 namespace editor {
@@ -17,7 +17,7 @@ ProjectManager::ProjectManager(ToastManager* toast_manager)
 absl::Status ProjectManager::CreateNewProject(const std::string& template_name) {
   if (template_name.empty()) {
     // Create default project
-    current_project_ = core::YazeProject();
+    current_project_ = project::YazeProject();
     current_project_.name = "New Project";
     current_project_.filepath = GenerateProjectFilename("New Project");
     
@@ -49,7 +49,7 @@ absl::Status ProjectManager::LoadProjectFromFile(const std::string& filename) {
     // TODO: Implement actual project loading from JSON/YAML
     // For now, create a basic project structure
     
-    current_project_ = core::YazeProject();
+    current_project_ = project::YazeProject();
     current_project_.filepath = filename;
     current_project_.name = std::filesystem::path(filename).stem().string();
     
@@ -223,7 +223,7 @@ absl::Status ProjectManager::CreateFromTemplate(const std::string& template_name
   // TODO: Implement template-based project creation
   // This would copy template files and customize them
   
-  current_project_ = core::YazeProject();
+  current_project_ = project::YazeProject();
   current_project_.name = project_name;
   current_project_.filepath = GenerateProjectFilename(project_name);
   

src/app/editor/system/project_manager.h

@@ -4,7 +4,7 @@
 #include <string>
 
 #include "absl/status/status.h"
-#include "app/core/project.h"
+#include "core/project.h"
 
 namespace yaze {
 namespace editor {
@@ -41,8 +41,8 @@ class ProjectManager {
   absl::Status ValidateProject();
   
   // Project information
-  core::YazeProject& GetCurrentProject() { return current_project_; }
-  const core::YazeProject& GetCurrentProject() const { return current_project_; }
+  project::YazeProject& GetCurrentProject() { return current_project_; }
+  const project::YazeProject& GetCurrentProject() const { return current_project_; }
   bool HasActiveProject() const { return !current_project_.filepath.empty(); }
   std::string GetProjectName() const;
   std::string GetProjectPath() const;
@@ -53,7 +53,7 @@ class ProjectManager {
                                  const std::string& project_name);
 
  private:
-  core::YazeProject current_project_;
+  project::YazeProject current_project_;
   ToastManager* toast_manager_ = nullptr;
   
   // Helper methods

src/app/editor/system/shortcut_configurator.cc

@@ -12,7 +12,7 @@
 #include "app/editor/ui/ui_coordinator.h"
 #include "app/editor/ui/workspace_manager.h"
 #include "app/editor/system/popup_manager.h"
-#include "app/core/project.h"
+#include "core/project.h"
 
 namespace yaze::editor {
 
@@ -164,7 +164,7 @@ void ConfigureEditorShortcuts(const ShortcutDependencies& deps,
   RegisterIfValid(shortcut_manager, "Load Last ROM",
                   {ImGuiMod_Ctrl, ImGuiKey_R},
                   [editor_manager]() {
-                    auto& recent = core::RecentFilesManager::GetInstance();
+                    auto& recent = project::RecentFilesManager::GetInstance();
                     if (!recent.GetRecentFiles().empty() && editor_manager) {
                       editor_manager->OpenRomOrProject(
                           recent.GetRecentFiles().front());

src/app/editor/ui/ui_coordinator.cc

@@ -7,7 +7,7 @@
 #include <vector>
 
 #include "absl/strings/str_format.h"
-#include "app/core/project.h"
+#include "core/project.h"
 #include "app/editor/editor.h"
 #include "app/editor/editor_manager.h"
 #include "app/editor/system/editor_registry.h"
@@ -706,7 +706,7 @@ void UICoordinator::DrawGlobalSearch() {
       // Recent Files Tab
       if (ImGui::BeginTabItem(
               absl::StrFormat("%s Recent Files", ICON_MD_HISTORY).c_str())) {
-        auto& manager = core::RecentFilesManager::GetInstance();
+        auto& manager = project::RecentFilesManager::GetInstance();
         auto recent_files = manager.GetRecentFiles();
 
         if (ImGui::BeginTable("RecentFilesTable", 3,

src/app/editor/ui/welcome_screen.cc

@@ -9,8 +9,8 @@
 #include "absl/strings/str_format.h"
 #include "absl/time/clock.h"
 #include "absl/time/time.h"
-#include "app/core/project.h"
-#include "app/core/timing.h"
+#include "core/project.h"
+#include "app/platform/timing.h"
 #include "app/gui/core/icons.h"
 #include "app/gui/core/theme_manager.h"
 #include "imgui/imgui.h"
@@ -255,7 +255,7 @@ bool WelcomeScreen::Show(bool* p_open) {
       
       // Smooth interpolation to target position (faster response)
       // Use TimingManager for accurate delta time
-      float lerp_speed = 8.0f * yaze::core::TimingManager::Get().GetDeltaTime();
+      float lerp_speed = 8.0f * yaze::TimingManager::Get().GetDeltaTime();
       triforce_positions_[i].x += (target_pos.x - triforce_positions_[i].x) * lerp_speed;
       triforce_positions_[i].y += (target_pos.y - triforce_positions_[i].y) * lerp_speed;
       
@@ -424,7 +424,7 @@ void WelcomeScreen::RefreshRecentProjects() {
   recent_projects_.clear();
   
   // Use the ProjectManager singleton to get recent files
-  auto& recent_files = core::RecentFilesManager::GetInstance().GetRecentFiles();
+  auto& recent_files = project::RecentFilesManager::GetInstance().GetRecentFiles();
   
   for (const auto& filepath : recent_files) {
     if (recent_projects_.size() >= kMaxRecentProjects) break;