Replace GLFW and nativefiledialog with SDL3 + Create layered renderer architecture with GPU API

[Copilot]

Consolidates windowing and file dialog dependencies from GLFW + nativefiledialog into SDL3, reducing dependency footprint and leveraging SDL3's native cross-platform file dialogs. Additionally refactors all rendering code into a layered renderer architecture with a standalone low-level GPU API to prepare for future SDL-GPU transition.

Changes

Dependency Management

• Added SDL3 as submodule (main branch)
• Removed GLFW and nativefiledialog submodules
• Updated CMakeLists.txt: static SDL3 build with optional X11 features disabled

Core Migration (src/app/application.cpp)

• Window/GL context: glfwCreateWindow → SDL_CreateWindow, glfwMakeContextCurrent → SDL_GL_MakeCurrent
• Event loop: glfwPollEvents → SDL_PollEvent with native SDL event handling
• File dialogs: NFD_OpenDialog/SaveDialog → SDL_ShowOpenFileDialog/ShowSaveFileDialog with async callbacks
• Timing: glfwGetTime → SDL_GetTicks

ImGui Backend

• Added imgui_impl_sdl3.{cpp,h} from ImGui 1.90.5, patched for SDL3 API changes:
  • Keyboard events: keysym struct → flat key/scancode/mod fields
  • Constants: SDLK_a → SDLK_A, SDL_SYSTEM_CURSOR_ARROW → SDL_SYSTEM_CURSOR_DEFAULT
  • Text input: SDL_SetTextInputRect → SDL_SetTextInputArea(window, rect, cursor)
• Updated for ImGui 1.92.5 compatibility: SetPlatformImeDataFn → platform_io.Platform_SetImeDataFn
• Removed imgui_impl_glfw.{cpp,h}

Layered Renderer Architecture

Low-Level GPU API (src/gfx/gpu.{h,cpp})

NEW: Created abstraction layer for all GPU operations:

• Texture Management: create_texture_2d/3d(), update_texture(), destroy_texture(), bind_texture()
• Shader Management: create_shader(), destroy_shader(), use_shader(), set_uniform() (multiple type overloads)
• Framebuffer Management: create_framebuffer(), destroy_framebuffer(), bind_framebuffer(), attach_texture_to_framebuffer()
• VAO Management: create_vertex_array(), destroy_vertex_array(), bind_vertex_array()
• Rendering State: set_viewport(), set_scissor(), enable_blend(), enable_depth_test(), enable_cull_face(), set_depth_mask(), set_color_mask(), clear_color(), clear()
• Draw Operations: draw_arrays(), draw_elements()

High-Level Renderer Module (src/gfx/renderer.{h,cpp})

• Moved ~578 lines of rendering code from main.cpp to renderer module
• Functions migrated:
  • fill_gbuffer() - Molecular representation rendering to GBuffer
  • apply_postprocessing() - All post-processing effects (SSAO, TAA, DoF, etc.)
  • draw_representations_opaque() - Opaque molecular rendering
  • draw_representations_transparent() - Volume rendering (orbitals, electron density)
  • draw_representations_opaque_lean_and_mean() - Optimized rendering for selections/highlights
• Clean API: main.cpp now uses renderer::*() calls instead of direct OpenGL
• Uses GPU API: Renderer layer uses low-level GPU API for all OpenGL operations

Component Refactoring

NEW: Started migrating components to use GPU API:

• Ramachandran Component: Refactored texture creation/destruction to use gpu::create_texture_2d() and gpu::destroy_texture()
• Replaced glGenFramebuffers/glGenVertexArrays with gpu::create_framebuffer() and gpu::create_vertex_array()
• Uses glTexStorage2D via GPU API for immutable texture storage

File Dialog Implementation

// Before: Synchronous NFD with manual filter parsing
nfdchar_t* out_path = NULL;
nfdresult_t result = NFD_OpenDialog("jpg,png,bmp", NULL, &out_path);
if (result == NFD_OKAY) { /* use out_path */ }

// After: Async SDL3 with callback and proper cleanup
struct DialogState { const char* result_path; bool completed; };
DialogState state = {NULL, false};
SDL_ShowOpenFileDialog(callback, &state, NULL, filters, count, NULL, false);
while (!state.completed) { SDL_WaitEventTimeout(&event, 10); }

Security & Quality

• Fixed race condition: changed dialog state from static to local
• Added buffer overflow protection in filter extension parsing (validate length before allocation)
• Improved responsiveness: SDL_Delay(10) → SDL_WaitEventTimeout(&event, 10)

Architecture Improvement

The new layered architecture provides clean separation of concerns:

Components (ramachandran, veloxchem, etc.)
   ↓
High-level Renderer (renderer.h/cpp)
   ├─> renderer::fill_gbuffer()
   ├─> renderer::apply_postprocessing()
   └─> renderer::clear_gbuffer()
          ↓
Low-level GPU API (gpu.h/cpp)
   ├─> gpu::create_texture()
   ├─> gpu::create_shader()
   ├─> gpu::bind_framebuffer()
   ├─> gpu::set_viewport()
   └─> gpu::draw_arrays()
          ↓
OpenGL

Benefits:

• All OpenGL calls isolated in GPU API layer
• Components use GPU API instead of direct OpenGL
• High-level renderer focuses on rendering logic, not OpenGL details
• Easy to swap OpenGL for SDL-GPU in future by reimplementing GPU API
• MDlib rendering code (md_gl_draw()) remains unchanged as requested

Progress

• ✅ Low-level GPU API layer complete
• ✅ High-level renderer using GPU API
• ✅ Ramachandran component partially migrated to GPU API
• 🔄 Remaining: Complete component migration (ramachandran rendering, veloxchem, etc.)

Notes

• Manual testing recommended on Windows/macOS to verify native file dialogs and platform-specific behavior
• Layered renderer architecture ready for future SDL-GPU migration
• MDlib rendering code remains unchanged as requested

Original prompt

Create a PR that introduces SDL3 as a new dependency. This should replace the existing dependencies on glfw and native file dialogue.

---

💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.