CMake improvements: ccache, bundled Qt, MoltenVK, LTO, and Linux deps (#2622)

- Fix YUZU_USE_BUNDLED_QT on Linux (correct path is gcc_64 for Qt 6.8.3).
- Implement USE_CCACHE correctly (additional changes on #2580).
- Categorize and organize CMake options for clarity.
- Add missing Linux dependencies
- Set CMP0069 (LTO) default behavior to NEW to reduce warnings.
- Replace USE_SYSTEM_MOLTENVK with YUZU_APPLE_USE_BUNDLED_MONTENVK and remove duplicate download_moltenvk.

Reviewed-on: #2622
Reviewed-by: MaranBr <maranbr@eden-emu.dev>
Reviewed-by: CamilleLaVey <camillelavey99@gmail.com>
Co-authored-by: Caio Oliveira <caiooliveirafarias0@gmail.com>
Co-committed-by: Caio Oliveira <caiooliveirafarias0@gmail.com>

src/yuzu/CMakeLists.txt

@@ -366,10 +366,10 @@ if (APPLE)
     set_target_properties(yuzu PROPERTIES MACOSX_BUNDLE TRUE)
     set_target_properties(yuzu PROPERTIES MACOSX_BUNDLE_INFO_PLIST ${CMAKE_CURRENT_SOURCE_DIR}/Info.plist)
 
-    if (NOT USE_SYSTEM_MOLTENVK)
+    if (YUZU_APPLE_USE_BUNDLED_MONTENVK)
         set(MOLTENVK_PLATFORM "macOS")
         set(MOLTENVK_VERSION "v1.3.0")
-        download_moltenvk_external(${MOLTENVK_PLATFORM} ${MOLTENVK_VERSION})
+        download_moltenvk(${MOLTENVK_PLATFORM} ${MOLTENVK_VERSION})
     endif()
     find_library(MOLTENVK_LIBRARY MoltenVK REQUIRED)
     message(STATUS "Using MoltenVK at ${MOLTENVK_LIBRARY}.")