refactor: Restructure CLI File Organization and Update Includes

- Updated CMakeLists.txt to reflect new file paths for CLI components, enhancing project organization.
- Replaced instances of the deprecated z3ed.h with cli.h across multiple handler files, improving code consistency and maintainability.
- Organized CLI source files into a dedicated directory structure for better modularity and clarity.

src/cli/handlers/project.cc

@@ -1,5 +1,5 @@
 #include "app/core/project.h"
-#include "cli/z3ed.h"
+#include "cli/cli.h"
 #include "util/file_util.h"
 #include "util/bps.h"
 #include <filesystem>