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/agent/general_commands.cc

@@ -38,7 +38,7 @@
 #include "cli/service/resources/resource_context_builder.h"
 #include "cli/service/rom/rom_sandbox_manager.h"
 #include "cli/tui/chat_tui.h"
-#include "cli/z3ed.h"
+#include "cli/cli.h"
 #include "util/macro.h"
 
 ABSL_DECLARE_FLAG(std::string, rom);