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.cc

@@ -1,6 +1,6 @@
 #include "cli/handlers/agent/commands.h"
 #include "cli/handlers/agent/todo_commands.h"
-#include "cli/z3ed.h"
+#include "cli/cli.h"
 
 #include <string>
 #include <vector>