Refactor setup workflow and make install robust via virtualenv

- Introduce a dedicated Python virtualenv (deps target) and run all setup scripts through it
- Fix missing PyYAML errors in clean, CI, and Nix environments
- Refactor build defaults into cli/setup for clearer semantics
- Make setup deterministic and independent from system Python
- Replace early Makefile shell expansion with runtime evaluation
- Rename messy-test to test-messy and update deploy logic and tests accordingly
- Keep setup and test targets consistent across Makefile, CLI, and unit tests

https://chatgpt.com/share/693de226-00ac-800f-8cbd-06552b2f283c

main.py

@@ -209,7 +209,7 @@ def print_global_help(available, cli_dir):
         Fore.CYAN
     ))
     print(color_text(
-        "    corresponds to `cli/build/defaults/users.py`.",
+        "    corresponds to `cli/setup/users.py`.",
         Fore.CYAN
     ))
     print()