ci: standardize Python execution across workflows and improve venv caching robustness

- Changed all Python/pip commands to use `venv/bin/python -m` pattern instead of direct tool invocation or source activation
  - package-tests.yml: pip, mypy, black, pytest now use `venv/bin/python -m`
  - python-tests.yml: ruff, pip, pytest now use `venv/bin/python -m` or `venv/bin/pytest`
  - staking-tests.yml: pytest now uses `venv/bin/pytest` instead of `python3 -m pytest`
- Added missing dependencies to workflow

.gitea/workflows/cli-level1-tests.yml

@@ -41,7 +41,9 @@ jobs:
 
           bash scripts/ci/setup-python-venv.sh \
             --repo-dir "$PWD" \
-            --venv-dir "$PWD/venv"
+            --venv-dir "$PWD/venv" \
+            --requirements-file "$PWD/cli/requirements-cli.txt" \
+            --extra-packages "PyYAML requests cryptography"
           echo "✅ Python environment ready"
 
       - name: Verify CLI imports