Fix critical bugs, add tests, CI, and improve code quality

[tdpham2]

• Fix MACE optimizer bug: geo_opt_cell_opt called dyn1.run() instead of dyn.run(), so cell optimization was never actually executed
• Fix shell injection vulnerability in tobacco module by replacing subprocess.call(shell=True) with safe subprocess.run([...])
• Fix missing f-string prefix in raspa2 error message
• Remove unreachable code after raise in graspa and graspa_sycl
• Replace platform-dependent sed/rm subprocess calls with Python
• Standardize os.path usage to pathlib.Path across all modules
• Add init.py with re-exports for io, mlip, orca, utils modules
• Add 42 pytest tests covering CLI, graspa, raspa3, and utils
• Add GitHub Actions CI workflow (lint, test on 3.10-3.12, build)
• Add optional dependency groups (rdkit, mlip, dev) in pyproject.toml
• Add skills.md, CHANGELOG.md, and update README with accurate docs
• Add docstrings and type hints to all public functions
• Fix type hints: steps float->int, list[int,int,int]->list[int]
• Remove unused imports across cli.py, graspa.py, raspa2.py