chore(linting): add Black + Ruff PEP 8 tooling and apply project-wide formatting

- Add [tool.black] and [tool.ruff] sections to pyproject.toml
  * line-length = 88 (Black default)
  * Ruff rule sets: E/W, F, I (isort), UP, B, SIM, RUF
  * Pragmatic ignore list for scientific code conventions (Greek
    letters, en-dash separators, JAX device-first import order)
  * Per-file ignores for tests, examples, docs
- Add ruff and black to [project.optional-dependencies] dev
- Apply Black formatter to all 98 Python files
- Apply Ruff auto-fixes (408 issues resolved):
  * Unused imports removed, import order normalised (isort)
  * f-string placeholders fixed, UTF-8 encoding declarations removed
  * Type annotations modernised (PEP 604/585)
- Update .vscode/settings.json:
  * Replace legacy python.linting.pylintEnabled with Ruff extension
  * Enable format-on-save and import organisation via charliermarsh.ruff
- 138 remaining warnings deferred for iterative cleanup (unused vars,
  undefined names, simplification suggestions)