Update ruff to encourage use of modern typing

[oerc0122]

Large number of small changes.

Description of work

• Migrate ruff out of pyproject.toml to top-level ruff.toml (so shared between MDANSE & GUI).
• Use 3.9 typing features.
• Enable pyupgrade checks.
• Add encoding to most open statements.
• Restructure some functions to avoid opening files repeatedly.

Fixes Fixes #746

To test Standard tests, should be no functional changes.