Switch to ruff for linting and formatting

[tomjholland]

This pull request includes significant changes to the configuration and example files, focusing on code formatting and updating dependencies. The most important changes include switching from flake8 and other tools to ruff, and reformatting several Jupyter notebooks for better readability and consistency.

Configuration updates:

• .flake8: Removed the configuration file for flake8, including settings and plugin requirements.
• .pre-commit-config.yaml: Replaced flake8, isort, and black with ruff for linting and formatting.

Code formatting improvements:

• docs/source/examples/LEAN-differentiation.ipynb: Reformatted dictionary and function call syntax for better readability. [1] [2] [3] [4] [5]
• docs/source/examples/analysing-GITT-data.ipynb: Updated dictionary and function call syntax to use consistent formatting. [1] [2] [3] [4] [5] [6] [7]
• docs/source/examples/comparing-pyprobe-performance.ipynb: Applied consistent formatting to dictionary and function calls. [1] [2]

Minor changes:

• docs/source/_append_footbib.py and docs/source/conf.py: Added a newline for better code structure. [1] [2]