Codebase Refactor: Adding pre-commit checks and enforcing them.

We really should try to enforce linting and code quality checks locally when possible, as it can ensure our code quality is high and prevent some easy errors.

Using pre-commit is easy - we just need to add the .pre-commit-config.yaml.

However, while it is easy to push the yaml into the repo, we should actually ensure compliance with ruff and other tools so that we can ensure everything is going as expected.

The PR to be mentioned will contain this first change, but I'll push any PRs I can that address issues as separate issues and PRs. This issue should be closed when we can run the pre-commit mentioned without any major errors.

Hooks used:
ruff (lint and format)
shellcheck
trailing-whitespace
end-of-file-fixer
check-yaml
check-added-large-files
detect-private-key

Start by reviewing the repository and the proposed .pre-commit-config.yaml, then run the listed hooks to identify existing violations. Check ruff linting and formatting first, followed by shellcheck and the file-safety checks. Done means pre-commit runs without major errors and the repository complies with the configured hooks.