Promote usage of uv run (no more python vs python3)

[Avasam]

Using uv run is optional. "medium to advanced" python users already know to activate their venv and use the right py/python/python3 command if they want to.

Contributors who want to use uv run but with a custom venv can do so with uv run --active. I use that on WSL with a .venv-linux venv.

This is mostly simplifying the instructions, and reducing the risk of a command failing from an unactivated venv, for newer contributors. Documentation only, it doesn't change any actual flow.

#13597 promotes the usage of uv pip.

This also also enables running uv run without having to add --no-project every time. Until astral-sh/uv#8666, this requires adding a [project] section to pyproject.toml and .gitignoring the uv.lock file.

[Avasam]

Oh, no shebang update until astral-sh/ruff#13021, I'll revert those.

[Akuli]

Let's wait for #13597 (comment) to be resolved before merging this.