Remove `--version` from subcommands (#13108)
Supersedes https://github.com/astral-sh/uv/pull/12439 — does not use the
Clap macro so we retain control over the messages
Closes #12431
https://github.com/astral-sh/uv/pull/13108/commits/0077a67b34d22071dcfd42c9281c6929658bb7f9
pulls `uv run` and `uv tool run` test changes from
https://github.com/astral-sh/uv/pull/12439
