Remove some Clap-level conflicts in argument groups

[charliermarsh]

Summary

It turns out that if you have an environment variable set, Clap will consider that equivalent to passing the flag, even if it's set to (e.g.) something falsy or the default value.

So, e.g., this fails:

UV_SYSTEM=false uv pip install --python ./.venv/bin/python flask

Worse, this fails, because it thinks --no-index and --index-url are conflicting:

export UV_INDEX_URL=https://google.com
uv pip install flask --no-index

This PR removes some of the conflicts, namely those related to environment variables, such that:

• You can pass mixes of --no-index, --index-url, etc. If --no-index is provided, all the index URLs will be ignored (but we won't error).
• Passing --pre will always enable prereleases, even if --prerelease is also provided. (We could warn here, although honestly it's not trivial because we'd need to make --prerelease take an optional, then we'd lose the default argument from the --help.)
• You can pass --system and --python. If --python is provided, we use that, and ignore --system. (We could warn here.)

I guess the underlying problem here is that we can't differentiate between arguments passed on the CLI and those set as environment variables. But making bigger changes here seems out-of-scope.

Closes #3000.

[BurntSushi]

This seems like an improvement to me.

Does this take the order of flags into account? e.g., Are --no-index --index-url ... and --index-url ... --no-index the same? I think arguably the order should determine which one "wins." IIRC, this was difficult to do in Clap unfortunately. (Or at least, difficult to do in Clap 2. I'm unsure about Clap 4.)

[charliermarsh]

It doesn't, though in that specific case I actually think --no-index should still win...

[charliermarsh]

In general though, I agree that taking order into account would help here.