Currently, when we generate a `csv_summary` with LINs, we get a summary
at every single LIN rank, which is a lot of results and not very
helpful. LINgroups are our way of linking the LINs (e.g.
`14;1;0;0;0;0;0;0;0;0`) to a known name/taxonomic group (e.g. "Phylotype
I").

This PR changes the behavior of `csv_summary` when a `lingroup` file is
provided, limiting summarized reporting to just the named lingroups.
While the output is very similar to the `lingroup` output we already
have, the most important difference is that the sample name is included
in the output, meaning that we get intelligible results when running
`tax metagenome` on more than one sample.

Prior `tax metagenome` behavior was to always generate a `lingroup`
output file when a `lingroups` file is provided. Here, I disable that
for multiple queries, since the results wouldn't make sense. I do not
replace it with another default, but I did add a recommendation to the
help + doc.

In the future, we could consider changing the default `lingroup` output
to `csv_summary`, since it's actually useful for multiple files. Or, we
could modify the `lingroup` output to include query information.

- Also fixes #3315

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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>