MRG: adjust documentation to recommend tax over lca for taxonomic analysis

[ctb]

This PR adds cautionary notes to the command line docs, and updates the information on classifying signatures to suggest using tax instead of LCA, and even explains why :).

There is more work to be done - we need to add more tutorials, and adjust the language in classifying-signatures around gather and LCA - but this is a nice standalone PR!

Fixes #2562
Fixes #2772
Fixes #2773

Adds information from #2760
Addresses #2535

[ctb]

ready for review @bluegenes

[codecov]

Codecov Report

Merging #2777 (a59effc) into latest (256a705) will increase coverage by 6.93%.
The diff coverage is n/a.

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+ Coverage   85.91%   92.85%   +6.93%     
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+ Misses       1785      587    -1198     
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hypothesis-py	25.81% <ø> (-0.01%)	⬇️
python	92.85% <ø> (-0.01%)	⬇️
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[bluegenes]

This looks good and provides some good context for why gather --> tax over lca.

Only thought - do you want to add a sentence on where LCA is still useful? E.g. tracking down individual k-mers/sequences, exploratory work, etc?

[ctb]

Only thought - do you want to add a sentence on where LCA is still useful? E.g. tracking down individual k-mers/sequences, exploratory work, etc?

Added in #2777 (review)

(I had originally put in something like that, and then removed as confusing, so your prompt was a nice reality check!)