deprecate sourmash multigather for 5.0

[ctb]

IMO.

code is messy, is not as well tested as gather, it was never that much faster than gather, and doesn't support picklists. our goal should be to continue to make gather even faster :)

[ctb]

an alternative brainstormed in #1624 would be to make multigather faster by doing a prefetch on all signatures combined - that is, optimize around multiple queries, rather than multiple databases (which was the original intent of multigather).

[ctb]

A few thoughts here -

• @olgabot and @dkoslicki are finding multigather useful (as evidenced in MRG: Uniquify csv output from multigather #2065 and multigather only saves first match to CSV #2321/[MRG] Fix multigather so that the output CSV contains all matches. #2322!)
• note the discussion in multigather CSV output uses signature filename as basename. #2328 about improving multigather output, which is potentially addressed in MRG: Uniquify csv output from multigather #2065
• instead of deprecating/removing multigather, we could make it a plugin
• note that the pyo3_branchwater plugin has fastmultigather which is indeed much faster than multigather also; so we could upgrade fastmultigather to do what people want and need

[ctb]

• instead of deprecating/removing multigather, we could make it a plugin

• note that the pyo3_branchwater plugin has fastmultigather which is indeed much faster than multigather also; so we could upgrade fastmultigather to do what people want and need

after ~6 months or so, I'm doubling down on this opinion - see #2722 (comment),

@bluegenes is doing different experiments in re output files with fastmultigather over in sourmash-bio/sourmash_plugin_branchwater#197, and so I think we have routes to explore better output over there.

It might be that a long-term future for multigather is to deprecate it in sourmash and direct people to fastmultigather, which is actually much faster than multigather.

[ctb]

note: as of sourmash_plugin_branchwater v0.9.5 link, the results from fastgather and fastmultigather are now identical to those from sourmash gather. So I think we should just update to say, "use fastmultigather".