[MRG] fix doc titles in command-line.md and update description a bit

[ctb]

Minor updates to command-line docs, initiated because I noticed that the prefetch section headers were at the wrong level.

This PR affects only command-line.md, and:

• adjusts prefetch section headers
• adds containment to the comment about similarity
• removes an outdated warning
• adds a reference to the gather preprint

Addresses #1789 but doesn't fix it.

[codecov]

Codecov Report

Merging #1874 (4a106df) into latest (ba38d14) will increase coverage by 7.93%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           latest    #1874      +/-   ##
==========================================
+ Coverage   82.52%   90.46%   +7.93%     
==========================================
  Files         121       91      -30     
  Lines       13061     8859    -4202     
  Branches     1751     1751              
==========================================
- Hits        10779     8014    -2765     
+ Misses       2016      579    -1437     
  Partials      266      266              

Flag	Coverage Δ
python	90.46% <ø> (ø)
rust	?

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Impacted Files	Coverage Δ
src/core/src/sketch/hyperloglog/mod.rs
src/core/src/index/sbt/mod.rs
src/core/src/storage.rs
src/core/src/index/linear.rs
src/core/src/signature.rs
src/core/src/index/sbt/mhbt.rs
src/core/src/ffi/hyperloglog.rs
src/core/src/index/bigsi.rs
src/core/tests/minhash.rs
src/core/src/index/mod.rs
... and 20 more

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[ctb]

Ready for review & merge @sourmash-bio/devs

(I'm aware we need lots of doc updates around FracMinHash. Please don't ask me to do more in this PR :)

[bluegenes]

minor suggestion, otherwise lgtm :)