[MRG] fix docs build

[ctb]

Fix some docs issues:

• version pinning of Sphinx, myst-parser, jinja2 all updated to avoid some of the recent ReadTheDocs build problems.
• myst_parser configuration of internal linking/references
• fix many different internal linking/references

Review of this probably needs to skim through the docs to look for major formatting errors. I've checked the command-line execution and error messages and there's nothing obvious wrong; I'll look at the online formatting and make a little checklist for the reviewer for what I checked, once the ReadTheDocs build passes.

CTB's doc checklist

• the logs for the build over at https://readthedocs.org/projects/sourmash/builds/ have no obvious errors
• cross-references within the sourmash documentation work (-> no missing reference errors when building the docs on the command line)
• the sourmash Python API docs in api.html have content / did not fail importing from packages
• the notebooks were built and formatted properly (e.g. kmers-and-minhash.html)

[codecov]

Codecov Report

Merging #1897 (b49788c) into latest (03f2fae) will increase coverage by 7.90%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           latest    #1897      +/-   ##
==========================================
+ Coverage   82.75%   90.65%   +7.90%     
==========================================
  Files         122       92      -30     
  Lines       13206     9004    -4202     
  Branches     1780     1780              
==========================================
- Hits        10928     8163    -2765     
+ Misses       2014      577    -1437     
  Partials      264      264              

Flag	Coverage Δ
python	90.65% <ø> (ø)
rust	?

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Impacted Files	Coverage Δ
src/core/src/ffi/cmd/compute.rs
src/core/src/index/bigsi.rs
src/core/src/ffi/utils.rs
src/core/src/index/mod.rs
src/core/src/index/linear.rs
src/core/src/index/revindex.rs
src/core/src/ffi/index/revindex.rs
src/core/src/index/sbt/mhbt.rs
src/core/src/errors.rs
src/core/src/ffi/index/mod.rs
... and 20 more

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[ctb]

ready for review and merge @sourmash-bio/devs

[luizirber]

I ran npx broken-link-checker -- <link-to-rtd-PR-docs> and found one "broken" link, but only because the checker wasn't following redirects.
I also bumped the rtd python to 3.8, since 3.7 is deprecated.