MRG: update docs for v0.9.0

[ctb]

After #197 and #211, we need to switch up our documentation and references for using the branchwater plugin.

This PR also adds documentation for pairwise and suggests .rocksdb as the suffix for index output.

Finally, this PR bumps the version to v0.9.0 in preparation for a release. 🎉

The updated doc/README.md is here.

HackMD version of doc/README.md for nicer viewing/editing: https://hackmd.io/_DqWfa8BS364lfjhnvfnOg?view

• Fixes revise "Notes on concurrency and efficiency" #212
• Fixes change index documentation to suggest/recommend .rocksdb suffix #210
• Fixes add documentation for pairwise #190

[ctb]

@bluegenes I am now using a hackmd to edit doc/README.md! It's directly linked via github in case you want to add or edit, but also happy to take comments and suggestions here on github rather than on hackmd. Whatever works for you.

(I, for one, welcome our new tabulatory overlords!)

If you have time or interest and want to double-check the new table of query/database types, that would be useful - but by no means necessary.

[ctb]

hmm.

  × Preparing editable metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [15 lines of output]
      error: failed to select a version for `env_logger`.
          ... required by package `sourmash_plugin_branchwater v0.8.7-dev (/home/ctbrown/pyo3_branchwater)`
      versions that meet the requirements `^0.11.1` (locked to 0.11.1) are: 0.11.1
     
      the package `sourmash_plugin_branchwater` depends on `env_logger`, with features: `anstream` but `env_logger` does not have these features.
       It has an optional dependency with that name, but that dependency uses the "dep:" syntax in the features table, so it does not have an implicit feature with that name.
     
     
      failed to select a version for `env_logger` which could resolve this conflict
      � maturin failed
        Caused by: Cargo metadata failed. Does your crate compile with `cargo build`?
        Caused by: `cargo metadata` exited with an error:
      Error running maturin: Command '['maturin', 'pep517', 'write-dist-info', '--metadata-directory', '/scratch/tmp/pip-modern-metadata-bkog6pe2', '--interpreter', '/home/ctbrown/mambaforge/envs/sourmash-dev/bin/python']' returned non-zero exit status 1.
      Checking for Rust toolchain....
      Running `maturin pep517 write-dist-info --metadata-directory /scratch/tmp/pip-modern-metadata-bkog6pe2 --interpreter /home/ctbrown/mambaforge/envs/sourmash-dev/bin/python`
      [end of output]

[ctb]

maybe broken by #209 - will try reverting.

[ctb]

(reversion works)

[ctb]

Ready for review & merge @bluegenes!

[bluegenes]

made a few suggestions -- otherwise looks good!!

[bluegenes]

backing up on purpose?

[ctb]

yes, it causes build problems on linux