Update the taxonomy and reference DBs

Currently the taxonomy and Kraken DB are from 2022-12. This is getting quite old!

Approach for getting up to date:

Come up with a name that shows files were processed under a more recent taxonomy. I'm leaning towards sticking it in the stage path, so instead of processed/ we'll now have processed-2024-06/. All the old files will still be there.
Move human-viruses-raw.tsv, human-viruses.tsv, plus, within dashboard, *.dmp, top_species_counts, and top_species_scratch into a scratch location. Delete hvreads, readlengths, ribofrac, cladecounts and allmatches.
Update download-taxonomy.sh to pull the latest taxonomy at the time we're making the change
Update run.py to use new timestamp-based directories for processed/ and everything downstream from it.
Update prepare-shm-kraken.sh to pull the latest KrakenDB
- Currently that's 2024-01-12, but historically these have come out in the early summer so we may be about to see an update
  - https://github.com/BenLangmead/aws-indexes/issues/29
- While we're at it, we should probably stop using the Standard16 and move to Standard, despite the higher memory requirements
Reprocess bioprojects as needed

naobservatory / mgs-pipeline