Update pathway analysis materials

[sjspielman]

Closes #902
Closes #903
Closes #904
Towards #798
Closes #881 (I snuck in the updated diagram here, renders fine! context: #881 (comment))

This PR tackles updated associated with pathway-materials, as well as one bonus update I tossed in (slightly by accident into this branch, but seems fine) to update the Harmony diagram - it's quite a bit smaller than the previous file size which was pretty big, but still actually technically pretty big.

Main changes:

• For 2024 August issues: Pathway and bulk materials #798, I swapped in fs::dir_create() in all the pathway notebooks: 2024 August issues: Pathway and bulk materials #798 (comment)
• ORA notebook changes:
  • msigdbr usage updates
  • Also from 2024 August issues: Pathway and bulk materials #798 I updated the data frame that I think was being referred to here: 2024 August issues: Pathway and bulk materials #798 (comment) (note a separate PR will be landing for RNA-seq module changes)
  • rendered notebook: 01-overrepresentation_analysis.nb.html. See Update pathway-analysis ORA notebook #902 for some context - notebook output is slightly different but expected given the KEGG update
• GSEA notebook changes:
  • set the seed as noted: 2024 August issues: Pathway and bulk materials #798 (comment)
  • msigdbr usage updates
  • rendered notebook: 02-gene_set_enrichment_analysis.nb.html. Note that the same pathways we plot at the end are at the same relative rankings in results, so no changes to these plots were needed
• GSVA changes
  • no longer use biocparallel for gsva; runtime is immediate and it doesn't play nicely anymore for multiple gene sets
  • purrr syntax updates away from ~
  • rendered notebook: 03-gene_set_variation_analysis.nb.html

Some amount of recreational spacing updates included!

As needed to support review, see August 2024 schedule for previous rendered versions: https://alexslemonade.github.io/2024-august-training/workshop/SCHEDULE.html