This is great, thank you! There is one problem however. While the defaults: worked and both journals and essays now have the permalinks that I want, the .md files don’t get assigned to a category based on the directory name in which they are located in.
For example, when I apply the file structure that you suggested:
_posts
\essays
yyyy-mm-dd-your-essay-title.md
yyyy-mm-dd-another-essay-title.md
...
\journals
yyyy-mm-dd-your-journal-title.md
yyyy-mm-dd-another-journal-title.md
...
The essays are not present in site.categories.essays variable, nor are the journals in the site.categories.journals variable.