Readwise and Other Highlights
Two folders I don't write by hand: readwise/, synced from Readwise, and highlights/, saved by a separate reading app.
Two folders hold highlights that tools write into the notebook. Notes link to them, but they're never edited by hand, since the next sync could overwrite the change.
Readwise highlights
readwise/ has one file per book or article, synced daily from Readwise. The Readwise Highlights page groups them by category, and each page lists its highlights as quotes. See Walden and The Way to Wealth.
Other highlights
highlights/ has passages I've saved with a separate reading app, from articles, PDFs, and newsletters, each with a summary of the source. The Other Highlights page lists them newest first. See Self-Reliance.
Searching them
They're left out of search unless asked for, since there are far more highlights than notes. See How Search Works.