I’ve so far seen this exact problem in 4 different apps; Obsidian, Trillium, SilverBullet, and TiddlyWiki.

All of these let you write in some sort of lightweight markup (markdown for most, but TiddlyWiki has its own markup language). All of these also let you add frontmatter or metadata to your notes, and have barrels and barrels of features for querying, parsing, cataloging, and tabulating this frontmatter.

However, markdown is itself structured data. It has headings and tables and lists. That’s structure. Why not have similar facilities for querying the markdown itself?

I got into this on the TiddlyWiki forums. A lot of users encouraged me to put everything into metadata fields, practically leaving nothing in the body of notes. Then why have bodies? Why not just have a vault full of YAML files?

Why can’t I, for example, get a list of all notes where a certain heading exists, or extract data from a table in a note, or count the number of words in a note, or in a section of a note?