I have a feeling you’re looking for something different, but: mine is a big todo.txt document that I open with fzf. I just add lines to it and tack on @keywords.

If your needs are more hierarchical and structured, fzf, I’d still try to stick with a plain-text and fuzzy-search based solution, and split stuff up into different files.

IMHO, you’re starting from a good place (plain text files). Maybe you just need a little tooling for searching and keyword filtering.