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I have notes.org (emacs org mode) which contain basically all of my notes ever written.

Sure the org mode collapse thing is fine but the killer feature is being able to grep all of my notes in milliseconds.

org-rifle may be better for searching org notes, because it searches for multiple words occuring in individual notes which is more efficient than simple line-base grepping:

https://news.ycombinator.com/item?id=24916536

Please see also org-ql, which mostly obsoletes org-rifle and is much faster as well.

How do you use that day to day? I also use Org, but it has slowed down quite a bit for me. Perhaps one of my files is too big, and I also use the agenda, which takes at least a few seconds to regenerate.

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