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Hmmm... I can't seem to escape to take notes abou note-taking. But then again, note-taking is a form of PIM.
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Future-proofing your notes is only worth if the future is relevant
At some point, your notes will be a gigantic mess. Even if you Add a desktop search engine for your digital library and know the structure, it's not always worth with the overwhelming pile that will accumulate further since you always navigate certain notes through a fixed path. Similar to certain software projects like Xorg, Rust language, magit, and org-roam, there will be a point where you have to redesign them. 1 You have to assign a garbage day at some point.
Future-proofing your notes creates pressure on managing your note-taking seriously and efficiently. You don't want to take notes haphazardly and the overall notes structure will stay the same throughout a year. They should eventually evolve into Evergreen notes, branching out of the original notes structure and making a better graph for navigation.
An alternative to trashing your notes is to Create an inbox to store your thoughts.
Xorg has Wayland as the successor, the Rust community can revise the language freely through editions, magit did have a crownfunding campaign to pay the developer to rewrite it for a year, and org-roam is recently through a major redesign.