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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.
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.