A notebook that survives its tools
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Summary
Every note-taking app eventually becomes the thing you are managing. Plain files, explicit links and one boring index outlast all of them.
Constraint first
Assume the current app will be gone in five years. Any feature that cannot be exported as text is a feature you are renting.
The index is the product
Search finds what you remember to look for. An index tells you what you have. Writing the index by hand is slow, which is precisely why it stays honest.