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EncryptPad
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I'm kinda surprised no one mentioned cherrytree yet.
Hey! I make an app that I think matches all your needs and am open to suggestions. The latest version is available on flathub. https://github.com/LukeBriggsDev/Pepys
Hazama worked for me.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.