If you really want to be future proof and interoperable, I suggest you to use something like a git repository + vscode + foam (https://github.com/foambubble/foam). All of the tech is open source and relatively easy to use, especially if you already know git.
Treedome on the other hand can be abandoned. It can be swallowed by the sands of time. It uses a custom file format after all. But because of its open-source nature, as long as you have the code, you can open the notes. But that's a good idea, to be able to export to a plaintext file. You could make a request here if you want https://codeberg.org/solver-orgz/treedome/issues
Could've put the app into maintenance mode instead of archiving it.