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Available for linux users Encfs stores files in an encrypted folder. To read these files, they must be mounted to an empty directory.
1. Install encfs
This process varies depending on your linux distribution.
This example works for Arch Linux:
pacman -S encfs
apt-get install encfs
2. Move existing zim files
Important: Close Zim
mv ~/Notes Notes-old
3. Setup encfs folders
Hidden folder stores encrypted contents. Note the '.' dot.
Same name as the folder Zim normally uses. Unencrypted files will be accessible here when mounted`
4. Start encryption
encfs ~/.Notes ~/Notes
this first time through, you will be prompted for a password, and some security settings. In the future, you will only need to supply a password. You will need to run this command each time you restart your computer before running zim
5. Move encrypt old notes
rsync -av ~/Notes-old ~/Notes
6. Remove old notes (optional)
Make sure zim starts normally and you can access your encrypted notebook first!
There is an interesting solution using Truecrypt and Dropbox. Your notebook can be encrypted inside a truecrypt container and that container can be synchronized over the cloud using Dropbox. The catch here is that when you open the container and make changes to your notebook and close it again, Dropbox wouldn't synchronize the whole container, only the bits that've changed.