how to encrypt an existing directory

Thank you for your question.

To encrypt an existing directory, you can rename it temporarily, create a new stash with the old foldername as either the mount point or the stash directory depending on whether you want to access the files through the old directory or use it to contain the encrypted files and then move the files into the newly created stash.

E.g. if you have an existing directory "someFolder" and if you want the files to be accessible though the old "someFolder" directory, you could do the following in a terminal:

rename the directory
$ mv someFolder someFolder.tmp

create a stash that mounts into "someFolder" and stores the encrypted files in ".someFolder"
$ gnome-encfs-manager create_stash .someFolder someFolder

move the files into the new stash and remove the temporary directory
$ mv someFolder.tmp/* someFolder && rmdir someFolder.tmp

I hope this helps and kind regards,
Moritz