I assume the sqlite database got corrupted or is too big. There is an article here [0] which describes why this could happen. Diodon uses Zeitgeist to store clipboard items and zeitgeist manages the sqlite database itself.
So you find the database at ~/.local/share/zeitgeist/. Best have a look what size the database has in this folder to see whether that is the issue. Simply renaming/removing the zeitgeist folder should fix the issue. (I guess you need to stop/kill the zeitgeist-daemon first though) Oliver [0] https://stackoverflow.com/questions/5274202/sqlite3-database-or-disk-is-full-the-database-disk-image-is-malformed
