MindTouch does not do any encryption at the application layer. Therefore, all the data in the DB is plaintext. It may be possible to encrypt data before storing but that would require a lot changes in the MindTouch codebase.
There are third-party tools that claim to offer transparent encrytion at the database or table level.
I have not used any of these third-party tools so I'm not exaclty sure how they work
The /var/lib/mysql directory could be installed on an encrypted filesystem. This would provide security if the disk was ever compromised. However, the filesystem would be mounted at boot time so anyone able to get root access would be able to access the database unencrypted.
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