Kumagusu is a file-based note app for Android. It stores and organizes plain text and encrypted files using directories. The encryption format is compatible with Tombo (its dated encryption format).

Related tools like Tombo* allow desktop and command-line interaction with encrypted files, including Git integration for diff and three-way merge support, as well as plugins for text editors like Vim and SciTE, and grep-like tools for searching encrypted files.

*Tombo:
https://github.com/clach04/