In other instances this would be my recommendation, but OP needs to somehow capture relationships between data-items in ways that referential integrity will be

In other instances this would be my recommendation, but OP needs to somehow capture relationships between data-items in ways that referential integrity will be maintained: this is a non-trivial challenge, because it requires application logic to enforce that referential integrity, and therefore requires an application, not just a format alone. If the requirement were merely to store some flat or hierarchical data, any run-of-the-mill file-based filesystem would fit the bill, and folder structure alone could be used to express relationships, but without simplifying the data model, this does not seem to be sufficient. SQLite manages to provide this capability and logic, and its installed base is very large, and thus lessens the likelihood that it or compatible systems disappear outright. I believe for your usecase, leaning on SQLite is preferable to coming up with your custom format to express data relationships, and your custom code to enforce those relationships. But consider the points raised elsewhere: plain text remains partially recoverable if damaged, while binary files often exhibit more brittleness.