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Wow, I never thought about storing build data in an SQLite file. That's quite clever.
One of SQLite's recommended use cases is as an alternate to proprietary binary formats: https://sqlite.org/appfileformat.html. Programs often store data in binary files for performance, but you get a lot of the same functionality included with SQLite (fast random access, concurrent usage, atomicity, updates that don't need to rewrite the whole file, etc) without having to implement a file format yourself.
I'm not sure if this is still the case, but Facebook'a HHVM used to store the compiled bytecode for the whole site in a single SQLite database: https://docs.hhvm.com/docs/hhvm/advanced-usage/repo-authoritative/. Every pageload loaded the bytecode for all required files from the DB.
They also have a (one-time fee) encryption extension.
Fascinating read, I should definitely also make way more use of sqlite for little side projects.
Thanks for the link!