I did this for MBTiles, for storing (at the time, raster) map tiles at Mapbox. I was working on the iPad wing of R&D early in the company and we were focusing on offline mapping for the iPad. Problem was, moving lots of tiny map tiles (generally 256px square PNGs) was tedious over USB and network. We had a thing called Maps on a Stick for moving things around by USB, but it just didn’t scale well to the iPad interface & file transfer needs.

Bundled the tiles into SQLite (I was inspired by seeing Dr. Hipp speak at a conference) and voila, things both easy to move and to checksum. Tiles were identified by X & Y offset at a given (Z)oom level, which made for super easy indexing in a relational DB like SQLite. On the iPad, it was then easy to give map bundles an application icon, associated datatype from file extension, metadata in a table, etc. At the time, I was fairly intimidated by the idea of creating a file format, but databases, I knew. And then making some CLI tools for working with the files in any language was trivial after that.