Flatpak is built on top of a technology called OSTree, which is influenced by and very similar to the Git version control system. Like Git, OSTree allows versioned data to be tracked and to be distributed between different repositories. However, where Git is designed to track source files, OSTree is designed to track binary files and other large data.

Storing applications in a local OSTree repository has other advantages. For example, it allows files that are stored on disk to be deduplicated, so the same file that belongs to multiple applications (or runtimes) is only stored once.

The underlying architecture might be summarized as “git for operating system binaries”.