Package managers have to deal with dependencies – too many of them. Over time things have gotten complicated: there are now soft dependencies, reverse dependencies and boolean conditions. So complicated that you can probably do general computation in the dependency solver now.
Of course, thats not the whole story. Lets take a look.
The only hard dependencies in Flatpak are between an app and the runtime that it uses.
Every app uses exactly one runtime. When installing the app, Flatpak will automatically install the runtime it needs, and it will refuse to uninstall the runtime as long as there are apps using it. You can override this using the –force-remove option.
The common term Flatpak uses for apps and runtimes is refs. Apart from dependencies, Flatpak has a notion of related refs. These are what other packaging systems might classify as soft dependencies, and they come in various forms and shapes.
The first group are standard pieces that get split off at build time, like .Locale and .Debug refs. The first contain translations and are similar to what other packaging systems call langpacks. The second contain debug information for binaries, and are the equivalent of debuginfo packages in other systems.
The next group are extensions. Both applications and runtimes can declare extension points, and flatpak will look for refs that match those when setting up a sandbox, and mounts the ones it finds inside the sandbox.
Some extensions are a bit more special, in that they are conditional on some condition of the system. For example, they might only be relevant if the system has an Nvidia GPU, or apply for a certain GTK+ theme.
Another kind of relationship exists between a runtime and its matching sdk.
Whats used ?
The Flatpak uninstall command has a –unused option that makes an educated guess about what refs are no longer needed on your system. For each ref, it looks if it is an application, or the runtime of an installed application, or related to one of these. In each of these cases, it considers the ref used and skips it. Whatever is left afterwards get removed.
There are some heuristics involved when looking at related refs, and we are still fine-tuning these. One change that we’re recently made is to consider sdks used, to make –unused usable for developers.
There is still more fine-tuning to be done. For example, Flatpak will happily use a runtime from the system installation to run an application from the user installation. But the uninstall command works only on a single installation, so it does not see these dependencies, and might remove the runtime. Thankfully, it is easy to recover, should this happen to you: just install the runtime again.