I installed an application using a command of the following form:

flatpak --user install -y --app --bundle "$DIR/Suphead.flatpak"

I uninstalled it using a command of the following form:

flatpak --user uninstall org.flatpaklinux.Suphead

However, after uninstall, I still see many files on the system associated with the application, files at all of the following sorts of directories:


Should Flatpak not remove directories like these and their contents? Should I just do an rm -rf on them?

3 Answers 3


It's usual for package management tools to leave files in the home directory alone, so that user preferences, etc. are retained on reinstallation. You can choose to delete them if you wish, but I wouldn't expect flatpak (or any other software installation tool) to delete configuration files in my home directory. And that's what ~/.var/app is, looking at the example in the flatpak wiki:

└── app
    └── org.gnome.GEdit
        ├── data
        ├── config
        └── cache

~/.local/share/flatpak/repo/refs/remotes/org.flatpaklinux.Suphead-origin looks like it's part of flatpak's state, and it could be using it to track it what it had installed and where from (such data is also often kept around after package removal, and anyway they don't occupy much space). From the flatpak wiki:

Flatpak uses OSTree to distribute and manage applications and runtimes. The repo/ in the above tree is the local OSTree repository. Flatpak creates the active/ directories of applications and runtimes as symlinks to OSTree checkouts (in the same directory). Using OSTree has the advantage that the checkouts are automatically deduped and share diskspace, since OSTree is using hardlinks and content-based addressing. OSTree also makes it easy to roll back to an earlier version, should the need arise.

refs/remotes/org.flatpaklinux.Suphead-origin looks very like something from a Git repo:

$ cat .git/refs/remotes/origin/master

If that is indeed the case, then that file just indicates which commit of the remote source was at the last time you fetched something from there.

If you think flatpak is taking up too much space even after removing an app, check the output of flatpak list -d --app --runtime to see what apps and runtimes are still installed and the space they take.

  • 2
    Hey, thanks for the solution there, and for the detailed description of how Flatpak stores things. Nov 28, 2017 at 15:34

As mentioned here,

flatpak uninstall --delete-data  # Delete app data

will remove already uninstalled app data still left on ~/.var/app.

By default will ask for each app, Delete data for Application_ID? [y/n]:.


You can uninstall these by using the --unsed modifier.

flatpak uninstall --unused

Ref: http://docs.flatpak.org/en/latest/flatpak-command-reference.html?highlight=uninstall#flatpak-uninstall

  • 3
    this is to remove unused apps not for the files remaining after uninstalling an app
    – v_sukt
    Sep 6, 2019 at 4:47

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