Almost all installed apps are now displayed as system ones (since build 41.0-4 in F35)
Latest Fedora 35 Beta. I am not sure what exactly happened, but since today's update (that contained gnome-software-41.0-4.fc35.x86_64), most of my apps are displayed as system and it is not possible to uninstall them:
Here is a log from opening details page for, for example, Lutris:
23:31:11:0676 Gs pushing back entry for installed
23:31:11:0677 Gs Chaining cancellation from 0x5622e9d645e0 to 0x5622ea8291e0
23:31:11:0677 Gs Looking for icon for net.lutris.Lutris, at size 128×1, with fallback (null)
23:31:11:0677 Gs Considering icon of type GFileIcon (/usr/share/app-info/icons/fedora/64x64/net.lutris.Lutris.png), width 64×1
23:31:11:0677 Gs Considering icon of type GFileIcon (/usr/share/app-info/icons/fedora/128x128/net.lutris.Lutris.png), width 128×1
23:31:11:0680 Gs running refine with dedupe-flags=7 with timeout=60 on apps system/package/fedora/net.lutris.Lutris/*, elapsed time since creation 3ms
23:31:11:0680 Gs content rating system is guessed as PEGI from cs_CZ.UTF-8
23:31:11:0680 Gs content rating system is guessed as PEGI from cs_CZ.UTF-8
23:31:11:0680 Gs content rating system is guessed as PEGI from cs_CZ.UTF-8
23:31:11:0680 Gs GsApp: [0x7f64dc33b5e0]
kind: desktop-application
state: installed
quirk: provenance,compulsory
progress: unknown
id: net.lutris.Lutris
unique-id: system/package/fedora/net.lutris.Lutris/*
scope: system
bundle-kind: package
kudos: recent-release|has-keywords|has-screenshots|hi-dpi-icon
kudo-percentage: 65
name: Lutris
icon: /usr/share/app-info/icons/fedora/64x64/net.lutris.Lutris.png
icon: /usr/share/app-info/icons/fedora/128x128/net.lutris.Lutris.png
version: 0.5.8.3-7.fc35
version-ui: 0.5.8.3
summary: open source gaming platform
description: Lutris is an Open Source gaming platform. It installs and launches games so you can start playing without the hassle of setting up your games. Get your games from GOG, Steam, Battle.net, Origin, Uplay and many other sources running on any Linux powered gaming machine.
screenshot-00: https://lutris.net/static/images/lutris-window.png [<none>]
source-00: lutris
source-id-00: lutris;0.5.8.3-7.fc35;x86_64;installed:fedora
content-age: 0
content-rating: oars-1.1
url{homepage}: https://lutris.net
launchable{desktop-id}: net.lutris.Lutris.desktop
license: GPL-3.0-or-later
license-is-free: yes
management-plugin: packagekit
origin: fedora
origin-appstream: fedora
origin-hostname: fedoraproject.org
rating: 75
review-rating: [0:0]
review-rating: [1:24]
review-rating: [2:7]
review-rating: [3:6]
review-rating: [4:17]
review-rating: [5:65]
reviews: 1
provided: 8
install-date: 1
release-date: 1611273600
size-installed: 2,4 MB
size-download: unknowable
history: */*/*/net.lutris.Lutris/*
category: Game
{ODRS::user_skey}: ae9de7fa3ef67d6579bef909b42665c078c99408
{GnomeSoftware::PackagingFormat}: RPM
{appstream::source-file}: /usr/share/app-info/xmls/fedora.xml.gz
{GnomeSoftware::Creator}: appstream
23:31:11:0690 Gs Looking for icon for net.lutris.Lutris, at size 128×1, with fallback (null)
23:31:11:0690 Gs Considering icon of type GFileIcon (/usr/share/app-info/icons/fedora/64x64/net.lutris.Lutris.png), width 64×1
23:31:11:0690 Gs Considering icon of type GFileIcon (/usr/share/app-info/icons/fedora/128x128/net.lutris.Lutris.png), width 128×1
23:31:11:0690 Gs Chaining cancellation from 0x5622e9d645e0 to 0x5622ea817f60
23:31:11:0690 Gs Chaining cancellation from 0x5622e9d645e0 to 0x5622ea5b7220
23:31:11:0690 Gs Disconnecting cancellable 0x5622e9d645e0
23:31:11:0692 Gs running refine with dedupe-flags=7 with refine-flags=require-size,require-rating,require-reviews,require-review-ratings,require-runtime with timeout=60 on apps system/package/fedora/net.lutris.Lutris/*, elapsed time since creation 1ms
23:31:11:0698 Gs running get-alternates on plugin=flatpak with interactive=True with timeout=60 on apps system/package/fedora/net.lutris.Lutris/*, elapsed time since creation 8ms
23:31:11:0704 Gs Disconnecting cancellable 0x5622e9d645e0
23:31:11:0704 Gs Disconnecting cancellable 0x5622e9d645e0
23:31:11:0705 Gs content rating system is guessed as PEGI from cs_CZ.UTF-8
23:31:11:0705 Gs content rating system is guessed as PEGI from cs_CZ.UTF-8
23:31:11:0705 Gs content rating system is guessed as PEGI from cs_CZ.UTF-8
23:31:11:0705 Gs content rating system is guessed as PEGI from cs_CZ.UTF-8
23:31:11:0705 Gs content rating system is guessed as PEGI from cs_CZ.UTF-8
23:31:11:0705 Gs content rating system is guessed as PEGI from cs_CZ.UTF-8
23:31:11:0705 Gs content rating system is guessed as PEGI from cs_CZ.UTF-8
23:31:11:0705 Gs content rating system is guessed as PEGI from cs_CZ.UTF-8
23:31:11:0705 Gs content rating system is guessed as PEGI from cs_CZ.UTF-8
23:31:11:0705 Gs content rating system is guessed as PEGI from cs_CZ.UTF-8
There is also a lot of flatpak Error marking directory as changed: Permission denied
errors in log and flatpak-1.12.0-1.fc35.x86_64 was also a part of today's update, so this may be also related.
Edited by Daniel Rusek