I recently updated my system to Fedora 42. The upgrade broke several things, but I have been able to fix most of them. One issue I have not been able to resolve is to do with flatpaks. I have a few apps installed via flatpak, and they have worked very well for quite some time. Unfortunately, some of them are no longer able to launch normally, returning the error “bwrap: execvp application: No such file or directory” when launching through the desktop icons or using “flatpak run org.publisher.application”. Investigating further, I pulled the commands from the line EXEC= in each .desktop file to rule them out as the problem, each of the form “/usr/bin/flatpak run --branch=stable --arch=x86_64 --command=application --file-forwarding org.publisher.application”, but they did not work in the terminal either. However, if I first cd into the directory (/usr/bin) and then use "flatpak run --branch=stable . . . " in the terminal, the flatpak launches just fine.
I have tried updating and repairing (latest version [although it has not been updated in weeks, so it could not be the app’s fault anyway], nothing broken on the app end), fully reinstalled each of the applications, both retaining and clearing their data, ran flatpak override --reset --user, and tested on other platforms (Fedora 41, Debian, SteamOS) on which they function properly, so I assume the issue is something related to Fedora 42 specifically. Unfortunately, one of these applications is only available (for Linux) on flathub, so I need to find a solution because I like the ease of just clicking an icon. What might prevent bubblewrap from identifying the binary file from / but not from /usr/bin? Is there any way I can rebuild the desktop icon from scratch? Since the flatpak itself works, surely this problem is limited to something else. I do not know much about flatpaks, so I hope someone else might be able to answer that. Perhaps the issue could be tracked down from there. Many thanks for reading.