Applications that I installed using an *.AppImage file and by creating a *.Desktop file are no more appearing in the Show Applications window

I am new in Ubuntu, only decided to install it like I did two years ago on a old laptop, and disconnected from other commonly used OS. I am very happy since then, but I have a lot to learn, as I only manage to give some basic commands, but I cannot say that I know the system and how all folders / files are used.

I am using Ubuntu 22.04.3 on a Toshiba Satellite laptop.

In the past, I installed multiple applications by downloading an "*.AppImage" file, creating myself the corresponding *.desktop file, adapt the property to allow "Run" and then copy it in the /home/yvan/.local/share/applications folder. Once this done, when I restart the computer, then the corresponding application with the assigned icon was appearing in the list of applications under "Show Applications".

Then if I wanted, I right-clicked on the icon and selected "Add to Favorites" to get a shortcut on my Favorites bar to make it easy to start the application without finally have to browse each time the *.AppImage file. So it was before, I know how to do, and everything was working fine.

My computer had some difficulties, probably hardware related, did sudden power off, was not restarting properly, even didn't show the very first Toshiba Logo to go to BIOS. I disconnected physically the HDD, the CD-ROM, to avoid them to suffer multiple restart and power cycles. I managed to restore the proper start by removing / putting back RAM modules, remove CMOS BIOS battery and completely RESET the BIOS, then reconnected the HDD and the CD-ROM drive.

Finally my computer was back to normal start, but after this, as I do almost each day, I tried to start the Software Updater to look for eventual updates, then I got a message that some updates were not completed, and I was proposed to do partial update. I was not immediately able to fix this without damages. The only way to get out was sudo apt-get dist-upgrade

I was surprised seeing this was removing A LOT OF PACKAGES ! After this my system was restarting in only kind of terminal mode, prompting me to input the login and password.

I ran:

sudo apt-get install --reinstall ubuntu-desktop
sudo apt-get update
sudo apt-get upgrade
sudo apt-get purge
sudo apt-get clean
sudo apt-get autoremove
sudo update-desktop-database

Now my system is starting back all normal, with my original graphical interface, but .... !!! And it is precisely why I am opening this request.

• All applications that were previously installed via AppImage files are NO MORE VISIBLE in the "Show Applications" window.
• My previously icons for these applications are still in the favorite bar, and the applications are still working fine.
• If I try to install a new application, or I try to upgrade an existing one using the new AppImage file version, IT DOES NOT WORK , the app does not appear in the "Show Applications" and therefore I cannot add the icon to my Favorites.

Questions:

• How to get back existing applications visible inside the "Show Applications" window?
• How to install a new application ? => I suppose this will resolve together with above question.

I don't know if it is important, nor if there is any link with the problem, but I have seen a file called "mimeapps.list" in the /home/yvan/.local/share/applications folder, where I put the *.Desktop files; and I noticed this file is completely empty (its size is zero bytes).

Correct desktop files in the correct location should continue to be picked up automatically in the menu within seconds. That hints that your system may still not be fully healthy again, despite appearing so.

Lacking to find a specific cause (who knows another more specific solution may come around), you may repair your system by doing a reinstall. There is a possibility to do a reinstallation in place: such installation refreshes the entire operating system, but keeps user data and configuration.

To do so, load the live CD of the same Ubuntu edition you currently use, in the installer, select "Something else" and manually assign your current system partition. Make sure to unselect the checkmark "Format" for that partition. Then let the installer run. It will do a fresh installation, however without erasing the disk, i.e., leaving your user data and config, but overwriting system files and configuration.

Do this only after you have made sure that the backups of your user data are fully up to date in case something goes wrong.