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You can use Alacarte program to do these tasks easily (point & click). Install this program by issuing a command line $ sudo apt-get install alacarte. Find Alacarte in your desktop menu then by searching for "alacarte".
1. Know The Command Line
Every Flatpak software installed on your system in a different directory compared to software installed from default channel (APT). This requires you to run the software by different command line too, not the same as the default system. The typical Flatpak software can be run by this command line:
$ flatpak run thename.of.Program
For the LibreOffice case previously, we know that the command is:
$ flatpak run org.libreoffice.LibreOffice
For each of specific programs of LibreOffice, we know that each command is:
$ flatpak run org.libreoffice.LibreOffice --writer
$ flatpak run org.libreoffice.LibreOffice --calc
$ flatpak run org.libreoffice.LibreOffice --impress
$ flatpak run org.libreoffice.LibreOffice --base
$ flatpak run org.libreoffice.LibreOffice --draw
We will try one of these to create an entry on Ubuntu desktop menu.
2. Add That Command Line to Alacarte
Open Alacarte > select a category on the left panel > press New Item button > type the command line on the box "Command:" > choose a picture as you wish on box on the left (this will be the menu icon of the program).
3. Name It
Give this new entry "LibreOffice from Flatpak" so it's easier to remember the name. Press OK and then close Alacarte.
4. Try It
Search for the name "libreoffice from flatpak" in Ubuntu menu and you get the icon and now you can run the software by clicking o its icon. You just need to repeat these steps for another Flatpak software packages in your system.