To run flatpak installed apps from dmenu.

flatpak-dmenu.md

To run a flatpak app from dmenu, you can create a symlink for the app in /usr/bin. You can find the flatpak apps binary link in /var/lib/flatpak/exports/bin/ on ubuntu. E.g. to run Rocket Chat (installed from flatpak via software center), you can do something like this:

sudo ln -s /var/lib/flatpak/exports/bin/chat.rocket.RocketChat /usr/bin/rocket-chat

This way you will be able to find it in the dmenu.

Resources:

• i3wm dmenu add .desktop file
• How To Create Menu Icon in Ubuntu for Installed Flatpak Application
• How to launch flatpak apps from dmenu/rofi?
• Where to find application after flatpak installation (gimp)

I have tried using what @alissonzuza and @mlaiseca3 have suggested, and while it works, you have to type in the full name of the application instead of the short name.
For example, if you want to open the flatpak of DBeaver, you have to type in io., which will then make the io.DBeaver.DBeaverCommunity option appear.
If you were to type in DBeaver, it would not appear.

Because I did not like this behavior, I modified my dmenu_run file to be as follows:

#!/bin/zsh

export linkFlatpakFolder="$HOME/.config/flatpak-shortcuts"
export PATH=$PATH:$linkFlatpakFolder
local systemFlatpakFolder="/var/lib/flatpak/exports/bin"
local userFlatpakFolder="$HOME/.local/share/flatpak/exports/bin"


local systemFlatpaks=$(ls -1 -a "$systemFlatpakFolder" 2>/dev/null | grep -v '^\.$' | grep -v '^\.\.$')
local userFlatpaks=$(ls -1 -a "$userFlatpakFolder" 2>/dev/null | grep -v '^\.$' | grep -v '^\.\.$')
# 1 line per flatpak. If any of the two directories does not exist, the variable will be empty


#Let's create syslinks to the flatpak binaries without including the full name
#NOTE: We need to ensure that there are no entries with the same name

rm -rf "$linkFlatpakFolder" 2>/dev/null

mkdir -p "$linkFlatpakFolder"


for (( i=1; i<=$(echo "$systemFlatpaks" | wc -l); i++ )); do
  local currentFlatpak=$(echo "$systemFlatpaks" | head -n $i | tail -n 1) #This is going to contain the full name
  local currentShortName=$(echo "$currentFlatpak" | awk -F. '{print $NF}') #The application name is always last.
  local currentShortName=$(echo "${(L)currentShortName}") #Make first letter of the name lower-case. (Use C instead of L for upper case)
  local fullPathToShortcut="${linkFlatpakFolder}/${currentShortName}"
  local duplicateIndex=1
  while [ -f "$fullPathToShortcut" ]; do #If the shortcut already exists, then add a suffix
    fullPathToShortcut="${fullPathToShortcut}-${duplicateIndex}"
	duplicateIndex=$(( 1 + $duplicateIndex ))
  done
  #Now create the symbolic link
  ln -s "${systemFlatpakFolder}/${currentFlatpak}" "${fullPathToShortcut}"
done

for (( i=1; i<=$(echo "$userFlatpaks" | wc -l); i++ )); do
  local currentFlatpak=$(echo "$userFlatpaks" | head -n $i | tail -n 1) #This is going to contain the full name
  local currentShortName=$(echo "$currentFlatpak" | awk -F. '{print $NF}') #The application name is always last.
  local currentShortName=$(echo "${(L)currentShortName}") #Make first letter of the name lower-case. (Use C instead of L for upper case)
  local fullPathToShortcut="${linkFlatpakFolder}/${currentShortName}"
  local duplicateIndex=1
  while [ -f "$fullPathToShortcut" ]; do #If the shortcut already exists, then add a suffix
    fullPathToShortcut="${fullPathToShortcut}-${duplicateIndex}"
	duplicateIndex=$(( 1 + $duplicateIndex ))
  done
  #Now create the symbolic link
  ln -s "${systemFlatpakFolder}/${currentFlatpak}" "${fullPathToShortcut}"
done

dmenu_path | dmenu "$@" | ${SHELL:-"/bin/sh"} &

Then, back in the terminal, I executed the following

rm "$HOME/.cache/dmenu_run" && cd "$HOME/programs/suckless/dmenu" && sudo make clean install 

And boom, it worked.

What the script does is that it creates symbolic links to the real flatpaks. The symbolic links do not carry the entire fully qualified name, but rather just the short name.

This way, I can just type DBeaver, and it will appear listed.

A solution that while not as short and elegant as the two above, works very well for me.

After you install a new flatpak, the link containing the symbolic links will be recreated, so you will always have all the flatpaks listed in dmenu