the repentogon launcher only loads vanilla when using the steam flatpak even when the repentogon option is selected, after some trial and error i made a symlink from ~/.var/app/com.valvesoftware.Steam/.local/share/Steam to ~/.steam/steam and selected the isaac executable to be the one in the symlink and it worked, i hope that these issues can be resolved so that it becomes a plug and play solution for other steam flatpak users
the repentogon launcher only loads vanilla when using the steam flatpak even when the repentogon option is selected, after some trial and error i made a symlink from ~/.var/app/com.valvesoftware.Steam/.local/share/Steam to ~/.steam/steam and selected the isaac executable to be the one in the symlink and it worked, i hope that these issues can be resolved so that it becomes a plug and play solution for other steam flatpak users