$ cat flatpaks.txt

NOTE: you need to match up the runtime with the application, we'll use fs-uae as an example here

application                         version                 runtime                                          vkBasalt Branch
net.fsuae.FS-UAE                    3.1.66                  org.kde.Platform/x86_64/5.15-24.08               24.08
org.zdoom.GZDoom                    4.12.2                  org.freedesktop.Platform/x86_64/24.08            24.08
re.chiaki.Chiaki                    2.2.0                   org.freedesktop.Platform/x86_64/23.08            23.08
com.blitterstudio.amiberry          v6.3.4                  org.freedesktop.Platform/x86_64/23.08            23.08
com.carpeludum.KegaFusion           3.63x                   org.freedesktop.Platform/x86_64/23.08            23.08
com.dosbox_x.DOSBox-X               2024.07.01              org.freedesktop.Platform/x86_64/23.08            23.08
com.epicgames.ut2004                3369.2                  org.freedesktop.Platform/x86_64/24.08            24.08
com.epicgames.ut99                  469d                    org.freedesktop.Platform/x86_64/24.08            24.08
com.etlegacy.ETLegacy               2.82.1                  org.freedesktop.Platform/x86_64/24.08            24.08
com.valvesoftware.SteamLink         1.3.9.258               org.freedesktop.Platform/x86_64/23.08            23.08
net.sf.VICE                         3.8                     org.freedesktop.Platform/x86_64/23.08            23.08
org.speed_dreams.SpeedDreams        2.3.0                   org.freedesktop.Platform/x86_64/21.08            21.08
net.pcsx2.PCSX2                     v2.1.71                 org.kde.Platform/x86_64/6.7                      23.08
org.flycast.Flycast                 v2.3.2                  org.freedesktop.Platform/x86_64/23.08            23.08
org.duckstation.DuckStation         0.1-7371-gb2577ef8b     org.kde.Platform/x86_64/6.7                      23.08

installation 
 usual flatpak installation for application and required runtime e.g 

    install application flatpak
       flatpak install net.fsuae.FS-UAE//3.1.66

    check the runtime branch used by the application flatpak (e.g. 24.08)
       flatpak info --show-runtime net.fsuae.FS-UAE
        org.kde.Platform/x86_64/5.15-24.08

    check if the runtime metadata supports vulkan
       flatpak info --show-metadata org.kde.Platform/x86_64/5.15-24.08 | grep -A1 Vulkan
        [Extension org.freedesktop.Platform.VulkanLayer]
        version=24.08

    install the matching vkbasalt runtime
       flatpak install org.freedesktop.Platform.VulkanLayer.vkBasalt//24.08

    confirm the runtime now sees the vkbasalt extension
       flatpak info --show-extensions org.kde.Platform/x86_64/5.15-24.08 | grep vkBasalt
        Extension: runtime/org.freedesktop.Platform.VulkanLayer.vkBasalt/x86_64/24.08

setup
 provide the VKBASALT=1 env var to the application flatpak, i do this with 
 overrides file

    $ cat $HOME/.local/share/flatpak/overrides/net.fsuae.FS-UAE 
    [Environment]
    ENABLE_VKBASALT=1

vkbasalt
 create a vkBasalt.conf for your shader and place it in the required location
 for the flatpak, yes you'll probably need to manage multiple which is annoying

 per application
    $HOME/.var/app/net.fsuae.FS-UAE/config/vkBasalt/vkBasalt.conf

 global for system installation
    /var/lib/flatpak/runtime/org.freedesktop.Platform.VulkanLayer.vkBasalt//[runtime-version]/active/files/etc/vkBasalt/vkBasalt.conf

 global for user installation
    $HOME/.local/share/flatpak/runtime/org.freedesktop.Platform.VulkanLayer.vkBasalt/[runtime-version]/active/files/etc/vkBasalt/vkBasalt.conf

opengl flatpaks
 have opengl applications use the zink renderer through env vars so it runs on 
 a vulkan layer then you can use shaders with opengl applications, these are
 the same env vars zinkrun sets. Retain the VKBASALT=1 env var. again i do this
 with an overrides file

    $ cat $HOME/.local/share/flatpak/overrides/net.fsuae.FS-UAE 
    [Environment]
    ENABLE_VKBASALT=1
    __GLX_VENDOR_LIBRARY_NAME=mesa
    MESA_LOADER_DRIVER_OVERRIDE=zink
    GALLIUM_DRIVER=zink
    LIBGL_KOPPER_DRI2=1

shaders
 provide an override for the path that contains your shaders so your flatpak can access them

    $ cat ~/.local/share/flatpak/overrides/net.fsuae.FS-UAE 
    [Context]
    filesystems=/opt/reshade-shaders;