diff --git a/.github/workflows/flatpak.yml b/.github/workflows/flatpak.yml
index c50b8a28..bd8cb679 100644
--- a/.github/workflows/flatpak.yml
+++ b/.github/workflows/flatpak.yml
@@ -14,6 +14,9 @@ jobs:
     - name: Configure flatpak
       run: flatpak remote-add --if-not-exists --user flathub https://dl.flathub.org/repo/flathub.flatpakrepo
 
+    - name: Install flatpak-builder
+      run: flatpak --user install --or-update --noninteractive flathub org.flatpak.Builder
+
     - name: Configure git
       run: git config --global protocol.file.allow always
       # Have to do this because for a while git's handling of submodules was broken
@@ -81,7 +84,7 @@ jobs:
       run: mv openchemistry/avogadroapp/flatpak/org.openchemistry.Avogadro2.yaml ./
 
     - name: Build with flatpak-builder
-      run: flatpak-builder --force-clean --user --install-deps-from=flathub --arch=x86_64 --default-branch=test --repo=repo builddir org.openchemistry.Avogadro2.yaml
+      run: dbus-run-session flatpak run org.flatpak.Builder --force-clean --user --install-deps-from=flathub --arch=x86_64 --default-branch=test --repo=repo builddir org.openchemistry.Avogadro2.yaml
 
     - name: Create bundle
       run: flatpak build-bundle repo Avogadro2.flatpak org.openchemistry.Avogadro2 test
diff --git a/flatpak/org.openchemistry.Avogadro2.yaml b/flatpak/org.openchemistry.Avogadro2.yaml
index 5e13f4f0..ebc9ae27 100644
--- a/flatpak/org.openchemistry.Avogadro2.yaml
+++ b/flatpak/org.openchemistry.Avogadro2.yaml
@@ -1,7 +1,7 @@
 app-id: org.openchemistry.Avogadro2
 runtime: org.kde.Platform
 sdk: org.kde.Sdk
-runtime-version: "6.7"
+runtime-version: "6.8"
 command: avogadro2
 appdata-license: BSD-3-Clause AND GPL-2.0-only
 finish-args:
@@ -11,7 +11,6 @@ finish-args:
   - --device=dri  # OpenGL rendering
   - --share=network  # For plugin downloads
 cleanup:
-  - /include
   - /lib/cmake
   - '*.la'
   - '*.a'
@@ -24,6 +23,10 @@ modules:
   - name: rapidjson
     buildsystem: cmake-ninja
     builddir: true
+    config-opts:
+      - -DRAPIDJSON_BUILD_DOC=OFF
+      - -DRAPIDJSON_BUILD_EXAMPLES=OFF
+      - -DRAPIDJSON_BUILD_TESTS=OFF
     sources:
       - type: git
         url: https://github.com/Tencent/rapidjson.git
@@ -38,7 +41,7 @@ modules:
     no-make-install: true  # Superbuild doesn't have `install` command defined
     config-opts:
       # Match GitHub builds as much as possible, which generally means using defaults
-      - -DCMAKE_BUILD_TYPE=Release
+      - -DCMAKE_BUILD_TYPE=Debug
       - -DUSE_VTK=ON
       - -DBUILD_GPL_PLUGINS=ON
       - -DBUILD_MOLEQUEUE=OFF
@@ -107,5 +110,9 @@ modules:
 
     post-install:
       # Manually copy contents of prefix dir over into main build dir
-      # -a option is recursive should preserve permissions and symlinks
-      - cp -a prefix/* -t ${FLATPAK_DEST}/
+      # -a option is recursive, should preserve permissions and symlinks
+      - cp -a prefix/bin -t ${FLATPAK_DEST}/
+      - cp -a prefix/lib -t ${FLATPAK_DEST}/
+      - cp -a prefix/lib64/* -t ${FLATPAK_DEST}/lib/  # Merge with lib
+      - ln -rs ${FLATPAK_DEST}/lib ${FLATPAK_DEST}/lib64  # Add a symlink so plugins get found
+      - cp -a prefix/share -t ${FLATPAK_DEST}/