diff --git a/.github/workflows/build_cmake.yml b/.github/workflows/build_cmake.yml
index 6b0913c249..f900fb9359 100644
--- a/.github/workflows/build_cmake.yml
+++ b/.github/workflows/build_cmake.yml
@@ -11,7 +11,7 @@ env:
   # this is different from MACOSX_DEPLOYMENT_TARGET to prevent build problems
   # we set MACOSX_DEPLOYMENT_TARGET later
   MACOS_TARGET: 10.12
-  FEATURES: -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF -DUSE_VTK=ON
+  FEATURES: -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF -DUSE_VTK=ON -DUSE_3DCONNEXION=ON
   CACHE: -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
   SCCACHE_GHA_ENABLED: "true"
 
@@ -106,6 +106,18 @@ jobs:
         repository: openchemistry/avogadroapp
         path: avogadroapp
 
+    - name: Checkout molecules
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/molecules
+        path: molecules
+
+    - name: Checkout i18n
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogadro-i18n
+        path: avogadro-i18n
+
     - name: Checkout avogadrolibs
       uses: actions/checkout@v4
       with:
@@ -122,7 +134,7 @@ jobs:
       uses: jurplel/install-qt-action@v3
       with:
         cache: True
-        tools: 'tools_openssl_x64'
+        tools: 'tools_opensslv3_x64'
         version: ${{ env.QT_VERSION }}
         host: 'windows'
         target: 'desktop'
@@ -181,6 +193,15 @@ jobs:
         done
         otool -L libinchi.?.?.?.dylib
         cp -p libinchi* ../Avogadro2.app/Contents/Frameworks/
+        # finally, fixup the binaries
+        cd ../bin
+        for exe in obabel obmm eht_bind genXrdPattern; do
+          for libpath in `otool -L ${exe} | grep '/Users/runner/work' | awk '{print $1}'`; do 
+            export lib=`echo $libpath | cut -d '/' -f 9`;
+            echo "Fixing $exe $lib $libpath"
+            install_name_tool -change $libpath @executable_path/../Frameworks/$lib $exe
+          done
+        done
 
     - name: Run tests
       if: matrix.config.os == 'ubuntu-20.04'
@@ -234,18 +255,18 @@ jobs:
           fi # certificate exists
         fi # password exists
 
-    - name: Pack
-      if: matrix.config.artifact != 0
+    - name: Create Mac and Windows Packages
+      if: matrix.config.os == 'windows-latest' || matrix.config.os == 'macos-latest'
       shell: bash
       run: |
         if [ -z "${P12_PASSWORD}" ]; then
           unset CODESIGN_IDENTITY # to prevent cpack failing when trying to sign
         fi
         cpack ${{ matrix.config.cpack_flags }}
+      working-directory: ${{ runner.workspace }}/build/avogadroapp
       env:
         P12_PASSWORD: ${{ secrets.P12_PASSWORD }}
         CODESIGN_IDENTITY: ${{ secrets.CODESIGN_ID }}
-      working-directory: ${{ runner.workspace }}/build/avogadroapp
 
     - name: AppImage
       if: matrix.config.os == 'ubuntu-20.04' && matrix.config.build_type == 'Release'
@@ -263,16 +284,11 @@ jobs:
         chmod a+x appdir/AppRun
         ./appimagetool-x86_64.AppImage appdir
         mv Avogadro2*.AppImage avogadroapp # for upload
-        # remove the cpack files
-        rm avogadroapp/Avogadro2*Linux.*
       working-directory: ${{ runner.workspace }}/build
 
     - name: Notarize Mac DMG
       if: runner.os == 'macOS'
       run: |
-        # check current directory (failing signing)
-        echo `pwd`
-        ls -ld
         # check if we have the password and the username
         if [ -n "${NOTARIZE_PASSWORD}" ] && [ -n "${NOTARIZE_USERNAME}" ]; then
           codesign -s "$CODESIGN_IDENTITY" --timestamp Avogadro2*.dmg
diff --git a/.github/workflows/build_m1.yml b/.github/workflows/build_m1.yml
index 7f9e31142b..87b4dcaf33 100644
--- a/.github/workflows/build_m1.yml
+++ b/.github/workflows/build_m1.yml
@@ -6,7 +6,7 @@ env:
   # this is different from MACOSX_DEPLOYMENT_TARGET to prevent build problems
   # we set MACOSX_DEPLOYMENT_TARGET later
   MACOS_TARGET: 10.12
-  FEATURES: -DUSE_VTK=ON -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF
+  FEATURES: -DUSE_VTK=ON -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF -DUSE_3DCONNEXION=ON
 
 jobs:
   build:
@@ -48,6 +48,12 @@ jobs:
         repository: openchemistry/avogadroapp
         path: avogadroapp
 
+    - name: Checkout molecules
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/molecules
+        path: molecules
+
     - name: Checkout avogadrolibs
       uses: actions/checkout@v4
       with:
@@ -59,19 +65,10 @@ jobs:
         repository: openchemistry/avogadro-i18n
         path: avogadro-i18n
 
-    - name: Grab cache files
-      uses: actions/cache@v3
-      with:
-        path: |
-          ${{ runner.workspace }}/build/thirdparty
-          ${{ runner.workspace }}/build/Downloads
-        key: ${{ matrix.config.name }}-thirdparty
-
     - name: Configure
       run: |
         if [ ! -d "${{ runner.workspace }}/build" ]; then mkdir "${{ runner.workspace }}/build"; fi
         cd "${{ runner.workspace }}/build"
-        # won't have any effect except on Mac
         echo "MACOSX_DEPLOYMENT_TARGET=${{ env.MACOS_TARGET }}" >> $GITHUB_ENV
         CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake $GITHUB_WORKSPACE ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}}
       shell: bash
@@ -87,22 +84,32 @@ jobs:
       working-directory: ${{ runner.workspace }}/build/prefix/lib/openbabel 
       run: |
         for plugin in *.so; do
-          for libpath in `otool -L ${plugin} | grep '/Users/runner/work' | awk '{print $1}'`; do 
-            export lib=`echo $libpath | cut -d '/' -f 9`;
+          for libpath in `otool -L ${plugin} | grep '/Users/runner' | awk '{print $1}'`; do 
+            export lib=`echo $libpath | cut -d '/' -f 10`;
             echo "Fixing $plugin $lib $libpath"
             install_name_tool -change $libpath @executable_path/../Frameworks/$lib $plugin
           done
         done
         cd .. # build/prefix/lib
         for plugin in libinchi.?.?.?.dylib; do
-          for libpath in `otool -L ${plugin} | grep '/Users/runner/work' | awk '{print $1}'`; do 
-            export lib=`echo $libpath | cut -d '/' -f 9`;
+          for libpath in `otool -L ${plugin} | grep '/Users/runner' | awk '{print $1}'`; do 
+            export lib=`echo $libpath | cut -d '/' -f 10`;
             echo "Fixing $plugin $lib $libpath"
             install_name_tool -change $libpath @executable_path/../Frameworks/$lib $plugin
           done
         done
         otool -L libinchi.?.?.?.dylib
         cp -p libinchi* ../Avogadro2.app/Contents/Frameworks/
+        # finally, fixup the binaries
+        cd ../bin
+        for exe in obabel obmm eht_bind genXrdPattern; do
+          for libpath in `otool -L ${exe} | grep '/Users/runner' | awk '{print $1}'`; do 
+            export lib=`echo $libpath | cut -d '/' -f 10`;
+            echo "Fixing $exe $lib $libpath"
+            install_name_tool -change $libpath @executable_path/../Frameworks/$lib $exe
+          done
+        done
+
 
     - name: Install the Apple certificate
       # From GitHub docs: https://docs.github.com/en/actions/guides/installing-an-apple-certificate-on-macos-runners-for-xcode-development
@@ -139,39 +146,34 @@ jobs:
           fi # certificate exists
         fi # password exists
 
-    - name: Pack
-      if: matrix.config.artifact != 0
+    - name: Create Mac and Windows Packages
       shell: bash
       run: |
         if [ -z "${P12_PASSWORD}" ]; then
           unset CODESIGN_IDENTITY # to prevent cpack failing when trying to sign
         fi
         cpack ${{ matrix.config.cpack_flags }}
+      working-directory: ${{ runner.workspace }}/build/avogadroapp
       env:
         P12_PASSWORD: ${{ secrets.P12_PASSWORD }}
         CODESIGN_IDENTITY: ${{ secrets.CODESIGN_ID }}
-      working-directory: ${{ runner.workspace }}/build/avogadroapp
 
     - name: Notarize Mac DMG
       if: runner.os == 'macOS'
       run: |
-        pwd
-        ls -l
         # check if we have the password and the username
         if [ -n "${NOTARIZE_PASSWORD}" ] && [ -n "${NOTARIZE_USERNAME}" ]; then
-          echo "codesign DMG"
           codesign -s "$CODESIGN_IDENTITY" --timestamp Avogadro2*.dmg
-          echo "notarizing"
           xcrun notarytool submit Avogadro2*.dmg --apple-id "$NOTARIZE_USERNAME" --team-id "$NOTARIZE_TEAM" --password "$NOTARIZE_PASSWORD" --verbose --wait
           xcrun stapler staple -v Avogadro2*.dmg
         fi
+      working-directory: ${{ runner.workspace }}/build/avogadroapp
       env:
+        NOTARIZE_TEAM: ${{ secrets.AC_TEAM }}
         NOTARIZE_USERNAME: ${{ secrets.AC_USERNAME }}
         NOTARIZE_PASSWORD: ${{ secrets.AC_PASSWORD }}
         CODESIGN_IDENTITY: ${{ secrets.CODESIGN_ID }}
-        NOTARIZE_TEAM: ${{ secrets.AC_TEAM }}
       continue-on-error: true
-      working-directory: ${{ runner.workspace }}/build/avogadroapp
 
     - name: Upload
       if: matrix.config.artifact != 0