diff --git a/.github/workflows/cooker-selfhosted-persistent.yml b/.github/workflows/cooker-selfhosted-persistent.yml
index bf45a7b1..dced323f 100644
--- a/.github/workflows/cooker-selfhosted-persistent.yml
+++ b/.github/workflows/cooker-selfhosted-persistent.yml
@@ -64,7 +64,7 @@ jobs:
 
       - name: "Build flatpak: download only"
         id: "flatpak-download"
-        run: "/bin/bash ${GITHUB_WORKSPACE}/automation_tools/flatpak_build_download_only.sh"
+        run: "/bin/bash ${GITHUB_WORKSPACE}/automation_tools/flatpak_build_download_only_persistent.sh"
         continue-on-error: true
 
       # Sometimes flatpak download fails, in this case it tries a second time
@@ -76,10 +76,10 @@ jobs:
           rm -f "{GITHUB_WORKSPACE}/net.retrodeck.retrodeck.yml"
           cp "${GITHUB_WORKSPACE}/net.retrodeck.retrodeck.yml.bak" "${GITHUB_WORKSPACE}/net.retrodeck.retrodeck.yml"
           "${GITHUB_WORKSPACE}/automation_tools/pre_build_automation.sh"
-          "${GITHUB_WORKSPACE}/automation_tools/flatpak_build_download_only.sh"
+          "${GITHUB_WORKSPACE}/automation_tools/flatpak_build_download_only_persistent.sh"
 
       - name: Build flatpak
-        run: "/bin/bash ${GITHUB_WORKSPACE}/automation_tools/flatpak_build_only.sh"
+        run: "/bin/bash ${GITHUB_WORKSPACE}/automation_tools/flatpak_build_only_persistent.sh"
 
       - name: Create Artifact for flathub
         run: | 
@@ -90,7 +90,7 @@ jobs:
         continue-on-error: true
 
       - name: Create Bundle
-        run: "/bin/bash ${GITHUB_WORKSPACE}/automation_tools/flatpak_build_bundle.sh"
+        run: "/bin/bash ${GITHUB_WORKSPACE}/automation_tools/flatpak_build_bundle_persistent.sh"
 
       - name: Set environment variable with current branch name
         run: echo "GITHUB_REF_SLUG=$(git rev-parse --abbrev-ref HEAD)" >> $GITHUB_ENV
diff --git a/automation_tools/flatpak_build_bundle.sh b/automation_tools/flatpak_build_bundle.sh
index e0aa0101..3568ebb7 100755
--- a/automation_tools/flatpak_build_bundle.sh
+++ b/automation_tools/flatpak_build_bundle.sh
@@ -2,17 +2,8 @@
 
 # This is building the bundle RetroDECK.flatpak after the download and build steps are done
 
-if [ $PERSISTENCE==true ]; then
-    GITHUB_WORKSPACE_BACKUP="$GITHUB_WORKSPACE"
-    GITHUB_WORKSPACE="$HOME/cooker-persistent"
-fi
-
 if [ "${GITHUB_REF##*/}" = "main" ]; then
-    flatpak build-bundle ${GITHUB_WORKSPACE}/.local $GITHUB_WORKSPACE/RetroDECK.flatpak net.retrodeck.retrodeck
+    flatpak build-bundle "${GITHUB_WORKSPACE}/.local" "$GITHUB_WORKSPACE/RetroDECK.flatpak" net.retrodeck.retrodeck
 else
-    flatpak build-bundle ${GITHUB_WORKSPACE}/.local $GITHUB_WORKSPACE/RetroDECK-cooker.flatpak net.retrodeck.retrodeck
-fi
-
-if [ $PERSISTENCE==true ]; then
-    GITHUB_WORKSPACE="$GITHUB_WORKSPACE_BACKUP"
+    flatpak build-bundle "${GITHUB_WORKSPACE}/.local" "$GITHUB_WORKSPACE/RetroDECK-cooker.flatpak" net.retrodeck.retrodeck
 fi
\ No newline at end of file
diff --git a/automation_tools/flatpak_build_bundle_persistent.sh b/automation_tools/flatpak_build_bundle_persistent.sh
new file mode 100755
index 00000000..ca6f1b5a
--- /dev/null
+++ b/automation_tools/flatpak_build_bundle_persistent.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+
+# This is building the bundle RetroDECK.flatpak after the download and build steps are done
+
+BUILD_DIR="$HOME/cooker-persistent"
+mkdir -p "$BUILD_DIR"
+
+if [ "${GITHUB_REF##*/}" = "main" ]; then
+    flatpak build-bundle "${BUILD_DIR}/.local" "$GITHUB_WORKSPACE/RetroDECK.flatpak" net.retrodeck.retrodeck
+else
+    flatpak build-bundle "${BUILD_DIR}/.local" "$GITHUB_WORKSPACE/RetroDECK-cooker.flatpak" net.retrodeck.retrodeck
+fi
diff --git a/automation_tools/flatpak_build_download_only.sh b/automation_tools/flatpak_build_download_only.sh
index 707c3e40..8c779fbb 100755
--- a/automation_tools/flatpak_build_download_only.sh
+++ b/automation_tools/flatpak_build_download_only.sh
@@ -12,32 +12,13 @@ else
     FOLDER=retrodeck-flatpak-cooker
 fi
 
-if [ $PERSISTENCE==true ]; then
-    GITHUB_WORKSPACE_BACKUP="$GITHUB_WORKSPACE"
-    GITHUB_WORKSPACE="$HOME/cooker-persistent"
+mkdir -vp "${GITHUB_WORKSPACE}"/{.local,retrodeck-flatpak-cooker}
 
-    mkdir -vp "${GITHUB_WORKSPACE}"/{local,retrodeck-flatpak-cooker}
-
-    flatpak-builder --user --force-clean \
+flatpak-builder --user --force-clean \
     --install-deps-from=flathub \
     --install-deps-from=flathub-beta \
     --repo="${GITHUB_WORKSPACE}/.local" \
     --download-only \
     "${GITHUB_WORKSPACE}/${FOLDER}" \
-    "${GITHUB_WORKSPACE_BACKUP}/net.retrodeck.retrodeck.yml"
-
-    GITHUB_WORKSPACE="$GITHUB_WORKSPACE_BACKUP"
-
-else
-
-    mkdir -vp "${GITHUB_WORKSPACE}"/{.local,retrodeck-flatpak-cooker}
-
-    flatpak-builder --user --force-clean \
-        --install-deps-from=flathub \
-        --install-deps-from=flathub-beta \
-        --repo="${GITHUB_WORKSPACE}/.local" \
-        --download-only \
-        "${GITHUB_WORKSPACE}/${FOLDER}" \
-        net.retrodeck.retrodeck.yml
-    
-fi
+    net.retrodeck.retrodeck.yml
+    
\ No newline at end of file
diff --git a/automation_tools/flatpak_build_download_only_persistent.sh b/automation_tools/flatpak_build_download_only_persistent.sh
new file mode 100755
index 00000000..7b05fa57
--- /dev/null
+++ b/automation_tools/flatpak_build_download_only_persistent.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+# This script is downloading the needed files to prepare the manifest build
+
+git config --global protocol.file.allow always
+
+if [[ "${GITHUB_REF##*/}" == "main" ]]; then
+    BUNDLE_NAME="RetroDECK.flatpak"
+    FOLDER=retrodeck-flatpak
+else
+    BUNDLE_NAME="RetroDECK-cooker.flatpak"
+    FOLDER=retrodeck-flatpak-cooker
+fi
+
+BUILD_DIR="$HOME/cooker-persistent"
+mkdir -p "$BUILD_DIR"
+mkdir -vp "${BUILD_DIR}"/{.local,retrodeck-flatpak-cooker}
+
+flatpak-builder --user --force-clean \
+--install-deps-from=flathub \
+--install-deps-from=flathub-beta \
+--repo="${BUILD_DIR}/.local" \
+--download-only \
+"${BUILD_DIR}/${FOLDER}" \
+"${GITHUB_WORKSPACE}/net.retrodeck.retrodeck.yml"
+
diff --git a/automation_tools/flatpak_build_only.sh b/automation_tools/flatpak_build_only.sh
index a72347fb..c7f84d82 100755
--- a/automation_tools/flatpak_build_only.sh
+++ b/automation_tools/flatpak_build_only.sh
@@ -12,35 +12,13 @@ else
     FOLDER=retrodeck-flatpak-cooker
 fi
 
-if [ $PERSISTENCE==true ]; then
+mkdir -vp ${GITHUB_WORKSPACE}/.local
+mkdir -vp ${GITHUB_WORKSPACE}/"$FOLDER"
 
-    GITHUB_WORKSPACE_BACKUP="$GITHUB_WORKSPACE"
-    GITHUB_WORKSPACE="$HOME/cooker-persistent"
-
-    mkdir -vp ${GITHUB_WORKSPACE}/.local
-    mkdir -vp ${GITHUB_WORKSPACE}/"$FOLDER"
-
-    flatpak-builder --user --force-clean \
+flatpak-builder --user --force-clean \
     --install-deps-from=flathub \
     --install-deps-from=flathub-beta \
-    --repo="${GITHUB_WORKSPACE}/.local" \
+    --repo=${GITHUB_WORKSPACE}/.local \
     --disable-download \
-    "${GITHUB_WORKSPACE}/${FOLDER}" \
-    "${GITHUB_WORKSPACE_BACKUP}/net.retrodeck.retrodeck.yml"
-
-    GITHUB_WORKSPACE="$GITHUB_WORKSPACE_BACKUP"
-
-else
-
-    mkdir -vp ${GITHUB_WORKSPACE}/.local
-    mkdir -vp ${GITHUB_WORKSPACE}/"$FOLDER"
-
-    flatpak-builder --user --force-clean \
-        --install-deps-from=flathub \
-        --install-deps-from=flathub-beta \
-        --repo=${GITHUB_WORKSPACE}/.local \
-        --disable-download \
-        ${GITHUB_WORKSPACE}/"$FOLDER" \
-        net.retrodeck.retrodeck.yml
-
-fi
\ No newline at end of file
+    "${GITHUB_WORKSPACE}/$FOLDER" \
+    net.retrodeck.retrodeck.yml
\ No newline at end of file
diff --git a/automation_tools/flatpak_build_only_persistent.sh b/automation_tools/flatpak_build_only_persistent.sh
new file mode 100755
index 00000000..4121cf9f
--- /dev/null
+++ b/automation_tools/flatpak_build_only_persistent.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+# This script is downloading the needed files to prepare the manifest build
+
+git config protocol.file.allow always
+
+if [ "${GITHUB_REF##*/}" = "main" ]; then
+    BUNDLE_NAME="RetroDECK.flatpak"
+    FOLDER=retrodeck-flatpak-main
+else
+    BUNDLE_NAME="RetroDECK-cooker.flatpak"
+    FOLDER=retrodeck-flatpak-cooker
+fi
+
+BUILD_DIR="$HOME/cooker-persistent"
+mkdir -vp ${$BUILD_DIR}/.local
+mkdir -vp ${$BUILD_DIR}/"$FOLDER"
+
+flatpak-builder --user --force-clean \
+--install-deps-from=flathub \
+--install-deps-from=flathub-beta \
+--repo="${BUILD_DIR}/.local" \
+--disable-download \
+"${BUILD_DIR}/${FOLDER}" \
+"${GITHUB_WORKSPACE}/net.retrodeck.retrodeck.yml"