diff --git a/.github/workflows/cooker-selfhosted.yml b/.github/workflows/cooker-selfhosted.yml
index 12d4512b..fc96a040 100644
--- a/.github/workflows/cooker-selfhosted.yml
+++ b/.github/workflows/cooker-selfhosted.yml
@@ -65,46 +65,16 @@ jobs:
 
       - name: "Build flatpak: download only"
         id: "flatpak-download"
-        run: |
-          git config --global protocol.file.allow always
-          mkdir -vp ${GITHUB_WORKSPACE}/local
-          mkdir -vp ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker
-          flatpak-builder --user --force-clean \
-            --install-deps-from=flathub \
-            --install-deps-from=flathub-beta \
-            --repo=${GITHUB_WORKSPACE}/local \
-            --download-only \
-            ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker \
-            net.retrodeck.retrodeck.yml
+        run: "/bin/bash ${GITHUB_WORKSPACE}/automation_tools/flatpak_build_download_only.sh"
         continue-on-error: true
 
       # Sometimes flatpak download fails, in this case it tries a second time
       - name: "Build flatpak: download only (retry)"
         if: steps.flatpak-download.outcome == 'failure'
-        run: |
-          git config --global protocol.file.allow always
-          mkdir -vp ${GITHUB_WORKSPACE}/local
-          mkdir -vp ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker
-          flatpak-builder --user --force-clean \
-            --install-deps-from=flathub \
-            --install-deps-from=flathub-beta \
-            --repo=${GITHUB_WORKSPACE}/local \
-            --download-only \
-            ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker \
-            net.retrodeck.retrodeck.yml
+        run: "/bin/bash ${GITHUB_WORKSPACE}/automation_tools/flatpak_build_download_only.sh"
 
       - name: Build flatpak
-        run: |
-          git config --global protocol.file.allow always
-          mkdir -vp ${GITHUB_WORKSPACE}/local
-          mkdir -vp ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker
-          flatpak-builder --user --force-clean \
-            --install-deps-from=flathub \
-            --install-deps-from=flathub-beta \
-            --repo=${GITHUB_WORKSPACE}/local \
-            --disable-download \
-            ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker \
-            net.retrodeck.retrodeck.yml
+        run: "/bin/bash ${GITHUB_WORKSPACE}/automation_tools/flatpak_build_only.sh"
 
       - name: Create Artifact for flathub
         run: | 
@@ -115,8 +85,7 @@ jobs:
         continue-on-error: true
 
       - name: Create Bundle
-        run: |
-          flatpak build-bundle ${GITHUB_WORKSPACE}/local RetroDECK-cooker.flatpak net.retrodeck.retrodeck
+        run: "/bin/bash ${GITHUB_WORKSPACE}/automation_tools/flatpak_build_bundle.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/.github/workflows/main-selfhosted.yml b/.github/workflows/main-selfhosted.yml
index c380622f..b71961c6 100644
--- a/.github/workflows/main-selfhosted.yml
+++ b/.github/workflows/main-selfhosted.yml
@@ -52,50 +52,23 @@ jobs:
         
       - name: Check versions (main only)
         id: check_version_string
-        run: "automation_tools/version_checker.sh"
+        run: "automation_tools/main_version_checker.sh"
+
+      - name: "[DEBUG] Outputting manifest"
+        run: cat net.retrodeck.retrodeck.yml
 
       - name: "Build flatpak: download only"
         id: "flatpak-download"
-        run: |
-          git config --global protocol.file.allow always
-          mkdir -vp ${GITHUB_WORKSPACE}/local
-          mkdir -vp ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker
-          flatpak-builder --user --force-clean \
-            --install-deps-from=flathub \
-            --install-deps-from=flathub-beta \
-            --repo=${GITHUB_WORKSPACE}/local \
-            --download-only \
-            ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker \
-            net.retrodeck.retrodeck.yml
+        run: "/bin/bash ${GITHUB_WORKSPACE}/automation_tools/flatpak_build_download_only.sh"
         continue-on-error: true
 
       # Sometimes flatpak download fails, in this case it tries a second time
       - name: "Build flatpak: download only (retry)"
         if: steps.flatpak-download.outcome == 'failure'
-        run: |
-          git config --global protocol.file.allow always
-          mkdir -vp ${GITHUB_WORKSPACE}/local
-          mkdir -vp ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker
-          flatpak-builder --user --force-clean \
-            --install-deps-from=flathub \
-            --install-deps-from=flathub-beta \
-            --repo=${GITHUB_WORKSPACE}/local \
-            --download-only \
-            ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker \
-            net.retrodeck.retrodeck.yml
+        run: "/bin/bash ${GITHUB_WORKSPACE}/automation_tools/flatpak_build_download_only.sh"
 
       - name: Build flatpak
-        run: |
-          git config --global protocol.file.allow always
-          mkdir -vp ${GITHUB_WORKSPACE}/local
-          mkdir -vp ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker
-          flatpak-builder --user --force-clean \
-            --install-deps-from=flathub \
-            --install-deps-from=flathub-beta \
-            --repo=${GITHUB_WORKSPACE}/local \
-            --disable-download \
-            ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker \
-            net.retrodeck.retrodeck.yml
+        run: "/bin/bash ${GITHUB_WORKSPACE}/automation_tools/flatpak_build_only.sh"
 
       - name: Create Artifact for flathub
         run: | 
@@ -106,8 +79,7 @@ jobs:
         continue-on-error: true
 
       - name: Create Bundle
-        run: |
-          flatpak build-bundle ${GITHUB_WORKSPACE}/local RetroDECK.flatpak net.retrodeck.retrodeck
+        run: "/bin/bash ${GITHUB_WORKSPACE}/automation_tools/flatpak_build_bundle.sh"
 
       - name: Getting version info
         id: version
diff --git a/automation_tools/cooker_flatpak_portal_add.sh b/automation_tools/cooker_flatpak_portal_add.sh
old mode 100644
new mode 100755
diff --git a/automation_tools/flatpak_build_bundle.sh b/automation_tools/flatpak_build_bundle.sh
new file mode 100755
index 00000000..8c155810
--- /dev/null
+++ b/automation_tools/flatpak_build_bundle.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+# This is building the bundle RetroDECK.flatpak after the download and build steps are done
+
+flatpak build-bundle ${GITHUB_WORKSPACE}/local RetroDECK-cooker.flatpak net.retrodeck.retrodeck
\ No newline at end of file
diff --git a/automation_tools/flatpak_build_download_only.sh b/automation_tools/flatpak_build_download_only.sh
new file mode 100755
index 00000000..55352780
--- /dev/null
+++ b/automation_tools/flatpak_build_download_only.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+# This script is downloading the needed files to prepare the manifest build
+
+git config --global protocol.file.allow always
+mkdir -vp ${GITHUB_WORKSPACE}/local
+mkdir -vp ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker
+flatpak-builder --user --force-clean \
+    --install-deps-from=flathub \
+    --install-deps-from=flathub-beta \
+    --repo=${GITHUB_WORKSPACE}/local \
+    --download-only \
+    ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker \
+    net.retrodeck.retrodeck.yml
\ No newline at end of file
diff --git a/automation_tools/flatpak_build_only.sh b/automation_tools/flatpak_build_only.sh
new file mode 100755
index 00000000..d2ed3fe5
--- /dev/null
+++ b/automation_tools/flatpak_build_only.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+# This script is building the flatpak is the needed files are already downloaded
+
+git config --global protocol.file.allow always
+mkdir -vp ${GITHUB_WORKSPACE}/local
+mkdir -vp ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker
+flatpak-builder --user --force-clean \
+    --install-deps-from=flathub \
+    --install-deps-from=flathub-beta \
+    --repo=${GITHUB_WORKSPACE}/local \
+    --disable-download \
+    ${GITHUB_WORKSPACE}/retrodeck-flatpak-cooker \
+    net.retrodeck.retrodeck.yml
\ No newline at end of file
diff --git a/automation_tools/force_update_submodules.sh b/automation_tools/force_update_submodules.sh
old mode 100644
new mode 100755
diff --git a/automation_tools/version_checker.sh b/automation_tools/main_version_checker.sh
similarity index 100%
rename from automation_tools/version_checker.sh
rename to automation_tools/main_version_checker.sh