diff --git a/ci-automation/ci_automation_common.sh b/ci-automation/ci_automation_common.sh
index a0745b25ec..2a7408b6d5 100644
--- a/ci-automation/ci_automation_common.sh
+++ b/ci-automation/ci_automation_common.sh
@@ -34,7 +34,7 @@ function update_and_push_version() {
     fi
 
     # Add and commit local changes
-    git add "sdk_container/.repo/manifests/version.txt"
+    git add "manifests/version.txt"
 
     git commit --allow-empty -m "New version: ${version}"
 
diff --git a/ci-automation/garbage_collect.sh b/ci-automation/garbage_collect.sh
index 3e0d0a8d58..c36f92fd89 100644
--- a/ci-automation/garbage_collect.sh
+++ b/ci-automation/garbage_collect.sh
@@ -82,8 +82,13 @@ function _garbage_collect_impl() {
         echo "#### Processing version '${version}' ####"
         echo
 
-        git checkout "${version}" -- sdk_container/.repo/manifests/version.txt
-        source sdk_container/.repo/manifests/version.txt
+        vertxt=manifests/version.txt
+        if ! git checkout "${version}" -- "${vertxt}"; then
+            echo 'Trying to check out the old location of the version.txt then.'
+            vertxt=sdk_container/.repo/manifests/version.txt
+            git checkout "${version}" -- "${vertxt}"
+        fi
+        source "${vertxt}"
 
         # Assuming that the SDK build version also has the same OS version
         local os_vernum="${FLATCAR_VERSION}"
@@ -151,7 +156,7 @@ function _garbage_collect_impl() {
     echo
 
     local mantle_ref
-    mantle_ref=$(cat sdk_container/.repo/manifests/mantle-container)
+    mantle_ref=$(cat manifests/mantle-container)
     docker run --pull always --rm --net host \
       --env AZURE_AUTH_CREDENTIALS --env AZURE_PROFILE \
       --env AWS_ACCESS_KEY_ID --env AWS_SECRET_ACCESS_KEY \
diff --git a/ci-automation/image.sh b/ci-automation/image.sh
index 0cb5b7e118..4a1608d183 100644
--- a/ci-automation/image.sh
+++ b/ci-automation/image.sh
@@ -13,7 +13,7 @@
 #
 # PREREQUISITES:
 #
-#   1. SDK version and OS image version are recorded in sdk_container/.repo/manifests/version.txt
+#   1. SDK version and OS image version are recorded in manifests/version.txt
 #   2. Scripts repo version tag of OS image version to be built is available and checked out.
 #   3. Flatcar packages container is available via build cache server
 #       from "/containers/[VERSION]/flatcar-packages-[ARCH]-[FLATCAR_VERSION].tar.gz"
@@ -63,7 +63,7 @@ function _image_build_impl() {
     source ci-automation/ci_automation_common.sh
     source ci-automation/gpg_setup.sh
 
-    source sdk_container/.repo/manifests/version.txt
+    source manifests/version.txt
     local vernum="${FLATCAR_VERSION}"
     local docker_vernum="$(vernum_to_docker_image_version "${vernum}")"
 
diff --git a/ci-automation/image_changes.sh b/ci-automation/image_changes.sh
index 82d9857c7e..23af10c70d 100644
--- a/ci-automation/image_changes.sh
+++ b/ci-automation/image_changes.sh
@@ -40,7 +40,7 @@ function image_changes() (
     if [ "${channel}" = "developer" ]; then
             channel="alpha"
     fi
-    vernum=$(source sdk_container/.repo/manifests/version.txt; echo "${FLATCAR_VERSION}")
+    vernum=$(source manifests/version.txt; echo "${FLATCAR_VERSION}")
 
     local -a package_diff_env package_diff_params_b
     local -a size_changes_env size_changes_params_b
diff --git a/ci-automation/packages-tag.sh b/ci-automation/packages-tag.sh
index 053f893546..f8acbc511b 100644
--- a/ci-automation/packages-tag.sh
+++ b/ci-automation/packages-tag.sh
@@ -14,7 +14,7 @@
 #
 # PREREQUISITES:
 #
-#   1. SDK version is recorded in sdk_container/.repo/manifests/version.txt
+#   1. SDK version is recorded in manifests/version.txt
 #   2. SDK container is either
 #       - available via ghcr.io/flatcar/flatcar-sdk-[ARCH]:[VERSION] (official SDK release)
 #       OR
@@ -41,7 +41,7 @@
 #
 #   1. Updated scripts repository
 #        - version tag
-#        - sdk_container/.repo/manifests/version.txt denotes new FLATCAR OS version
+#        - manifests/version.txt denotes new FLATCAR OS version
 #   2. "./skip-build" as flag file to signal that the build should stop
 
 function packages_tag() {
@@ -63,7 +63,7 @@ function _packages_tag_impl() {
 
     check_version_string "${version}"
 
-    source sdk_container/.repo/manifests/version.txt
+    source manifests/version.txt
     local sdk_version="${FLATCAR_SDK_VERSION}"
 
     # Create new tag in scripts repo w/ updated versionfile
diff --git a/ci-automation/packages.sh b/ci-automation/packages.sh
index e6e984f7f3..4ef2538aa2 100644
--- a/ci-automation/packages.sh
+++ b/ci-automation/packages.sh
@@ -13,7 +13,7 @@
 #
 # PREREQUISITES:
 #
-#   1. SDK version and OS image version are recorded in sdk_container/.repo/manifests/version.txt
+#   1. SDK version and OS image version are recorded in manifests/version.txt
 #   2. Scripts repo version tag of OS image version to be built is available and checked out.
 #   3. SDK container is either
 #       - available via ghcr.io/flatcar/flatcar-sdk-[ARCH]:[VERSION] (official SDK release)
@@ -64,7 +64,7 @@ function _packages_build_impl() {
     source ci-automation/ci_automation_common.sh
     source ci-automation/gpg_setup.sh
 
-    source sdk_container/.repo/manifests/version.txt
+    source manifests/version.txt
     local sdk_version="${FLATCAR_SDK_VERSION}"
 
     # Get SDK from either the registry or import from build cache
@@ -90,7 +90,7 @@ function _packages_build_impl() {
         ./build_packages --board="${arch}-usr"
 
     # run_sdk_container updates the version file, use that version from here on
-    source sdk_container/.repo/manifests/version.txt
+    source manifests/version.txt
     local vernum="${FLATCAR_VERSION}"
     local docker_vernum="$(vernum_to_docker_image_version "${vernum}")"
     local packages_image="flatcar-packages-${arch}"
diff --git a/ci-automation/push_pkgs.sh b/ci-automation/push_pkgs.sh
index 0cb1a0187c..1d4d31259b 100644
--- a/ci-automation/push_pkgs.sh
+++ b/ci-automation/push_pkgs.sh
@@ -15,7 +15,7 @@
 #
 # PREREQUISITES:
 #
-#   1. SDK version and OS image version are recorded in sdk_container/.repo/manifests/version.txt
+#   1. SDK version and OS image version are recorded in manifests/version.txt
 #   2. Scripts repo version tag of OS image version to be built is available and checked out.
 #   3. Flatcar packages container is available via build cache server
 #       from "/containers/[VERSION]/flatcar-packages-[ARCH]-[FLATCAR_VERSION].tar.gz"
@@ -79,7 +79,7 @@ function _push_packages_impl() {
     source ci-automation/ci_automation_common.sh
     source ci-automation/gpg_setup.sh
 
-    source sdk_container/.repo/manifests/version.txt
+    source manifests/version.txt
     local vernum="${FLATCAR_VERSION}"
     local docker_vernum="$(vernum_to_docker_image_version "${vernum}")"
 
diff --git a/ci-automation/release.sh b/ci-automation/release.sh
index 90fb1c59db..bff9ae6f72 100644
--- a/ci-automation/release.sh
+++ b/ci-automation/release.sh
@@ -13,9 +13,9 @@
 #
 # PREREQUISITES:
 #
-#   1. SDK version and OS image version are recorded in sdk_container/.repo/manifests/version.txt
+#   1. SDK version and OS image version are recorded in manifests/version.txt
 #   2. Scripts repo version tag of OS image version to be built is available and checked out.
-#   3. Mantle container docker image reference is stored in sdk_container/.repo/manifests/mantle-container.
+#   3. Mantle container docker image reference is stored in manifests/mantle-container.
 #   4. Vendor image to run tests for are available on buildcache
 #         ( images/[ARCH]/[FLATCAR_VERSION]/ )
 #   5. SDK container is either
@@ -74,7 +74,7 @@ function _inside_mantle() {
 
     source sdk_lib/sdk_container_common.sh
     source ci-automation/ci_automation_common.sh
-    source sdk_container/.repo/manifests/version.txt
+    source manifests/version.txt
     # Needed because we are not the SDK container here
     source sdk_container/.env
     CHANNEL="$(get_git_channel)"
@@ -189,7 +189,7 @@ function _release_build_impl() {
     source ci-automation/ci_automation_common.sh
     source ci-automation/gpg_setup.sh
 
-    source sdk_container/.repo/manifests/version.txt
+    source manifests/version.txt
     # Needed because we are not the SDK container here
     source sdk_container/.env
     local sdk_version="${FLATCAR_SDK_VERSION}"
@@ -201,7 +201,7 @@ function _release_build_impl() {
 
     local container_name="flatcar-publish-${docker_vernum}"
     local mantle_ref
-    mantle_ref=$(cat sdk_container/.repo/manifests/mantle-container)
+    mantle_ref=$(cat manifests/mantle-container)
     # A job on each worker prunes old mantle images (docker image prune), no need to do it here
     echo "docker rm -f '${container_name}'" >> ./ci-cleanup.sh
 
diff --git a/ci-automation/sdk_bootstrap.sh b/ci-automation/sdk_bootstrap.sh
index 3540ec9023..d3ea8d1691 100644
--- a/ci-automation/sdk_bootstrap.sh
+++ b/ci-automation/sdk_bootstrap.sh
@@ -47,7 +47,7 @@
 #   1. SDK tarball (gentoo catalyst output) of the new SDK, pushed to buildcache.
 #   2. Updated scripts repository
 #        - version tag
-#        - sdk_container/.repo/manifests/version.txt denotes new SDK version
+#        - manifests/version.txt denotes new SDK version
 #   3. "./ci-cleanup.sh" with commands to clean up temporary build resources,
 #        to be run after this step finishes / when this step is aborted.
 #   4. If signer key was passed, signatures of artifacts from point 1, pushed along to buildcache.
@@ -147,7 +147,7 @@ function _sdk_bootstrap_impl() {
     # push SDK tarball to buildcache
     # Get Flatcar version number format (separator is '+' instead of '-',
     # equal to $(strip_version_prefix "$version")
-    source sdk_container/.repo/manifests/version.txt
+    source manifests/version.txt
     local dest_tarball="flatcar-sdk-${ARCH}-${FLATCAR_SDK_VERSION}.tar.bz2"
 
     # change the owner of the files and directories in __build__ back
diff --git a/ci-automation/sdk_container.sh b/ci-automation/sdk_container.sh
index e387558191..57be39febd 100644
--- a/ci-automation/sdk_container.sh
+++ b/ci-automation/sdk_container.sh
@@ -15,7 +15,7 @@
 #
 # PREREQUISITES:
 #
-#   1. SDK version is recorded in sdk_container/.repo/manifests/version.txt and a matching
+#   1. SDK version is recorded in manifests/version.txt and a matching
 #       SDK tarball is available on BUILDCACHE/sdk/[ARCH]/[VERSION]/flatcar-sdk-[ARCH]-[VERSION].tar.bz2
 #
 # OPTIONAL INPUT:
@@ -56,7 +56,7 @@ function _sdk_container_build_impl() {
     source ci-automation/ci_automation_common.sh
     source ci-automation/gpg_setup.sh
 
-    source sdk_container/.repo/manifests/version.txt
+    source manifests/version.txt
     local vernum="${FLATCAR_SDK_VERSION}"
     local sdk_tarball="flatcar-sdk-${ARCH}-${vernum}.tar.bz2"
 
diff --git a/ci-automation/test.sh b/ci-automation/test.sh
index bdddb4a3b4..7026b2f736 100644
--- a/ci-automation/test.sh
+++ b/ci-automation/test.sh
@@ -16,9 +16,9 @@
 #
 # PREREQUISITES:
 #
-#   1. SDK version and OS image version are recorded in sdk_container/.repo/manifests/version.txt
+#   1. SDK version and OS image version are recorded in manifests/version.txt
 #   2. Scripts repo version tag of OS image version to be built is available and checked out.
-#   3. Mantle container docker image reference is stored in sdk_container/.repo/manifests/mantle-container.
+#   3. Mantle container docker image reference is stored in manifests/mantle-container.
 #   4. Vendor image to run tests for are available on buildcache
 #         ( images/[ARCH]/[FLATCAR_VERSION]/ )
 #
@@ -112,7 +112,7 @@ function _test_run_impl() {
     source ci-automation/ci_automation_common.sh
     source sdk_lib/sdk_container_common.sh
 
-    source sdk_container/.repo/manifests/version.txt
+    source manifests/version.txt
     local vernum="${FLATCAR_VERSION}"
     local docker_vernum
     docker_vernum="$(vernum_to_docker_image_version "${vernum}")"
@@ -130,7 +130,7 @@ function _test_run_impl() {
 
     local container_name="flatcar-tests-${arch}-${docker_vernum}-${image}"
     local mantle_ref
-    mantle_ref=$(cat sdk_container/.repo/manifests/mantle-container)
+    mantle_ref=$(cat manifests/mantle-container)
 
     local tap_merged_summary="results-${image}"
     local tap_merged_detailed="results-${image}-detailed"
diff --git a/ci-automation/util/fetch_image.sh b/ci-automation/util/fetch_image.sh
index 51c4ef3a42..5b65e13256 100755
--- a/ci-automation/util/fetch_image.sh
+++ b/ci-automation/util/fetch_image.sh
@@ -30,7 +30,7 @@ function fetch_image() {
     local script_root="$(dirname "${BASH_SOURCE[0]}")/../.."
     source "${script_root}/ci-automation/ci_automation_common.sh"
 
-    local vernum="$(source "${script_root}/sdk_container/.repo/manifests/version.txt";
+    local vernum="$(source "${script_root}/manifests/version.txt";
                     echo "${FLATCAR_VERSION}")"
     local docker_vernum="$(vernum_to_docker_image_version "${vernum}")"
 
diff --git a/ci-automation/vms.sh b/ci-automation/vms.sh
index 69f8fd5462..720689453d 100644
--- a/ci-automation/vms.sh
+++ b/ci-automation/vms.sh
@@ -13,7 +13,7 @@
 #
 # PREREQUISITES:
 #
-#   1. SDK version and OS image version are recorded in sdk_container/.repo/manifests/version.txt
+#   1. SDK version and OS image version are recorded in manifests/version.txt
 #   2. Scripts repo version tag of OS image version to be built is available and checked out.
 #   3. Flatcar packages container is available via build cache server
 #       from "/containers/[VERSION]/flatcar-images-[ARCH]-[FLATCAR_VERSION].tar.gz"
@@ -65,7 +65,7 @@ function _vm_build_impl() {
     source ci-automation/ci_automation_common.sh
     source ci-automation/gpg_setup.sh
 
-    source sdk_container/.repo/manifests/version.txt
+    source manifests/version.txt
     local vernum="${FLATCAR_VERSION}"
     local docker_vernum="$(vernum_to_docker_image_version "${vernum}")"