diff --git a/.github/workflows/common.sh b/.github/workflows/common.sh
index 0c3b11e011a..f584e313e8f 100644
--- a/.github/workflows/common.sh
+++ b/.github/workflows/common.sh
@@ -13,9 +13,10 @@ if [[ ! -d "${WORK_SCRIPTS_DIR:-}" ]]; then
   fail "WORK_SCRIPTS_DIR env var does not point to a directory. It should point to the scripts repo which will be updated."
 fi
 
+# Update these to use the new repo location once LTS has migrated.
 readonly SDK_OUTER_TOPDIR="${WORK_SCRIPTS_DIR}"
 readonly SDK_OUTER_OVERLAY="${SDK_OUTER_TOPDIR}/sdk_container/src/third_party/coreos-overlay"
-readonly SDK_INNER_SRCDIR="/mnt/host/source/src"
+readonly SDK_INNER_SRCDIR="/mnt/host/source/src/scripts/sdk_container/src"
 readonly SDK_INNER_OVERLAY="${SDK_INNER_SRCDIR}/third_party/coreos-overlay"
 
 readonly BUILDBOT_USERNAME="Flatcar Buildbot"
diff --git a/.github/workflows/portage-stable-packages-list b/.github/workflows/gentoo-subset-packages-list
similarity index 100%
rename from .github/workflows/portage-stable-packages-list
rename to .github/workflows/gentoo-subset-packages-list
diff --git a/.github/workflows/image_changes.sh b/.github/workflows/image_changes.sh
index 8008f0bd786..42fd2214151 100755
--- a/.github/workflows/image_changes.sh
+++ b/.github/workflows/image_changes.sh
@@ -25,8 +25,8 @@ function github_ricj_callback() {
     show_changes_env+=(
         # Override the default locations of repositories.
         "SCRIPTS_REPO=."
-        "COREOS_OVERLAY_REPO=../coreos-overlay"
-        "PORTAGE_STABLE_REPO=../portage-stable"
+        "FLATCAR_OVERLAY_REPO=../flatcar-overlay"
+        "GENTOO_SUBSET_REPO=../gentoo-subset"
     )
     show_changes_params+=(
         # We may not have a tag handy, so we tell show-changes
diff --git a/.github/workflows/update-portage-stable-packages-from-list.yaml b/.github/workflows/update-gentoo-subset-packages-from-list.yaml
similarity index 86%
rename from .github/workflows/update-portage-stable-packages-from-list.yaml
rename to .github/workflows/update-gentoo-subset-packages-from-list.yaml
index 044b77af865..d778df0b9f6 100644
--- a/.github/workflows/update-portage-stable-packages-from-list.yaml
+++ b/.github/workflows/update-gentoo-subset-packages-from-list.yaml
@@ -1,4 +1,4 @@
-name: Keep portage-stable packages updated
+name: Keep gentoo-subset packages updated
 on:
   schedule:
     - cron:  '0 7 * * 1'
@@ -35,10 +35,10 @@ jobs:
           git config --global user.name "Flatcar Buildbot"
           git config --global user.email "buildbot@flatcar-linux.org"
           old_head=$(git -C scripts rev-parse HEAD)
-          packages_list=$(realpath scripts/.github/workflows/portage-stable-packages-list)
+          packages_list=$(realpath scripts/.github/workflows/gentoo-subset-packages-list)
           gentoo_repo=$(realpath gentoo)
           build_scripts=$(realpath flatcar-build-scripts)
-          pushd scripts/sdk_container/src/third_party/portage-stable
+          pushd scripts/repos/gentoo-subset
           while read -r package; do
               if [[ ! -e "${package}" ]]; then
                   # If this happens, it means that the package was moved to overlay
@@ -50,7 +50,7 @@ jobs:
                   # If this happens, it means that the package was obsoleted or moved
                   # in Gentoo. The obsoletion needs to be handled in the case-by-case
                   # manner, while move should be handled by doing the same move
-                  # in portage-stable. The build should not break because of the move,
+                  # in gentoo-subset. The build should not break because of the move,
                   # because most likely it's already reflected in the profiles/updates
                   # directory.
                   echo "::warning title=${package}::Obsolete or moved package"
@@ -73,10 +73,10 @@ jobs:
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           path: scripts
-          branch: buildbot/weekly-portage-stable-package-updates-${{steps.update-listed-packages.outputs.TODAYDATE }}
+          branch: buildbot/weekly-gentoo-subset-package-updates-${{steps.update-listed-packages.outputs.TODAYDATE }}
           delete-branch: true
           base: main
-          title: Weekly portage-stable package updates ${{steps.update-listed-packages.outputs.TODAYDATE }}
+          title: Weekly gentoo-subset package updates ${{steps.update-listed-packages.outputs.TODAYDATE }}
           body: |
             CI: TODO
 
diff --git a/.github/workflows/update-metadata-glsa.yaml b/.github/workflows/update-metadata-glsa.yaml
index ead1c2a4065..de3af834112 100644
--- a/.github/workflows/update-metadata-glsa.yaml
+++ b/.github/workflows/update-metadata-glsa.yaml
@@ -15,7 +15,7 @@ jobs:
       - name: Update GLSA metadata
         id: update-glsa-metadata
         run: |
-          glsa_dir='sdk_container/src/third_party/portage-stable/metadata/glsa'
+          glsa_dir='repos/gentoo-subset/metadata/glsa'
           rm -rf "${glsa_dir}"
           mkdir --parents "${glsa_dir}"
           rsync --archive rsync://rsync.gentoo.org/gentoo-portage/metadata/glsa/* "${glsa_dir}"
@@ -30,6 +30,6 @@ jobs:
           base: main
           title: Monthly GLSA metadata ${{steps.update-glsa-metadata.outputs.TODAYDATE }}
           body: Updated GLSA metadata
-          commit-message: "portage-stable/metadata: Monthly GLSA metadata updates"
+          commit-message: "gentoo-subset/metadata: Monthly GLSA metadata updates"
           author: Flatcar Buildbot <buildbot@flatcar-linux.org>
           labels: main
diff --git a/PREFIX.md b/PREFIX.md
index e353a0d5b62..1d6b6d17106 100644
--- a/PREFIX.md
+++ b/PREFIX.md
@@ -35,7 +35,7 @@ Prefix uses a _staging environment_ to build binary packages, then installs thes
 The _staging environment_ contains toolchains and all build tools required to create binary packages (a full `@system`).
 The _final environment_ only contains run-time dependencies.
 
-Packages are built from ebuilds in coreos-overlay, portage-stable, and prefix-overlay.
+Packages are built from ebuilds in flatcar-overlay, gentoo-subset, and prefix-overlay.
 
 A QoL `emerge` wrapper is included to install packages to the prefix.
 
diff --git a/README.md b/README.md
index 262180cec55..9ad11ddad95 100644
--- a/README.md
+++ b/README.md
@@ -14,20 +14,18 @@ The SDK can be used to
 # Using the scripts repository
 
 The repository is meant to be the entry point for Flatcar builds and development.
-Ebuilds for all packages reside in one of 2 subdirectories - [coreos-overlay](sdk_container/src/third_party/coreos-overlay) and [portage-stable](sdk_container/src/third_party/portage-stable/):
+Ebuilds for all packages reside in one of 2 subdirectories - [flatcar-overlay](repos/flatcar-overlay) and [gentoo-subset](repos/gentoo-subset/):
 ```
 scripts
-   +--sdk_container
-          +---------src
-                     +--third_party
-                             +------coreos-overlay
-                             +------portage-stable
+   +--repos
+          +--flatcar-overlay
+          +--gentoo-subset
 ```
 
-`portage-stable` is kept in alignment with upstream Gentoo and should not contain any modifications (with only minor, well-justified exceptions).
+`gentoo-subset` is kept in alignment with upstream Gentoo and should not contain any modifications (with only minor, well-justified exceptions).
 Consider it a small sub-set of Gentoo.
 
-`coreos-overlay` contains significantly modified or even entirely self-written ebuilds.
+`flatcar-overlay` contains significantly modified or even entirely self-written ebuilds.
 
 The `scripts` repository makes ample use of tags to mark releases.
 Sometimes, local and origin tags can diverge (e.g. when re-tagging something locally to test a build).
@@ -52,7 +50,7 @@ While work on a native ARM64 native SDK is ongoing, it's unfortunately not ready
 
 The container can be run in one of two ways - "standalone", or integrated with the [scripts](https://github.com/flatcar/scripts) repo:
 * Standalone mode will use no host volumes and will allow you to play with the SDK in a sandboxed throw-away environment. In standalone mode, you interface with Docker directly to use the SDK container.
-* Integrated mode will closely integrate with the scripts repo directory and bind-mount it as well as the portage-stable and coreos-overlay directories into the container. Integrated mode uses wrapper scripts to interact with the SDK container. This is the recommended way for developing patches for Flatcar.
+* Integrated mode will closely integrate with the scripts repo directory and bind-mount it as well as the gentoo-subset and flatcar-overlay directories into the container. Integrated mode uses wrapper scripts to interact with the SDK container. This is the recommended way for developing patches for Flatcar.
 
 ## Standalone mode
 
@@ -82,7 +80,7 @@ To start a container in privileged mode with `/dev` available use:
 
 This is the preferred mode of working with the SDK.
 Interaction with the container happens via wrapper scripts from the scripts repository.
-Both the host's scripts repo as well as the ebuild paths (portage-stable and coreos-overlay) are made available in the container, allowing for work on these directly.
+Both the host's scripts repo as well as the ebuild paths (gentoo-subset and flatcar-overlay) are made available in the container, allowing for work on these directly.
 The wrapper scripts will re-use existing containers instead of creating new ones to preserve your work in the container, enabling consistency.
 
 To clone the scripts repo and pick a version:
diff --git a/bootstrap_sdk b/bootstrap_sdk
index 36bda6ecca9..051438338ae 100755
--- a/bootstrap_sdk
+++ b/bootstrap_sdk
@@ -18,13 +18,13 @@
 #     will be linked against the SEED SDK libraries, NOT against libraries built
 #     in stage 1.
 #
-# 3. stage2: Run portage-stable/scripts/bootstrap.sh
+# 3. stage2: Run gentoo-subset/scripts/bootstrap.sh
 #     This rebuilds the toolchain using Gentoo bootstrapping, ensuring it's not linked
 #     to or otherwise influenced by whatever was in the "seed" tarball.
 #     The toolchain rebuild may contain updated package ebuilds from
-#     third_party/(portage-stable|coreos-overlay).
-#     This and all following stages use portage-stable and coreos-overlay
-#     from third_party/... (see 1.)
+#     repos/(gentoo-subset|flatcar-overlay).
+#     This and all following stages use gentoo-subset and flatcar-overlay
+#     from repos/... (see 1.)
 #
 # 4. stage3: Run emerge -e system to rebuild everything using the fresh updated
 #     toolchain from 3., using the normal USE flags provided by the profile. This
@@ -95,13 +95,13 @@ chmod 1777 "${ROOT_OVERLAY}/tmp"
 cp "${BUILD_LIBRARY_DIR}/toolchain_util.sh" "${ROOT_OVERLAY}/tmp"
 
 
-# Stage 1 uses "known-good" ebuilds (from both coreos-overlay and portage-stable)
+# Stage 1 uses "known-good" ebuilds (from both flatcar-overlay and gentoo-subset)
 #  to build a minimal toolchain (USE="-*") for stage 2.
 #
-# No package updates must happen in stage 1, so we use the portage-stable and
-#  coreos-overlay paths included with the current SDK (from the SDK chroot's
-#  /var/gentoo/repos/). "Current SDK" refers to the SDK we entered with
-#  'cork enter', i.e. the SDK we run ./bootstrap_sdk in.
+# No package updates must happen in stage 1, so we use the gentoo-subset and
+#  flatcar-overlay paths included with the current SDK (from the SDK chroot's
+#  /mnt/host/source/src/scripts/repos/). "Current SDK" refers to the SDK we
+#  entered with 'cork enter', i.e. the SDK we run ./bootstrap_sdk in.
 #
 # Using ebuilds from the above mentioned sources will ensure that stage 1 builds
 #  a minimal stage 2 from known-good ebuild versions - the same ebuild versions
diff --git a/build_library/build_image_util.sh b/build_library/build_image_util.sh
index 7712141c36a..144d13c588f 100755
--- a/build_library/build_image_util.sh
+++ b/build_library/build_image_util.sh
@@ -365,7 +365,7 @@ get_metadata() {
             local mirror="$(echo "${v}" | grep mirror:// | cut -d '/' -f 3)"
             if [ -n "${mirror}" ]; then
                 # Take only first mirror, those not working should be removed
-                local location="$(grep "^${mirror}"$'\t' /mnt/host/source/src/third_party/portage-stable/profiles/thirdpartymirrors | cut -d $'\t' -f 2- | cut -d ' ' -f 1 | tr -d $'\t')"
+                local location="$(grep "^${mirror}"$'\t' /mnt/host/source/src/scripts/repos/gentoo-subset/profiles/thirdpartymirrors | cut -d $'\t' -f 2- | cut -d ' ' -f 1 | tr -d $'\t')"
                 v="$(echo "${v}" | sed "s#mirror://${mirror}/#${location}#g")"
             fi
             new_val+="${v} "
@@ -489,8 +489,8 @@ EOF
     local license_list # define before assignment because it would mask any error
     license_list="$(jq -r '.[] | "\(.licenses | .[])"' "${json_input}" | sort | uniq)"
     local license_dirs=(
-        "/mnt/host/source/src/third_party/coreos-overlay/licenses/"
-        "/mnt/host/source/src/third_party/portage-stable/licenses/"
+        "/mnt/host/source/src/scripts/repos/flatcar-overlay/licenses/"
+        "/mnt/host/source/src/scripts/repos/gentoo-subset/licenses/"
         "none"
     )
     for license_file in ${license_list}; do
diff --git a/build_library/catalyst.sh b/build_library/catalyst.sh
index 4512091dfc7..65423732d89 100644
--- a/build_library/catalyst.sh
+++ b/build_library/catalyst.sh
@@ -28,10 +28,10 @@ STAGES=
 
 DEFINE_string catalyst_root "${DEFAULT_CATALYST_ROOT}" \
     "Path to directory for all catalyst images and other files."
-DEFINE_string portage_stable "${SRC_ROOT}/third_party/portage-stable" \
-    "Path to the portage-stable git checkout."
-DEFINE_string coreos_overlay "${SRC_ROOT}/third_party/coreos-overlay" \
-    "Path to the coreos-overlay git checkout."
+DEFINE_string gentoo_subset "${SCRIPTS_DIR}/repos/gentoo-subset" \
+    "Path to the gentoo-subset git checkout."
+DEFINE_string flatcar_overlay "${SCRIPTS_DIR}/repos/flatcar-overlay" \
+    "Path to the flatcar-overlay git checkout."
 DEFINE_string seed_tarball "${DEFAULT_SEED}" \
     "Path to an existing stage tarball to start from."
 DEFINE_string version "${FLATCAR_VERSION}" \
@@ -62,8 +62,8 @@ storedir="$CATALYST_ROOT"
 distdir="$DISTDIR"
 envscript="$TEMPDIR/catalystrc"
 port_logdir="$CATALYST_ROOT/log"
-repo_basedir="/mnt/host/source/src/third_party"
-repo_name="portage-stable"
+repo_basedir="/mnt/host/source/src/scripts/repos"
+repo_name="gentoo-subset"
 EOF
 }
 
@@ -87,8 +87,8 @@ target: stage$1
 subarch: $ARCH
 rel_type: $TYPE
 portage_confdir: $TEMPDIR/portage
-repos: $FLAGS_coreos_overlay
-keep_repos: portage-stable coreos-overlay
+repos: $FLAGS_flatcar_overlay
+keep_repos: gentoo-subset flatcar-overlay
 profile: $FLAGS_profile
 snapshot_treeish: $FLAGS_version
 version_stamp: $FLAGS_version
@@ -231,7 +231,7 @@ write_configs() {
     info "Configuring Portage..."
     cp -r "${BUILD_LIBRARY_DIR}"/portage/ "${TEMPDIR}/"
 
-    ln -sfT '/mnt/host/source/src/third_party/coreos-overlay/coreos/user-patches' \
+    ln -sfT '/mnt/host/source/src/scripts/repos/flatcar-overlay/coreos/user-patches' \
         "${TEMPDIR}"/portage/patches
 }
 
@@ -264,10 +264,10 @@ build_stage() {
 build_snapshot() {
     local repo_dir snapshot snapshots_dir snapshot_path
 
-    repo_dir=${1:-"${FLAGS_portage_stable}"}
+    repo_dir=${1:-"${FLAGS_gentoo_subset}"}
     snapshot=${2:-"${FLAGS_version}"}
     snapshots_dir="${CATALYST_ROOT}/snapshots"
-    snapshot_path="${snapshots_dir}/portage-stable-${snapshot}.sqfs"
+    snapshot_path="${snapshots_dir}/gentoo-subset-${snapshot}.sqfs"
     if [[ -f ${snapshot_path} && $FLAGS_rebuild == $FLAGS_FALSE ]]
     then
         info "Skipping snapshot, ${snapshot_path} exists"
@@ -325,5 +325,5 @@ catalyst_build() {
     fi
 
     # Cleanup snapshots, we don't use them
-    rm -rf "$CATALYST_ROOT/snapshots/${FLAGS_portage_stable##*/}-${FLAGS_version}.sqfs"*
+    rm -rf "$CATALYST_ROOT/snapshots/${FLAGS_gentoo_subset##*/}-${FLAGS_version}.sqfs"*
 }
diff --git a/build_library/dev_container_util.sh b/build_library/dev_container_util.sh
index 3d702c32eb1..a2f877e32cb 100755
--- a/build_library/dev_container_util.sh
+++ b/build_library/dev_container_util.sh
@@ -20,11 +20,11 @@ configure_dev_portage() {
 
     # Need profiles at the bare minimum
     local repo
-    for repo in portage-stable coreos-overlay; do
+    for repo in gentoo-subset flatcar-overlay; do
         sudo mkdir -p "${root_fs_dir}/var/lib/portage/${repo}"
         sudo rsync -rtl --exclude=md5-cache \
-            "${SRC_ROOT}/third_party/${repo}/metadata" \
-            "${SRC_ROOT}/third_party/${repo}/profiles" \
+            "${SRC_ROOT}/scripts/repos/${repo}/metadata" \
+            "${SRC_ROOT}/scripts/repos/${repo}/profiles" \
             "${root_fs_dir}/var/lib/portage/${repo}"
     done
 
@@ -42,26 +42,26 @@ PORTAGE_BINHOST="$(get_binhost_url "${binhost}" "${update_group}" 'pkgs')
 $(get_binhost_url "${binhost}" "${update_group}" 'toolchain')"
 EOF
 
-    sudo_clobber "${root_fs_dir}/etc/portage/repos.conf/portage-stable.conf" <<EOF
+    sudo_clobber "${root_fs_dir}/etc/portage/repos.conf/gentoo-subset.conf" <<EOF
 [DEFAULT]
-main-repo = portage-stable
+main-repo = gentoo-subset
 
-[portage-stable]
-location = /var/lib/portage/portage-stable
+[gentoo-subset]
+location = /var/lib/portage/gentoo-subset
 EOF
 
-    sudo_clobber "${root_fs_dir}/etc/portage/repos.conf/coreos-overlay.conf" <<EOF
-[coreos-overlay]
-location = /var/lib/portage/coreos-overlay
+    sudo_clobber "${root_fs_dir}/etc/portage/repos.conf/flatcar-overlay.conf" <<EOF
+[flatcar-overlay]
+location = /var/lib/portage/flatcar-overlay
 EOF
 
     # Now set the correct profile, we do not use the eselect tool - it
     # does not seem to be usable outside of the chroot without using
     # deprecated PORTDIR and PORTDIR_OVERLAY environment variables.
     local profile_name=$(get_board_profile "${BOARD}")
-    # Turn coreos-overlay:coreos/amd64/generic into coreos/amd64/generic/dev
+    # Turn flatcar-overlay:coreos/amd64/generic into coreos/amd64/generic/dev
     profile_name="${profile_name#*:}/dev"
-    local profile_directory="${root_fs_dir}/var/lib/portage/coreos-overlay/profiles/${profile_name}"
+    local profile_directory="${root_fs_dir}/var/lib/portage/flatcar-overlay/profiles/${profile_name}"
     if [[ ! -d "${profile_directory}" ]]; then
         die "Not a valid profile: ${profile_name}"
     fi
diff --git a/build_library/prefix_util.sh b/build_library/prefix_util.sh
index a3c3db8a4d1..c15eaad3a17 100644
--- a/build_library/prefix_util.sh
+++ b/build_library/prefix_util.sh
@@ -67,7 +67,7 @@ function setup_prefix_dirs() {
   sudo cp -vR "${prefix_repo}/skel/etc/portage" "${STAGINGROOT}${EPREFIX}/etc/"
   sudo cp -vR "${prefix_repo}/skel/etc/portage" "${FINALROOT}${EPREFIX}/etc/"
 
-  local profile="/mnt/host/source/src/third_party/portage-stable/profiles/default/linux"
+  local profile="/mnt/host/source/src/scripts/repos/gentoo-subset/profiles/default/linux"
   case "${PREFIX_BOARD}" in
     amd64-usr) profile="${profile}/amd64/17.1/no-multilib/prefix/kernel-3.2+";;
     arm64-usr) profile="${profile}/arm64/17.0/prefix/kernel-3.2+";;
diff --git a/build_library/sysext_mangle_containerd-flatcar b/build_library/sysext_mangle_containerd-flatcar
index 1d3502d33ae..686e8dea257 100755
--- a/build_library/sysext_mangle_containerd-flatcar
+++ b/build_library/sysext_mangle_containerd-flatcar
@@ -9,7 +9,7 @@ echo ">>> NOTICE: $0: removing 'gen-manpages', 'containerd-stress' from sysext"
 rm -f "${rootfs}/usr/bin/gen-manpages" "${rootfs}/usr/bin/containerd-stress"
 
 script_root="$(cd "$(dirname "$0")/../"; pwd)"
-files_dir="${script_root}/sdk_container/src/third_party/coreos-overlay/coreos/sysext/containerd"
+files_dir="${script_root}/repos/flatcar-overlay/coreos/sysext/containerd"
 
 echo ">>> NOTICE $0: installing extra files from '${files_dir}'"
 cp -va "${files_dir}/"* "${rootfs}"
diff --git a/build_library/sysext_mangle_docker-flatcar b/build_library/sysext_mangle_docker-flatcar
index b2c055324dc..5188ddd33e9 100755
--- a/build_library/sysext_mangle_docker-flatcar
+++ b/build_library/sysext_mangle_docker-flatcar
@@ -8,7 +8,7 @@ echo ">>> NOTICE: $0: removing '/usr/lib/debug/', '/usr/share/docker/contrib' fr
 rm -rf "${rootfs}/usr/lib/debug/" "${rootfs}/usr/share/docker/contrib/"
 
 script_root="$(cd "$(dirname "$0")/../"; pwd)"
-files_dir="${script_root}/sdk_container/src/third_party/coreos-overlay/coreos/sysext/docker"
+files_dir="${script_root}/repos/flatcar-overlay/coreos/sysext/docker"
 
 echo ">>> NOTICE $0: installing extra files from '${files_dir}'"
 cp -va "${files_dir}/"* "${rootfs}"
diff --git a/build_library/toolchain_util.sh b/build_library/toolchain_util.sh
index 65848e91309..f304cdb1015 100644
--- a/build_library/toolchain_util.sh
+++ b/build_library/toolchain_util.sh
@@ -14,18 +14,18 @@ TOOLCHAIN_PKGS=(
 # This is only used as an intermediate step to be able to use the cross
 # compiler to build a full native toolchain. Packages are not uploaded.
 declare -A CROSS_PROFILES
-CROSS_PROFILES["x86_64-cros-linux-gnu"]="coreos-overlay:coreos/amd64/generic"
-CROSS_PROFILES["aarch64-cros-linux-gnu"]="coreos-overlay:coreos/arm64/generic"
+CROSS_PROFILES["x86_64-cros-linux-gnu"]="flatcar-overlay:coreos/amd64/generic"
+CROSS_PROFILES["aarch64-cros-linux-gnu"]="flatcar-overlay:coreos/arm64/generic"
 
 # Map board names to CHOSTs and portage profiles. This is the
 # definitive list, there is assorted code new and old that either
 # guesses or hard-code these. All that should migrate to this list.
 declare -A BOARD_CHOSTS BOARD_PROFILES
 BOARD_CHOSTS["amd64-usr"]="x86_64-cros-linux-gnu"
-BOARD_PROFILES["amd64-usr"]="coreos-overlay:coreos/amd64/generic"
+BOARD_PROFILES["amd64-usr"]="flatcar-overlay:coreos/amd64/generic"
 
 BOARD_CHOSTS["arm64-usr"]="aarch64-cros-linux-gnu"
-BOARD_PROFILES["arm64-usr"]="coreos-overlay:coreos/arm64/generic"
+BOARD_PROFILES["arm64-usr"]="flatcar-overlay:coreos/arm64/generic"
 
 BOARD_NAMES=( "${!BOARD_CHOSTS[@]}" )
 
@@ -169,7 +169,7 @@ get_sdk_arch() {
 }
 
 get_sdk_profile() {
-    echo "coreos-overlay:coreos/$(get_sdk_arch)/sdk"
+    echo "flatcar-overlay:coreos/$(get_sdk_arch)/sdk"
 }
 
 get_sdk_libdir() {
@@ -244,7 +244,7 @@ configure_crossdev_overlay() {
     echo "x-crossdev" | \
         "${sudo[@]}" tee "${root}${location}/profiles/repo_name" > /dev/null
     "${sudo[@]}" tee "${root}${location}/metadata/layout.conf" > /dev/null <<EOF
-masters = portage-stable coreos-overlay
+masters = gentoo-subset flatcar-overlay
 use-manifests = true
 thin-manifests = true
 EOF
@@ -271,7 +271,7 @@ _get_dependency_list() {
 
 # Configure a new ROOT
 # Values are copied from the environment or the current host configuration.
-# Usage: CBUILD=foo-bar-linux-gnu ROOT=/foo/bar SYSROOT=/foo/bar configure_portage coreos-overlay:some/profile
+# Usage: CBUILD=foo-bar-linux-gnu ROOT=/foo/bar SYSROOT=/foo/bar configure_portage flatcar-overlay:some/profile
 # Note: if using portageq to get CBUILD it must be called before CHOST is set.
 _configure_sysroot() {
     local profile="$1"
@@ -287,7 +287,7 @@ _configure_sysroot() {
     "${sudo[@]}" eselect profile set --force "$profile"
 
     local coreos_path
-    coreos_path=$(portageq get_repo_path "${ROOT}" coreos-overlay)
+    coreos_path=$(portageq get_repo_path "${ROOT}" flatcar-overlay)
     "${sudo[@]}" ln -sfT "${coreos_path}/coreos/user-patches" "${ROOT}/etc/portage/patches"
 
     echo "Writing make.conf for the sysroot ${SYSROOT}, root ${ROOT}"
diff --git a/build_library/vm_image_util.sh b/build_library/vm_image_util.sh
index ecaa792d5a5..6c41122f0b9 100644
--- a/build_library/vm_image_util.sh
+++ b/build_library/vm_image_util.sh
@@ -553,7 +553,7 @@ install_oem_sysext() {
         --metapkgs="${metapkg}"
     )
     local overlay_path mangle_fs
-    overlay_path=$(portageq get_repo_path / coreos-overlay)
+    overlay_path=$(portageq get_repo_path / flatcar-overlay)
     mangle_fs="${overlay_path}/${metapkg}/files/manglefs.sh"
     if [[ -x "${mangle_fs}" ]]; then
         build_sysext_flags+=(
diff --git a/build_sysext b/build_sysext
index 963391df567..38adb84b9c9 100755
--- a/build_sysext
+++ b/build_sysext
@@ -65,7 +65,7 @@ metapackage 'coreos-base/oem-azure' for the arm64 squashfs base at
 sudo build_sysext \\
      --board=arm64-usr \\
      --metapkgs=coreos-base/oem-azure \\
-     --mangle_fs=sdk_container/src/third_party/coreos-overlay/coreos-base/oem-azure/files/manglefs.sh \\
+     --mangle_fs=repos/flatcar-overlay/coreos-base/oem-azure/files/manglefs.sh \\
      --squashfs_base=build/artifacts/flatcar_production_image_sysext.squashfs \\
      --image_builddir=oem-images \\
      oem-azure
@@ -244,7 +244,7 @@ ROOT="${BUILD_DIR}/install-root" PORTAGE_CONFIGROOT="${BUILD_DIR}/install-root"
 if [[ "${FLAGS_strip_binaries}" = "${FLAGS_TRUE}" ]]; then
     chost="$("portageq-${BOARD}" envvar CHOST)"
     strip="${chost}-strip"
-    
+
     info "Stripping all non-stripped binaries in sysext using '${strip}'"
 
     # Find all non-stripped binaries, remove ':' from filepath, and strip 'em
diff --git a/changelog/changes/2024-07-15-repo-rename.md b/changelog/changes/2024-07-15-repo-rename.md
index 3683de4d077..ad97bb9e2b2 100644
--- a/changelog/changes/2024-07-15-repo-rename.md
+++ b/changelog/changes/2024-07-15-repo-rename.md
@@ -1 +1 @@
-- As part of the update to Catalyst 4 (used to build the SDK), the coreos package repository has been renamed to coreos-overlay to match its directory name. This will be reflected in package listings and package manager output. ([flatcar/scripts#2115](https://github.com/flatcar/scripts/pull/2115))
+- As part of the update to Catalyst 4 (used to build the SDK), the portage-stable and coreos package repositories has been moved to the `repos` directory and renamed to gentoo-subset and flatcar-overlay respectively. This will be reflected in package listings and package manager output. ([flatcar/scripts#2115](https://github.com/flatcar/scripts/pull/2115))
diff --git a/checkout b/checkout
index 5a18a255b63..f6774bc880c 100755
--- a/checkout
+++ b/checkout
@@ -17,13 +17,13 @@ usage() {
     echo "  Usage:"
     echo "  $0 [-t|-b] [-n] [-u <strategy>] <tag-or-branch>"
     echo "       Check our a tag or branch and synchronise git submodules"
-    echo "          coreos-overlay and portage-stable."
+    echo "          flatcar-overlay and gentoo-subset."
     echo "       By default, $0 tries to auto-detect whether to handle a tag or a branch,"
     echo "         with tags being prioritised over branches of the same name."
     echo
     echo "       <tag-or-branch> Name of the tag or branch to check out."
-    echo "                       BRANCH: Check out the branch in scripts, coreos-overlay"
-    echo "                                and portage-stable, and fast-forward to the"
+    echo "                       BRANCH: Check out the branch in scripts, flatcar-overlay"
+    echo "                                and gentoo-subset, and fast-forward to the"
     echo "                                latest changes by default (but see '-u' below)."
     echo "                       TAG:    Check out the tag in scripts, and update submodules."
     echo
@@ -90,8 +90,8 @@ esac
 
 # make sure submodules are initialised
 git submodule init
-for dir in sdk_container/src/third_party/coreos-overlay \
-           sdk_container/src/third_party/portage-stable ; do
+for dir in repos/flatcar-overlay \
+           repos/gentoo-subset ; do
     if [ ! -f "$dir"/.git ] ; then
         git submodule update -N "$dir"
     fi
@@ -111,10 +111,10 @@ function check_all() {
         return
     fi
 
-    local overlay="$(git -C sdk_container/src/third_party/coreos-overlay $gitcmd \
+    local overlay="$(git -C repos/flatcar-overlay $gitcmd \
                         | sed -e 's/^[[:space:]]*//' -e 's:remotes/[^/]\+/::' \
                         | grep -m1 -E "^$name\$")"
-    local portage="$(git -C sdk_container/src/third_party/portage-stable $gitcmd \
+    local portage="$(git -C repos/gentoo-subset $gitcmd \
                         | sed -e 's/^[[:space:]]*//' -e 's:remotes/[^/]\+/::' \
                         | grep -m1 -E "^$name\$")"
 
@@ -129,8 +129,8 @@ function check_all() {
 #
 if ! $force_branch; then
     for dir in . \
-        sdk_container/src/third_party/coreos-overlay \
-        sdk_container/src/third_party/portage-stable ; do
+        repos/flatcar-overlay \
+        repos/gentoo-subset ; do
         git -C "$dir" fetch --tags --force --prune --prune-tags
     done
     tag="$(check_all 'tag -l' "$name")"
@@ -166,8 +166,8 @@ echo
 echo "Checking out BRANCH '$branch'"
 echo "----------------------------------"
 for dir in . \
-    sdk_container/src/third_party/coreos-overlay \
-    sdk_container/src/third_party/portage-stable ; do
+    repos/flatcar-overlay \
+    repos/gentoo-subset ; do
 
     git -C "$dir" checkout "$branch"
     if [ -n "$update_strategy" ] ; then
@@ -175,4 +175,3 @@ for dir in . \
         git -C "$dir" pull "$update_strategy"
     fi
 done
-
diff --git a/ci-automation/README.md b/ci-automation/README.md
index aef5b76fa34..0760b02bf20 100644
--- a/ci-automation/README.md
+++ b/ci-automation/README.md
@@ -39,7 +39,7 @@ image_build amd64
 ### SDK bootstrap build
 
 1. SDK Bootstrap (`sdk.sh`): Use a seed SDK tarball and seed SDK container image to build a new SDK tarball.
-   The resulting SDK tarball will ship packages and versions from the updated coreos-overlay and portage-stable ebuild directories.
+   The resulting SDK tarball will ship packages and versions from the updated flatcar-overlay and gentoo-subset ebuild directories.
    This step updates the versionfile, recording the SDK container version just built.
    It will generate and push a new version tag to the scripts repo.
 2. SDK container build (`sdk_container.sh`) : use SDK tarball to build an SDK container image.
diff --git a/ci-automation/image_changes.sh b/ci-automation/image_changes.sh
index 6af4be47eb1..5ad51958a14 100644
--- a/ci-automation/image_changes.sh
+++ b/ci-automation/image_changes.sh
@@ -81,8 +81,8 @@ function ricj_callback() {
         "PATH=${PATH}:${PWD}/ci-automation/python-bin"
         # Override the default locations of repositories.
         "SCRIPTS_REPO=."
-        "COREOS_OVERLAY_REPO=../coreos-overlay"
-        "PORTAGE_STABLE_REPO=../portage-stable"
+        "FLATCAR_OVERLAY_REPO=../flatcar-overlay"
+        "GENTOO_SUBSET_REPO=../gentoo-subset"
     )
     show_changes_params+=(
         # The show-changes script expects a tag name, so using git tag
@@ -251,7 +251,7 @@ function get_oem_id_list() {
     arch=${1}; shift
     list_var_name=${1}; shift
 
-    local -a ebuilds=("${scripts_repo}/sdk_container/src/third_party/coreos-overlay/coreos-base/common-oem-files/common-oem-files-"*'.ebuild')
+    local -a ebuilds=("${scripts_repo}/repos/flatcar-overlay/coreos-base/common-oem-files/common-oem-files-"*'.ebuild')
     if [[ ${#ebuilds[@]} -eq 0 ]] || [[ ! -e ${ebuilds[0]} ]]; then
         echo "No coreos-base/common-oem-files ebuilds?!" >&2
         exit 1
diff --git a/find_overlay_dups b/find_overlay_dups
index c76a1042014..d41edb48e42 100755
--- a/find_overlay_dups
+++ b/find_overlay_dups
@@ -1,14 +1,14 @@
 #!/bin/bash
 
-# Prints packages which are in both portage-stable and coreos-overlay
+# Prints packages which are in both gentoo-subset and flatcar-overlay
 
 SCRIPT_ROOT=$(dirname $(readlink -f "$0"))
 . "${SCRIPT_ROOT}/common.sh" || exit 1
 
-DEFINE_string overlay_path "${SRC_ROOT}/third_party/coreos-overlay" \
+DEFINE_string overlay_path "${SCRIPT_ROOT}/repos/flatcar-overlay" \
     "Directory containing the overlay"
-DEFINE_string portage_stable_path "${SRC_ROOT}/third_party/portage-stable" \
-    "Path to portage-stable"
+DEFINE_string gentoo_subset_path "${SCRIPT_ROOT}/repos/gentoo-subset" \
+    "Path to gentoo-subset"
 
 # Parse flags
 FLAGS "$@" || exit 1
@@ -19,10 +19,10 @@ function get_tree_packages() {
 	find "$1" -maxdepth 3 -type f -name "*.ebuild" -printf "%P\n" | xargs dirname | sort | uniq
 }
 
-portage_stable_packages=$(get_tree_packages ${FLAGS_portage_stable_path})
+gentoo_subset_packages=$(get_tree_packages ${FLAGS_gentoo_subset_path})
 overlay_packages=$(get_tree_packages ${FLAGS_overlay_path})
 
-all_packages="$portage_stable_packages $overlay_packages"
+all_packages="$gentoo_subset_packages $overlay_packages"
 dups=$(sort <<< "$all_packages" | uniq -D | uniq)
 
 if [[ -z "$dups" ]]; then
diff --git a/generate_payload b/generate_payload
index 39bfddc44a3..ccdf359c53e 100755
--- a/generate_payload
+++ b/generate_payload
@@ -388,7 +388,7 @@ for d in ./data/*/*; do
     for FILE_PATH in "${DATA_DIR}"/*.sig; do
       gpg --verify "${FILE_PATH}"
     done
-    
+
     echo "Generating extension payloads for ${DATA_DIR}"
     shopt -s nullglob
     for EXTENSION_PATH in "${DATA_DIR}/flatcar-"*.raw "${DATA_DIR}/oem-"*.raw; do
@@ -401,7 +401,7 @@ for d in ./data/*/*; do
           --image "${EXTENSION_PATH}" \
           --output "${OUTPUT_PATH}" \
           --private_keys "${PRIVATE_KEYS}" \
-          --public_keys "/mnt/host/source/src/scripts/sdk_container/src/third_party/coreos-overlay/coreos-base/coreos-au-key/files/official-v2.pub.pem" \
+          --public_keys "/mnt/host/source/src/scripts/repos/flatcar-overlay/coreos-base/coreos-au-key/files/official-v2.pub.pem" \
           --keys_separator "+"
       else
         echo "ERROR: Found update payload already: ${OUTPUT_PATH}."
@@ -409,10 +409,10 @@ for d in ./data/*/*; do
       fi
     done
     shopt -u nullglob
-    
+
     echo "Extracting flatcar_production_update.bin.bz2 for ${DATA_DIR}"
     bunzip2 -f -k "${DATA_DIR}/flatcar_production_update.bin.bz2"
-    
+
     echo "Generating generic update payload for ${DATA_DIR}"
     OUTPUT_PATH="${DATA_DIR}/flatcar_production_update.gz"
     if [ ! -f "${OUTPUT_PATH}" ]; then
@@ -422,12 +422,12 @@ for d in ./data/*/*; do
             --kernel "${DATA_DIR}/flatcar_production_image.vmlinuz" \
             --output "${OUTPUT_PATH}" \
             --private_keys "${PRIVATE_KEYS}" \
-            --public_keys "/mnt/host/source/src/scripts/sdk_container/src/third_party/coreos-overlay/coreos-base/coreos-au-key/files/official-v2.pub.pem" \
+            --public_keys "/mnt/host/source/src/scripts/repos/flatcar-overlay/coreos-base/coreos-au-key/files/official-v2.pub.pem" \
             --keys_separator "+"
     else
         echo "ERROR: Found update payload already: ${OUTPUT_PATH}."
         exit 1
     fi
-    
+
     echo "Payload generated: ${OUTPUT_PATH}"
 done
diff --git a/jenkins/manifest.sh b/jenkins/manifest.sh
index 94573f89663..555e4fb35ec 100755
--- a/jenkins/manifest.sh
+++ b/jenkins/manifest.sh
@@ -117,11 +117,11 @@ then
 fi
 if [[ -n "${OVERLAY_REF}" ]]
 then
-        setup_manifest_ref coreos-overlay "${OVERLAY_REF}"
+        setup_manifest_ref flatcar-overlay "${OVERLAY_REF}"
 fi
 if [[ -n "${PORTAGE_REF}" ]]
 then
-        setup_manifest_ref portage-stable "${PORTAGE_REF}"
+        setup_manifest_ref gentoo-subset "${PORTAGE_REF}"
 fi
 
 ln -fns "${FLATCAR_BUILD_ID}.xml" manifest/default.xml
diff --git a/repos/flatcar-overlay/.travis.yml b/repos/flatcar-overlay/.travis.yml
deleted file mode 100644
index 5afcfddad57..00000000000
--- a/repos/flatcar-overlay/.travis.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-# Derived from https://github.com/mrueg/repoman-travis/
-
-sudo: required
-language: python
-python:
-    - pypy
-
-# For some reason portage is defaulting to lbzip2/lbunzip2 here and then complaining when they don't
-# exist, so use plain old b{,un}zip2.
-env:
-    - PORTAGE_VER="2.3.40" PORTAGE_BZIP2_COMMAND="bzip2" PORTAGE_BUNZIP2_COMMAND="bunzip2"
-
-before_install:
-    - sudo apt-get -qq update
-    - pip install lxml pyyaml
-
-before_script: ./.travis/setup_repoman.sh
-
-script:
-    - cd /usr/coreos-overlay
-    - /tmp/portage/portage-${PORTAGE_VER}/repoman/bin/repoman --experimental-repository-modules=y -dx full
diff --git a/repos/flatcar-overlay/.travis/coreos.conf b/repos/flatcar-overlay/.travis/coreos.conf
deleted file mode 100644
index f95be5e1788..00000000000
--- a/repos/flatcar-overlay/.travis/coreos.conf
+++ /dev/null
@@ -1,8 +0,0 @@
-[DEFAULT]
-main-repo = portage-stable
-
-[coreos]
-location = /usr/coreos-overlay
-
-[portage-stable]
-location = /usr/portage
diff --git a/repos/flatcar-overlay/.travis/setup_repoman.sh b/repos/flatcar-overlay/.travis/setup_repoman.sh
deleted file mode 100755
index bfad0f2cf6c..00000000000
--- a/repos/flatcar-overlay/.travis/setup_repoman.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/bash
-
-set -euo pipefail
-
-# Set up directory permissions/portage user and group.
-sudo chmod a+rwX /etc/passwd /etc/group /etc /usr
-echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
-echo "portage::250:portage,travis" >> /etc/group
-
-# Shuffle portage repositories around into the right places.
-mkdir -p /etc/portage/repos.conf /usr/coreos-overlay
-mv * /usr/coreos-overlay/
-mv .git /usr/coreos-overlay/
-git clone https://github.com/coreos/portage-stable /usr/portage/
-cp .travis/coreos.conf /etc/portage/repos.conf/
-ln -s /usr/coreos-overlay/profiles/coreos/amd64/sdk /etc/portage/make.profile
-mkdir -p /usr/portage/metadata/{dtd,xml-schema}
-wget -O /usr/portage/metadata/dtd/metadata.dtd https://www.gentoo.org/dtd/metadata.dtd
-wget -O /usr/portage/metadata/xml-schema/metadata.xsd https://www.gentoo.org/xml-schema/metadata.xsd
-
-# Download portage.
-mkdir /tmp/portage && cd /tmp/portage
-wget -qO - "https://gitweb.gentoo.org/proj/portage.git/snapshot/portage-${PORTAGE_VER}.tar.gz" | tar xz
diff --git a/repos/flatcar-overlay/README.md b/repos/flatcar-overlay/README.md
index 150fb7b6493..0abdb7773c1 100644
--- a/repos/flatcar-overlay/README.md
+++ b/repos/flatcar-overlay/README.md
@@ -3,7 +3,7 @@
 This overlay contains Container Linux specific packages and Gentoo packages
 that differ from their upstream Gentoo versions.
 
-See the [portage-stable](https://github.com/coreos/portage-stable) repo
+See the [gentoo-subset](https://github.com/flatcar/scripts/repos/gentoo-subset) repo
 for packages which do not have Container Linux specific changes.
 
 Licensing information can be found in the respective files, so consult
@@ -29,7 +29,7 @@ development or production image, plus any OEM specific packages.
 that belong in the OEM partition. Any RDEPENDS from these packages should
 be copied to the RDEPENDS in `board-packages` to ensure they are built.
 
-`coreos-base/coreos-oem-*` are metapackages for OEM specific ACIs. 
+`coreos-base/coreos-oem-*` are metapackages for OEM specific ACIs.
 
 # Updating
 
@@ -39,7 +39,7 @@ To update follow the following steps:
   upstream Gentoo, not only resetting the ebuild file but also any additional
   files like patches or downstream additions under `files`.
 * Run `~/trunk/src/scripts/update_ebuilds --portage_stable . CATEGORY/PACKAGE`
-  in the `coreos-overlay` folder to import a new version from upstream Gentoo.
+  in the `flatcar-overlay` folder to import a new version from upstream Gentoo.
   Drop the ebuild files that you don't plan to use.
 * Commit the changes with a message like `CATEGORY/PACKAGE: Sync from Gentoo`,
   and mention the the commit ID in the body (`git show update_ebuilds/master`).
diff --git a/repos/flatcar-overlay/app-containers/docker-cli/README.md b/repos/flatcar-overlay/app-containers/docker-cli/README.md
index 052c52cfc3f..99d075dee49 100644
--- a/repos/flatcar-overlay/app-containers/docker-cli/README.md
+++ b/repos/flatcar-overlay/app-containers/docker-cli/README.md
@@ -1 +1 @@
-This is a temporary overlay over portage-stable until Gentoo catches up with package versions.
+This is a temporary overlay over gentoo-subset until Gentoo catches up with package versions.
diff --git a/repos/flatcar-overlay/app-containers/docker/README.md b/repos/flatcar-overlay/app-containers/docker/README.md
index 052c52cfc3f..99d075dee49 100644
--- a/repos/flatcar-overlay/app-containers/docker/README.md
+++ b/repos/flatcar-overlay/app-containers/docker/README.md
@@ -1 +1 @@
-This is a temporary overlay over portage-stable until Gentoo catches up with package versions.
+This is a temporary overlay over gentoo-subset until Gentoo catches up with package versions.
diff --git a/repos/flatcar-overlay/coreos/user-patches/app-emulation/open-vm-tools/README.md b/repos/flatcar-overlay/coreos/user-patches/app-emulation/open-vm-tools/README.md
index 370ddcdaf48..2afc83bb305 100644
--- a/repos/flatcar-overlay/coreos/user-patches/app-emulation/open-vm-tools/README.md
+++ b/repos/flatcar-overlay/coreos/user-patches/app-emulation/open-vm-tools/README.md
@@ -1,6 +1,6 @@
 The patch for configure.ac is not upstreamable at all, we either need
 to modify the ebuild or the build system. We went with the latter, so
-the ebuild could eventually be moved to portage-stable.
+the ebuild could eventually be moved to gentoo-subset.
 
 Git repo of open-vm-tools has a different layout of files than the
 tarball. The files that are in toplevel directory in tarball (like
diff --git a/repos/flatcar-overlay/coreos/user-patches/sec-policy/flatcar-selinux-patches/README.md b/repos/flatcar-overlay/coreos/user-patches/sec-policy/flatcar-selinux-patches/README.md
index a7cb18f1641..399ae1055c1 100644
--- a/repos/flatcar-overlay/coreos/user-patches/sec-policy/flatcar-selinux-patches/README.md
+++ b/repos/flatcar-overlay/coreos/user-patches/sec-policy/flatcar-selinux-patches/README.md
@@ -5,7 +5,7 @@ The following steps were needed to make these patches:
 - Checkout the appropriate tag:
   - For example `RELEASE_2_20231002`.
 - Apply the Gentoo patch:
-  - See the sec-policy/selinux-base ebuild in portage-stable for the
+  - See the sec-policy/selinux-base ebuild in gentoo-subset for the
     patch tarball URL.
 - Apply our changes:
   - `git am -p2 <OUR_PATCH>` should do the trick. Try adding `-3` flag
diff --git a/repos/flatcar-overlay/metadata/layout.conf b/repos/flatcar-overlay/metadata/layout.conf
index a83f5b12222..0bae123418d 100644
--- a/repos/flatcar-overlay/metadata/layout.conf
+++ b/repos/flatcar-overlay/metadata/layout.conf
@@ -1,4 +1,4 @@
-masters = portage-stable
+masters = gentoo-subset
 thin-manifests = true
 use-manifests = strict
 cache-format = md5-dict
diff --git a/repos/flatcar-overlay/metadata/repoman/repository.yaml b/repos/flatcar-overlay/metadata/repoman/repository.yaml
index d38f71c6db0..aef02f4236f 100644
--- a/repos/flatcar-overlay/metadata/repoman/repository.yaml
+++ b/repos/flatcar-overlay/metadata/repoman/repository.yaml
@@ -15,7 +15,7 @@ repoman_version: 2.3.3
 #   noise than signal.
 # * The `profile` module, among other issues, generates a huge number (>10000) of dependency.bad
 #   errors. This is due to unmodified (or minimally modified) ebuilds from Gentoo upstream that
-#   depend on ebuilds not present in coreos-overlay or portage-stable. These dependencies are hidden
+#   depend on ebuilds not present in flatcar-overlay or gentoo-subset. These dependencies are hidden
 #   behind USE flags or otherwise unused in Container Linux, so the missing ebuilds aren't a
 #   problem, but the amount of noise generated by this module makes it unusable.
 #
diff --git a/repos/flatcar-overlay/profiles/coreos/amd64/parent b/repos/flatcar-overlay/profiles/coreos/amd64/parent
index b15d5c1cf90..947746e3149 100644
--- a/repos/flatcar-overlay/profiles/coreos/amd64/parent
+++ b/repos/flatcar-overlay/profiles/coreos/amd64/parent
@@ -1,2 +1,2 @@
-portage-stable:default/linux/amd64/17.1/no-multilib/hardened
+gentoo-subset:default/linux/amd64/17.1/no-multilib/hardened
 :coreos/base
diff --git a/repos/flatcar-overlay/profiles/coreos/arm64/parent b/repos/flatcar-overlay/profiles/coreos/arm64/parent
index ffc428f7733..3bcde1a5daf 100644
--- a/repos/flatcar-overlay/profiles/coreos/arm64/parent
+++ b/repos/flatcar-overlay/profiles/coreos/arm64/parent
@@ -1,2 +1,2 @@
-portage-stable:default/linux/arm64/17.0/hardened
+gentoo-subset:default/linux/arm64/17.0/hardened
 :coreos/base
diff --git a/repos/flatcar-overlay/profiles/coreos/base/package.accept_keywords b/repos/flatcar-overlay/profiles/coreos/base/package.accept_keywords
index d4a4548aa26..b88475412b1 100644
--- a/repos/flatcar-overlay/profiles/coreos/base/package.accept_keywords
+++ b/repos/flatcar-overlay/profiles/coreos/base/package.accept_keywords
@@ -23,7 +23,7 @@ dev-util/catalyst ~amd64 ~arm64
 =app-containers/podman-5.0.2 ~amd64 ~arm64
 =app-containers/runc-1.1.13 ~amd64 ~arm64
 
-# Seems to be the only available ebuild in portage-stable right now.
+# Seems to be the only available ebuild in gentoo-subset right now.
 =app-crypt/adcli-0.9.2 ~amd64 ~arm64
 
 # Needed by arm64-native SDK
diff --git a/repos/flatcar-overlay/profiles/coreos/base/package.mask b/repos/flatcar-overlay/profiles/coreos/base/package.mask
index 1b68e837616..30601e51512 100644
--- a/repos/flatcar-overlay/profiles/coreos/base/package.mask
+++ b/repos/flatcar-overlay/profiles/coreos/base/package.mask
@@ -11,7 +11,7 @@
 # certificate store provided in NSS rather than the Gentoo/Debian package.
 >=app-misc/ca-certificates-20000000
 
-# Python 3.12 is in portage-stable (currently testing), so avoid picking it
+# Python 3.12 is in gentoo-subset (currently testing), so avoid picking it
 # up. Update this to mask later versions when we switch to 3.11.
 >=dev-lang/python-3.12
 
diff --git a/repos/flatcar-overlay/profiles/coreos/base/package.unmask b/repos/flatcar-overlay/profiles/coreos/base/package.unmask
index 7eebbb56b18..0cd2429bb46 100644
--- a/repos/flatcar-overlay/profiles/coreos/base/package.unmask
+++ b/repos/flatcar-overlay/profiles/coreos/base/package.unmask
@@ -1,4 +1,4 @@
-# Overwrite portage-stable mask. We haven't seen LLVM related problems
+# Overwrite gentoo-subset mask. We haven't seen LLVM related problems
 # with rust so far, so keep using 1.70.0.
 ~dev-lang/rust-1.79.0
 ~virtual/rust-1.79.0
diff --git a/repos/flatcar-overlay/profiles/coreos/base/package.use b/repos/flatcar-overlay/profiles/coreos/base/package.use
index b4cba830553..993a026d626 100644
--- a/repos/flatcar-overlay/profiles/coreos/base/package.use
+++ b/repos/flatcar-overlay/profiles/coreos/base/package.use
@@ -146,7 +146,7 @@ net-analyzer/tcpdump -ssl -smi -samba
 # selinux: to find files with a particular SElinux label
 sys-apps/findutils selinux
 
-# Flatcar defaults formerly defined in coreos-overlay ebuilds
+# Flatcar defaults formerly defined in flatcar-overlay ebuilds
 app-containers/containerd btrfs device-mapper
 app-containers/docker btrfs device-mapper overlay seccomp
 app-containers/docker-cli hardened
diff --git a/repos/flatcar-overlay/profiles/coreos/base/package.use.mask b/repos/flatcar-overlay/profiles/coreos/base/package.use.mask
index 0e3644833e2..2bffe822e76 100644
--- a/repos/flatcar-overlay/profiles/coreos/base/package.use.mask
+++ b/repos/flatcar-overlay/profiles/coreos/base/package.use.mask
@@ -14,7 +14,7 @@ sys-libs/ncurses cxx
 # stage1, because ncurses >= 6.2_p20210619 which does not have the USE
 # flag at all.
 # To fix that, exclude the unicode USE flag from packages.use.force list,
-# which is defined in portage-stable.
+# which is defined in gentoo-subset.
 app-editors/nano unicode
 
 # Pulls dev-python/sphinx, which in turn pulls a lot of other python stuff.
diff --git a/repos/flatcar-overlay/profiles/coreos/base/parent b/repos/flatcar-overlay/profiles/coreos/base/parent
index e00b432785f..df895ded22d 100644
--- a/repos/flatcar-overlay/profiles/coreos/base/parent
+++ b/repos/flatcar-overlay/profiles/coreos/base/parent
@@ -1,2 +1,2 @@
-portage-stable:targets/systemd
+gentoo-subset:targets/systemd
 :features/systemd
diff --git a/repos/flatcar-overlay/profiles/coreos/base/profile.bashrc b/repos/flatcar-overlay/profiles/coreos/base/profile.bashrc
index 7abb2c7af01..a9cc9b10c27 100644
--- a/repos/flatcar-overlay/profiles/coreos/base/profile.bashrc
+++ b/repos/flatcar-overlay/profiles/coreos/base/profile.bashrc
@@ -3,7 +3,7 @@
 CROS_BUILD_BOARD_TREE="${SYSROOT}/build"
 CROS_BUILD_BOARD_BIN="${CROS_BUILD_BOARD_TREE}/bin"
 
-CROS_ADDONS_TREE="/mnt/host/source/src/third_party/coreos-overlay/coreos"
+CROS_ADDONS_TREE="/mnt/host/source/src/scripts/repos/flatcar-overlay/coreos"
 
 # Are we merging for the board sysroot, or for the cros sdk, or for
 # the target hardware?  Returns a string:
diff --git a/repos/flatcar-overlay/profiles/coreos/base/profile.bashrc.slsa-provenance b/repos/flatcar-overlay/profiles/coreos/base/profile.bashrc.slsa-provenance
index 66926477480..db59ac8372d 100644
--- a/repos/flatcar-overlay/profiles/coreos/base/profile.bashrc.slsa-provenance
+++ b/repos/flatcar-overlay/profiles/coreos/base/profile.bashrc.slsa-provenance
@@ -123,7 +123,7 @@ __slsa_provenance_resolved_dependencies() {
     einfo "    Provenance: recording ebuild material (input) '${spm_repo}/${ebuild}'"
 
     local repo_uri uri
-    repo_uri="https://raw.githubusercontent.com/flatcar/scripts/${scripts_hash}/sdk_container/src/third_party/${spm_repo}"
+    repo_uri="https://raw.githubusercontent.com/flatcar/scripts/${scripts_hash}/repos/${spm_repo}"
     uri="${repo_uri}/${ebuild}"
     __slsa_rd_printf "${uri}" 'sha1' "${csum}"
 
diff --git a/repos/flatcar-overlay/profiles/coreos/targets/generic/use.force b/repos/flatcar-overlay/profiles/coreos/targets/generic/use.force
index f29fb18c73e..f6caa9f531a 100644
--- a/repos/flatcar-overlay/profiles/coreos/targets/generic/use.force
+++ b/repos/flatcar-overlay/profiles/coreos/targets/generic/use.force
@@ -1,4 +1,4 @@
 # We don't have a separate /{bin,lib} and /usr/{bin,lib}. But the base
-# profile in portage-stable forces split-usr, so here we unforce it
+# profile in gentoo-subset forces split-usr, so here we unforce it
 # and in use.mask we mask it.
 -split-usr
diff --git a/repos/flatcar-overlay/profiles/coreos/targets/generic/use.mask b/repos/flatcar-overlay/profiles/coreos/targets/generic/use.mask
index 9a467dab418..8bfa1d9b89d 100644
--- a/repos/flatcar-overlay/profiles/coreos/targets/generic/use.mask
+++ b/repos/flatcar-overlay/profiles/coreos/targets/generic/use.mask
@@ -1,4 +1,4 @@
 # We don't have a separate /{bin,lib} and /usr/{bin,lib}. But the base
-# profile in portage-stable forces split-usr, so in use.force we
+# profile in gentoo-subset forces split-usr, so in use.force we
 # unforce it and here we mask it.
 split-usr
diff --git a/repos/flatcar-overlay/profiles/repo_name b/repos/flatcar-overlay/profiles/repo_name
index cf96a73002d..bbdbb6051a9 100644
--- a/repos/flatcar-overlay/profiles/repo_name
+++ b/repos/flatcar-overlay/profiles/repo_name
@@ -1 +1 @@
-coreos-overlay
+flatcar-overlay
diff --git a/repos/flatcar-overlay/sys-apps/ignition/files/README.md b/repos/flatcar-overlay/sys-apps/ignition/files/README.md
index f040413103d..ec7e5e4a5fc 100644
--- a/repos/flatcar-overlay/sys-apps/ignition/files/README.md
+++ b/repos/flatcar-overlay/sys-apps/ignition/files/README.md
@@ -12,7 +12,7 @@ For this, we can just apply the current patches and fix any broken stuff:
 git clone https://github.com/coreos/ignition
 cd ignition
 git checkout "${RELEASE}"
-git am --3way /path/to/coreos-overlay/sys-apps/ignition/files/00*
+git am --3way /path/to/flatcar-overlay/sys-apps/ignition/files/00*
 ```
 
 Once done, we can generate the new set of patches:
@@ -20,9 +20,9 @@ Once done, we can generate the new set of patches:
 git format-patch "${RELEASE}"
 ```
 
-Copy the new patches to `::coreos-overlay`
+Copy the new patches to `::flatcar-overlay`
 ```
-cp 00* /path/to/coreos-overlay/sys-apps/ignition/files/
+cp 00* /path/to/flatcar-overlay/sys-apps/ignition/files/
 ```
 
 :warning: We might need to update the applied patches' names in the Ignition ebuild.
diff --git a/repos/flatcar-overlay/sys-auth/pambase/README.md b/repos/flatcar-overlay/sys-auth/pambase/README.md
index 4b3cb979e10..382116d6a50 100644
--- a/repos/flatcar-overlay/sys-auth/pambase/README.md
+++ b/repos/flatcar-overlay/sys-auth/pambase/README.md
@@ -1,5 +1,5 @@
 This is a not-really-a-fork of gentoo's `sys-auth/pambase`
-package. The main reasons for having it in `coreos-overlay` are:
+package. The main reasons for having it in `flatcar-overlay` are:
 
 1. The `sys-apps/baselayout` package replaced it, so this package
    became a stub.
diff --git a/repos/flatcar-overlay/sys-boot/grub/files/grub-2.06-add-gpt-partition-scheme.patch b/repos/flatcar-overlay/sys-boot/grub/files/grub-2.06-add-gpt-partition-scheme.patch
index cef57e856a9..dad7b2d776f 100644
--- a/repos/flatcar-overlay/sys-boot/grub/files/grub-2.06-add-gpt-partition-scheme.patch
+++ b/repos/flatcar-overlay/sys-boot/grub/files/grub-2.06-add-gpt-partition-scheme.patch
@@ -13,7 +13,7 @@ gptrepair, search commands.
 
 The patch is prepared using the coreos/grub PRs, picking the only
 required ones, and dropping the others. The README.md file in the
-coreos-overlay/sys-boot/grub/ contains more contexual information
+flatcar-overlay/sys-boot/grub/ contains more contexual information
 along with the commits used to create the patch.
 
 Authored-by: Michael Marineau <michael.marineau@coreos.com>
diff --git a/repos/flatcar-overlay/sys-boot/grub/files/grub-2.06-add-verity-hash.patch b/repos/flatcar-overlay/sys-boot/grub/files/grub-2.06-add-verity-hash.patch
index ed892d90dd2..d4c748a1507 100644
--- a/repos/flatcar-overlay/sys-boot/grub/files/grub-2.06-add-verity-hash.patch
+++ b/repos/flatcar-overlay/sys-boot/grub/files/grub-2.06-add-verity-hash.patch
@@ -8,7 +8,7 @@ system via the kernel command line
 
 The patch is prepared using the coreos/grub PRs, picking the only
 required ones, and dropping the others. The README.md file in the
-coreos-overlay/sys-boot/grub/ contains more contexual information
+flatcar-overlay/sys-boot/grub/ contains more contexual information
 along with the commits used to create the patch.
 
 Authored-by: Matthew Garrett <mjg59@coreos.com>
diff --git a/repos/flatcar-overlay/sys-fs/lvm2/README.md b/repos/flatcar-overlay/sys-fs/lvm2/README.md
index 379916ebf07..1c9314e2f41 100644
--- a/repos/flatcar-overlay/sys-fs/lvm2/README.md
+++ b/repos/flatcar-overlay/sys-fs/lvm2/README.md
@@ -1,7 +1,7 @@
 We keep this package in overlay, because we carry one extra patch for
 the unit generator. It was posted upstream and remains
 unacknowledged. We could try sending the patch to gentoo, so we can
-bring this package back to portage-stable.
+bring this package back to gentoo-subset.
 
 The lvm2-activation(-early).service was triggered multiple times which
 if done too quickly leads to a failure like this:
diff --git a/repos/gentoo-subset/README.md b/repos/gentoo-subset/README.md
index 2d42d1b212b..db0faea5564 100644
--- a/repos/gentoo-subset/README.md
+++ b/repos/gentoo-subset/README.md
@@ -22,7 +22,7 @@ If you'd prefer to use a local copy of the portage tree, you can point
 Licensing information can be found in the respective files, so consult
 them directly. Most ebuilds are licensed under the GPL version 2.
 
-Upstream Gentoo sources: http://sources.gentoo.org/gentoo-x86/
+Upstream Gentoo sources: https://gitweb.gentoo.org/repo/gentoo.git/
 
 # Removing packages
 
@@ -55,7 +55,7 @@ Furthermore, the SDK bootstrapping process uses a list of packages defined the b
 file. Install `dev-util/catalyst` and run `/usr/lib64/catalyst/targets/stage1/build.py` to get a list of packages
 needed for the boostrapping process, then run `emerge --emptytree` on that list.
 
-A package's ebuild must be removed from `portage-stable` _and_ the package must be removed locally. If only the
+A package's ebuild must be removed from `gentoo-subset` _and_ the package must be removed locally. If only the
 ebuild is removed, the package will be silently elided in the `emerge --emptytree` dependency list.
 To see if there are any packages installed without ebuilds run `eix -tTc`. There are no `eix-<arch>-usr` wrappers, so double
 check the packages are also unmerged via the `emerge-<arch>-usr` commands. Make sure to run
@@ -72,9 +72,9 @@ See [this bug](https://bugs.gentoo.org/127956).
 ## grep, git grep, repo grep, ripgrep, find, etc
 
 Use your favorite grep variant to see if the package is used anywhere. Good places to double check are
-coreos-overlay, manifest, scripts, and portage-stable, as well as anything specific to the package.
+flatcar-overlay, manifest, scripts, and gentoo-subset, as well as anything specific to the package.
 
-Be sure to check `coreos-overlay` to ensure there are no use flags, accept_keywords, or other leftover bits
+Be sure to check `flatcar-overlay` to ensure there are no use flags, accept_keywords, or other leftover bits
 relating to the package being removed.
 
 ## Updating the metadata cache
@@ -82,9 +82,9 @@ relating to the package being removed.
 If you remove a package, make sure to delete the corresponding files in
 metadata/md5cache, or run use egencache to do it for you:
 ```
-    egencache --update --repo portage-stable
+    egencache --update --repo gentoo-subset
 ```
-There is also `scripts/update_metadata` which will update both `portage-stable` and `coreos-overlay`
+There is also `scripts/update_metadata` which will update both `gentoo-subset` and `flatcar-overlay`
 and optionally generate a commit message.
 
 ## Testing changes
diff --git a/repos/gentoo-subset/profiles/repo_name b/repos/gentoo-subset/profiles/repo_name
index 316c11ecc49..34eeccda8cf 100644
--- a/repos/gentoo-subset/profiles/repo_name
+++ b/repos/gentoo-subset/profiles/repo_name
@@ -1 +1 @@
-portage-stable
+gentoo-subset
diff --git a/sdk_container/src/third_party/coreos-overlay b/sdk_container/src/third_party/coreos-overlay
new file mode 120000
index 00000000000..ef693a03b09
--- /dev/null
+++ b/sdk_container/src/third_party/coreos-overlay
@@ -0,0 +1 @@
+../../../repos/flatcar-overlay
\ No newline at end of file
diff --git a/sdk_container/src/third_party/portage-stable b/sdk_container/src/third_party/portage-stable
new file mode 120000
index 00000000000..2b517835535
--- /dev/null
+++ b/sdk_container/src/third_party/portage-stable
@@ -0,0 +1 @@
+../../../repos/gentoo-subset
\ No newline at end of file
diff --git a/sdk_container/src/third_party/prefix-overlay/metadata/layout.conf b/sdk_container/src/third_party/prefix-overlay/metadata/layout.conf
index a83f5b12222..0bae123418d 100644
--- a/sdk_container/src/third_party/prefix-overlay/metadata/layout.conf
+++ b/sdk_container/src/third_party/prefix-overlay/metadata/layout.conf
@@ -1,4 +1,4 @@
-masters = portage-stable
+masters = gentoo-subset
 thin-manifests = true
 use-manifests = strict
 cache-format = md5-dict
diff --git a/sdk_container/src/third_party/prefix-overlay/skel/etc/portage/repos.conf/coreos.conf b/sdk_container/src/third_party/prefix-overlay/skel/etc/portage/repos.conf/coreos.conf
index d73d1434874..978e210ca26 100644
--- a/sdk_container/src/third_party/prefix-overlay/skel/etc/portage/repos.conf/coreos.conf
+++ b/sdk_container/src/third_party/prefix-overlay/skel/etc/portage/repos.conf/coreos.conf
@@ -1,8 +1,8 @@
 [DEFAULT]
-main-repo = portage-stable
+main-repo = gentoo-subset
 
-[coreos]
-location = /mnt/host/source/src/third_party/coreos-overlay
+[flatcar-overlay]
+location = /mnt/host/source/src/scripts/repos/flatcar-overlay
 
-[portage-stable]
-location = /mnt/host/source/src/third_party/portage-stable
+[gentoo-subset]
+location = /mnt/host/source/src/scripts/repos/gentoo-subset
diff --git a/sdk_lib/sdk_entry.sh b/sdk_lib/sdk_entry.sh
index 9ebc141771b..8cc441db0d1 100755
--- a/sdk_lib/sdk_entry.sh
+++ b/sdk_lib/sdk_entry.sh
@@ -10,13 +10,8 @@ fi
 
 chown -R sdk:sdk /home/sdk
 
-# Fix up SDK repo configuration to use the new coreos-overlay name.
-sed -i -r 's/^\[coreos\]/[coreos-overlay]/' /etc/portage/repos.conf/coreos.conf 2>/dev/null
-sed -i -r '/^masters =/s/\bcoreos(\s|$)/coreos-overlay\1/g' /usr/local/portage/crossdev/metadata/layout.conf 2>/dev/null
-
-# Check if the OS image version we're working on is newer than
-#  the SDK container version and if it is, update the boards
-#  chroot portage conf to point to the correct binhost.
+# Check if the OS image version we're working on is newer than the SDK container
+# version and if it is, update the configuration for the SDK and the boards.
 (
     source /etc/lsb-release # SDK version in DISTRIB_RELEASE
     source /mnt/host/source/.repo/manifests/version.txt # OS image version in FLATCAR_VERSION_ID
@@ -29,6 +24,9 @@ sed -i -r '/^masters =/s/\bcoreos(\s|$)/coreos-overlay\1/g' /usr/local/portage/c
     fi
 
     if [ "${version}" != "${DISTRIB_RELEASE}" ] ; then
+        # Fix up SDK repo configuration to use the new layout.
+        sudo su sdk -l -c "/home/sdk/trunk/src/scripts/update_chroot --setuponly"
+
         for target in amd64-usr arm64-usr; do
             if [ ! -d "/build/$target" ] ; then
                 continue
diff --git a/sdk_lib/sdk_init_selfcontained.sh b/sdk_lib/sdk_init_selfcontained.sh
index c5006f841e8..188a21df12b 100755
--- a/sdk_lib/sdk_init_selfcontained.sh
+++ b/sdk_lib/sdk_init_selfcontained.sh
@@ -30,8 +30,4 @@ function clone_version() {
 sudo chown -R sdk:sdk /home/sdk /mnt/host/source
 
 version="$(source /mnt/host/source/.repo/manifests/version.txt; echo $FLATCAR_VERSION)"
-
-rmdir /mnt/host/source/src/third_party
-ln -s /mnt/host/source/src/scripts/sdk_container/src/third_party /mnt/host/source/src/
-
 clone_version scripts /home/sdk/trunk/src/scripts "$version"
diff --git a/setup_board b/setup_board
index bba9251ab7e..9984b0ed496 100755
--- a/setup_board
+++ b/setup_board
@@ -154,8 +154,8 @@ fi
 get_board_and_variant $FLAGS_board $FLAGS_variant
 
 # Locations we will need
-COREOS_OVERLAY="${REPO_ROOT}/src/third_party/coreos-overlay"
-COREOS_CONFIG="${COREOS_OVERLAY}/coreos/config"
+FLATCAR_OVERLAY="${SCRIPTS_DIR}/repos/flatcar-overlay"
+COREOS_CONFIG="${FLATCAR_OVERLAY}/coreos/config"
 BOARD_ROOT="/build/${BOARD_VARIANT}"
 BOARD_ETC="${BOARD_ROOT}/etc"
 BOARD_ARCH=$(get_board_arch "$BOARD")
@@ -232,10 +232,10 @@ if [[ ! -L "${BOARD_ROOT}/packages" ]]; then
 fi
 
 info "Configuring portage in ${BOARD_ROOT}"
-sudo mkdir -p "${BOARD_ETC}/portage/"{profile,repos.conf}
-sudo ln -sfT "$(portageq get_repo_path / coreos-overlay)/coreos/user-patches" \
+sudo mkdir -p "${BOARD_ETC}/portage/profile
+sudo ln -sfT "$(portageq get_repo_path / flatcar-overlay)/coreos/user-patches" \
    "${BOARD_ETC}/portage/patches"
-sudo cp /etc/portage/repos.conf/* "${BOARD_ETC}"/portage/repos.conf/
+sudo rsync --archive --delete /etc/portage/repos.conf/ "${BOARD_ETC}"/portage/repos.conf/
 sudo ROOT="${BOARD_ROOT}" eselect profile set --force "${PORTAGE_PROFILE}"
 
 # Cleanup/migrate from older make.conf files
diff --git a/setup_prefix b/setup_prefix
index dd0c8ade678..20f451f6c5b 100755
--- a/setup_prefix
+++ b/setup_prefix
@@ -96,7 +96,7 @@ function check_force_dirs() {
 #
 
 set_prefix_vars "${name}" "${prefix}"
-prefix_repo="$(dirname "$(EPREFIX="" portageq get_repo_path / portage-stable)")/prefix-overlay"
+prefix_repo="$(dirname "$(EPREFIX="" portageq get_repo_path / gentoo-subset)")/prefix-overlay"
 
 if [ "${FLAGS_uninstall}" = "${FLAGS_TRUE}" ] ; then
   warn "Removing prefix '${name}' and all associated direcroties and wrappers."
diff --git a/tag_release b/tag_release
index f97ee53aac4..291f1dbe140 100755
--- a/tag_release
+++ b/tag_release
@@ -37,7 +37,7 @@ if [[ "${DEFAULT_MANIFEST}" != master.xml ]]; then
     DEFAULT_MAJOR=${CURRENT_VERSION[0]}
     DEFAULT_BRANCH=${FLAGS_TRUE}
 else
-    DEFAULT_BRANCH_PROJECTS='coreos-overlay portage-stable scripts'
+    DEFAULT_BRANCH_PROJECTS='flatcar-overlay gentoo-subset scripts'
 fi
 
 # Increment $MINOR if we already made a major release.
diff --git a/update_chroot b/update_chroot
index 2a9cbeb3212..15f5aa2e6ef 100755
--- a/update_chroot
+++ b/update_chroot
@@ -61,10 +61,10 @@ if [[ -n "${FLAGS_dev_builds_sdk}" ]]; then
   FLATCAR_DEV_BUILDS_SDK="${FLAGS_dev_builds_sdk}"
 fi
 
-PORTAGE_STABLE_OVERLAY="${REPO_ROOT}/src/third_party/portage-stable"
+GENTOO_SUBSET_OVERLAY="${SCRIPTS_DIR}/repos/gentoo-subset"
 CROSSDEV_OVERLAY="/usr/local/portage/crossdev"
-COREOS_OVERLAY="${REPO_ROOT}/src/third_party/coreos-overlay"
-COREOS_CONFIG="${COREOS_OVERLAY}/coreos/config"
+FLATCAR_OVERLAY="${SCRIPTS_DIR}/repos/flatcar-overlay"
+COREOS_CONFIG="${FLATCAR_OVERLAY}/coreos/config"
 PORTAGE_BINHOST="$FLAGS_binhost $(get_sdk_binhost)"
 
 # PORTAGE_USERNAME may already be in the env but set just to be safe.
@@ -83,7 +83,7 @@ info "Setting up portage..."
 sudo mkdir -p "${REPO_CACHE_DIR}/distfiles"
 sudo chown "${PORTAGE_USERNAME}:portage" "${REPO_CACHE_DIR}/distfiles"
 sudo mkdir -p /etc/portage/repos.conf /var/lib/portage/pkgs
-sudo ln -sfT "${COREOS_OVERLAY}/coreos/user-patches" '/etc/portage/patches'
+sudo ln -sfT "${FLATCAR_OVERLAY}/coreos/user-patches" '/etc/portage/patches'
 sudo touch /etc/portage/make.conf.user
 
 sudo_clobber "/etc/portage/make.conf" <<EOF
@@ -103,53 +103,20 @@ EMERGE_DEFAULT_OPTS="--verbose --oneshot"
 source "/etc/portage/make.conf.user"
 EOF
 
-sudo_clobber "/etc/portage/repos.conf/portage-stable.conf" <<EOF
+sudo_clobber "/etc/portage/repos.conf/gentoo-subset.conf" <<EOF
 [DEFAULT]
-main-repo = portage-stable
+main-repo = gentoo-subset
 
-[portage-stable]
-location = ${PORTAGE_STABLE_OVERLAY}
+[gentoo-subset]
+location = ${GENTOO_SUBSET_OVERLAY}
 EOF
 
-sudo_clobber "/etc/portage/repos.conf/coreos-overlay.conf" <<EOF
-[coreos-overlay]
-location = ${COREOS_OVERLAY}
+sudo_clobber "/etc/portage/repos.conf/flatcar-overlay.conf" <<EOF
+[flatcar-overlay]
+location = ${FLATCAR_OVERLAY}
 EOF
 
-# Automatically symlink any provided portage repo configurations into
-# the appropriate destination directory from "config/portage/repos".
-# CAUTON: Any repo configuration files with the same name, will be silently
-# relinked to the last file found.
-# Automatic file renaming to avoid this is challenging as it has to deal with
-# the case where we actually do want the files overwritten and so is outside
-# the scope of this function for now.
-# If your taking advantage of this functionality in the build toolchain
-# you probably found out about it from these code comments so we can assume
-# for now at least, that you have been somewhat warned.
-
-# If any directories match config/portage/repos/*/repos.conf
-if [[ -n $(sudo find /mnt/host/source/config/portage/repos \
-  -maxdepth 2 -mindepth 2 -type d -name "repos.conf") ]]; then
-  # If any files match config/portage/repos/*/repos.conf/*
-  if [[ -n $(sudo find /mnt/host/source/config/portage/repos \
-    -maxdepth 3 -mindepth 3 -path "*/repos.conf/*" -type f) ]]; then
-    info "Symlinking portage repo configuration files into repos.conf dir..."
-    # Do not name any of your repo configs "coreos-overlay.conf" bad things will happen.
-    # We abort if any file matches config/portage/repos/*/repos.conf/coreos-overlay.conf
-    if [[ -n $(sudo find /mnt/host/source/config/portage/repos \
-      -maxdepth 3 -mindepth 3 -path "*/repos.conf/*" -name "coreos-overlay.conf") ]]; then
-      die_notrace "One of the portage repo configuration files to be symlinked is " \
-        "named \"coreos-overlay.conf\" which will conflict with the main configuation file " \
-        "called \"coreos-overlay.conf\" which is created during the chroot build process."
-    fi
-    # We run through all the other files matching config/portage/repos/*/repos.conf/*
-    # and symlink them to the right place for portage.
-    sudo find /mnt/host/source/config/portage/repos \
-      -maxdepth 3 -mindepth 3 -path "*/repos.conf/*" -type f \
-      -exec bash -c 'ln -sf {} /etc/portage/repos.conf/$(basename {})' \;
-  fi
-fi
-
+sudo rm -f /etc/portage/repos.conf/{portage-stable,coreos-overlay,coreos}.conf
 sudo eselect profile set --force "$(get_sdk_profile)"
 
 # Create crossdev repo_name and metadata
diff --git a/update_distfiles b/update_distfiles
index 00abd37fab8..eb4e6682e35 100755
--- a/update_distfiles
+++ b/update_distfiles
@@ -26,7 +26,7 @@ eval set -- "${FLAGS_ARGV}"
 switch_to_strict_mode
 
 if [[ $# -eq 0 ]]; then
-    eval set -- portage-stable coreos-overlay
+    eval set -- gentoo-subset flatcar-overlay
 fi
 
 GSUTIL_OPTS=
diff --git a/update_ebuilds b/update_ebuilds
index 07eab2f9c44..2ca3ce0c7cd 100755
--- a/update_ebuilds
+++ b/update_ebuilds
@@ -12,14 +12,14 @@ RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force
 
 DEFINE_string portage "git" \
     "Path to a local portage tree or 'rsync' or 'git' to fetch from remote."
-DEFINE_string portage_stable "${SRC_ROOT}/third_party/portage-stable" \
-    "Path to the portage-stable git checkout."
+DEFINE_string gentoo_subset "${SCRIPT_ROOT}/repos/gentoo-subset" \
+    "Path to the gentoo-subset git checkout."
 DEFINE_string git "https://github.com/gentoo/gentoo.git" \
     "git location for the gentoo portage repo (for use with --portage=git)"
 DEFINE_string rsync "rsync://rsync.gentoo.org/gentoo-portage" \
     "Rsync location for gentoo-portage to use with --portage=rsync"
 DEFINE_boolean commit ${FLAGS_FALSE} \
-    "Commit all changes after updating portage-stable."
+    "Commit all changes after updating gentoo-subset."
 
 
 # Parse flags
@@ -36,7 +36,7 @@ if [[ -z "$*" ]]; then
     die "No packages provided"
 fi
 
-cd "$FLAGS_portage_stable"
+cd "$FLAGS_gentoo_subset"
 
 for pkg in "$@"; do
     # Only allow packages, not categories or the whole tree
@@ -68,7 +68,7 @@ for pkg in "$@"; do
 
     # Make sure we don't change the repo name to 'gentoo'
     if [[ "$pkg" =~ ^profiles ]]; then
-        echo portage-stable > profiles/repo_name
+        echo gentoo-subset > profiles/repo_name
     fi
 
     git add -A "$pkg"
@@ -90,4 +90,3 @@ EOF
 else
     git status
 fi
-
diff --git a/update_metadata b/update_metadata
index fd9972d4fd5..ab648e54a5e 100755
--- a/update_metadata
+++ b/update_metadata
@@ -16,7 +16,7 @@ eval set -- "${FLAGS_ARGV}"
 switch_to_strict_mode
 
 if [[ $# -eq 0 ]]; then
-    eval set -- portage-stable coreos-overlay
+    eval set -- gentoo-subset flatcar-overlay
 fi
 
 update_overlay() {
diff --git a/update_sdk_container_image b/update_sdk_container_image
index b11f383f573..60b9971a2d2 100755
--- a/update_sdk_container_image
+++ b/update_sdk_container_image
@@ -23,7 +23,7 @@ cleanup=""
 usage() {
     echo "  $0 - Update SDK container image."
     echo "       Create a new container image based on the current SDK ($base_sdk_version)"
-    echo "       with current changes from coreos-overlay and portage-stable."
+    echo "       with current changes from flatcar-overlay and gentoo-subset."
     echo
     echo "       Just like build_sdk_container_image the resulting container comes in 3 flavours:"
     echo "        1.    flatcar-sdk-all - includes both ARM64 and AMD64 support"