diff --git a/Dockerfile b/Dockerfile
index 063595d..e73a8c4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -36,7 +36,7 @@ RUN \
   sed -i -e 's/^root::/root:!:/' /root-out/etc/shadow
 
 # set version for s6 overlay
-ARG S6_OVERLAY_VERSION="3.1.0.1"
+ARG S6_OVERLAY_VERSION="3.1.2.1"
 ARG S6_OVERLAY_ARCH="x86_64"
 
 # add s6 overlay
@@ -51,13 +51,6 @@ RUN tar -C /root-out -Jxpf /tmp/s6-overlay-symlinks-noarch.tar.xz
 ADD https://github.com/just-containers/s6-overlay/releases/download/v${S6_OVERLAY_VERSION}/s6-overlay-symlinks-arch.tar.xz /tmp
 RUN tar -C /root-out -Jxpf /tmp/s6-overlay-symlinks-arch.tar.xz
 
-# copy ci-checks
-COPY ci-check/ /root-out/package/admin/s6-overlay-${S6_OVERLAY_VERSION}/etc/s6-rc/sources/top/contents.d
-
-# patch cont-init for docker-mods
-COPY patch/ /tmp/patch
-RUN  patch -u /root-out/package/admin/s6-overlay-${S6_OVERLAY_VERSION}/etc/s6-linux-init/skel/rc.init -i /tmp/patch/package/admin/s6-overlay-@VERSION@/etc/s6-linux-init/skel/rc.init.patch
-
 # Runtime stage
 FROM scratch
 COPY --from=rootfs-stage /root-out/ /
@@ -70,7 +63,9 @@ LABEL maintainer="TheLamer"
 ENV PS1="$(whoami)@$(hostname):$(pwd)\\$ " \
 HOME="/root" \
 TERM="xterm" \
-S6_CMD_WAIT_FOR_SERVICES_MAXTIME="0"
+S6_CMD_WAIT_FOR_SERVICES_MAXTIME="0" \
+S6_VERBOSITY=1 \
+S6_STAGE2_HOOK=/docker-mods
 
 RUN \
   echo "**** install runtime packages ****" && \
diff --git a/Dockerfile.aarch64 b/Dockerfile.aarch64
index 03c98fd..4bb7c91 100644
--- a/Dockerfile.aarch64
+++ b/Dockerfile.aarch64
@@ -36,7 +36,7 @@ RUN \
   sed -i -e 's/^root::/root:!:/' /root-out/etc/shadow
 
 # set version for s6 overlay
-ARG S6_OVERLAY_VERSION="3.1.0.1"
+ARG S6_OVERLAY_VERSION="3.1.2.1"
 ARG S6_OVERLAY_ARCH="aarch64"
 
 # add s6 overlay
@@ -51,13 +51,6 @@ RUN tar -C /root-out -Jxpf /tmp/s6-overlay-symlinks-noarch.tar.xz
 ADD https://github.com/just-containers/s6-overlay/releases/download/v${S6_OVERLAY_VERSION}/s6-overlay-symlinks-arch.tar.xz /tmp
 RUN tar -C /root-out -Jxpf /tmp/s6-overlay-symlinks-arch.tar.xz
 
-# copy ci-checks
-COPY ci-check/ /root-out/package/admin/s6-overlay-${S6_OVERLAY_VERSION}/etc/s6-rc/sources/top/contents.d
-
-# patch cont-init for docker-mods
-COPY patch/ /tmp/patch
-RUN  patch -u /root-out/package/admin/s6-overlay-${S6_OVERLAY_VERSION}/etc/s6-linux-init/skel/rc.init -i /tmp/patch/package/admin/s6-overlay-@VERSION@/etc/s6-linux-init/skel/rc.init.patch
-
 # Runtime stage
 FROM scratch
 COPY --from=rootfs-stage /root-out/ /
@@ -70,7 +63,9 @@ LABEL maintainer="TheLamer"
 ENV PS1="$(whoami)@$(hostname):$(pwd)\\$ " \
 HOME="/root" \
 TERM="xterm" \
-S6_CMD_WAIT_FOR_SERVICES_MAXTIME="0"
+S6_CMD_WAIT_FOR_SERVICES_MAXTIME="0" \
+S6_VERBOSITY=1 \
+S6_STAGE2_HOOK=/docker-mods
 
 RUN \
   echo "**** install runtime packages ****" && \
diff --git a/Dockerfile.armhf b/Dockerfile.armhf
index e46f1f3..02336c7 100644
--- a/Dockerfile.armhf
+++ b/Dockerfile.armhf
@@ -36,7 +36,7 @@ RUN \
   sed -i -e 's/^root::/root:!:/' /root-out/etc/shadow
 
 # set version for s6 overlay
-ARG S6_OVERLAY_VERSION="3.1.0.1"
+ARG S6_OVERLAY_VERSION="3.1.2.1"
 ARG S6_OVERLAY_ARCH="armhf"
 
 # add s6 overlay
@@ -51,13 +51,6 @@ RUN tar -C /root-out -Jxpf /tmp/s6-overlay-symlinks-noarch.tar.xz
 ADD https://github.com/just-containers/s6-overlay/releases/download/v${S6_OVERLAY_VERSION}/s6-overlay-symlinks-arch.tar.xz /tmp
 RUN tar -C /root-out -Jxpf /tmp/s6-overlay-symlinks-arch.tar.xz
 
-# copy ci-checks
-COPY ci-check/ /root-out/package/admin/s6-overlay-${S6_OVERLAY_VERSION}/etc/s6-rc/sources/top/contents.d
-
-# patch cont-init for docker-mods
-COPY patch/ /tmp/patch
-RUN  patch -u /root-out/package/admin/s6-overlay-${S6_OVERLAY_VERSION}/etc/s6-linux-init/skel/rc.init -i /tmp/patch/package/admin/s6-overlay-@VERSION@/etc/s6-linux-init/skel/rc.init.patch
-
 # Runtime stage
 FROM scratch
 COPY --from=rootfs-stage /root-out/ /
@@ -70,7 +63,9 @@ LABEL maintainer="TheLamer"
 ENV PS1="$(whoami)@$(hostname):$(pwd)\\$ " \
 HOME="/root" \
 TERM="xterm" \
-S6_CMD_WAIT_FOR_SERVICES_MAXTIME="0"
+S6_CMD_WAIT_FOR_SERVICES_MAXTIME="0" \
+S6_VERBOSITY=1 \
+S6_STAGE2_HOOK=/docker-mods
 
 RUN \
   echo "**** install runtime packages ****" && \
diff --git a/patch/package/admin/s6-overlay-@VERSION@/etc/s6-linux-init/skel/rc.init.patch b/patch/package/admin/s6-overlay-@VERSION@/etc/s6-linux-init/skel/rc.init.patch
deleted file mode 100644
index b01a7f0..0000000
--- a/patch/package/admin/s6-overlay-@VERSION@/etc/s6-linux-init/skel/rc.init.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- rc.init	2022-05-20 17:41:11.195721000 -0500
-+++ rc.init.patched	2022-05-20 17:41:37.646586700 -0500
-@@ -6,6 +6,8 @@
-   s6-chmod 0755 /run/s6/container_environment
- fi
- 
-+/docker-mods
-+
- if profile=`printcontenv S6_RUNTIME_PROFILE` ; then
-   etc="/etc/cont-profile.d/$profile"
- else
diff --git a/root/docker-mods b/root/docker-mods
index eae1e60..d69b801 100755
--- a/root/docker-mods
+++ b/root/docker-mods
@@ -1,6 +1,12 @@
 #!/usr/bin/with-contenv bash
 # shellcheck shell=bash
 
+# Define custom folder paths
+SCRIPTS_DIR_OLD="/config/custom-cont-init.d"
+SCRIPTS_DIR="/custom-cont-init.d"
+SERVICES_DIR_OLD="/config/custom-services.d"
+SERVICES_DIR="/custom-services.d"
+
 # Set executable bit on cont-init and services built into the image
 set_legacy_executable_bits() {
     mkdir -p /etc/{cont-init.d,services.d}
@@ -31,7 +37,7 @@ tamper_check() {
 tamper_check_legacy() {
     # Tamper check custom script locations
     if [[ -d "${SCRIPTS_DIR_OLD}" ]] && [[ -n "$(find ${SCRIPTS_DIR_OLD} ! -user root 2>/dev/null)" ]]; then
-        echo "**** Potential tampering with custom scripts detected ****"
+        echo "[custom-init] **** Potential tampering with custom scripts detected ****"
         randstr=$(
             tr </dev/urandom -dc _A-Z-a-z-0-9 | head -c8
             echo
@@ -266,12 +272,7 @@ run_mods() {
 
 # Main script loop
 
-SCRIPTS_DIR_OLD="/config/custom-cont-init.d"
-SCRIPTS_DIR="/custom-cont-init.d"
-SERVICES_DIR_OLD="/config/custom-services.d"
-SERVICES_DIR="/custom-services.d"
-
-if [ ! -d "/custom-cont-init.d" ] && [ ! -d "/custom-services.d" ]; then
+if [ ! -d "${SCRIPTS_DIR}" ] && [ ! -d "${SERVICES_DIR}" ]; then
     # Tamper check legacy custom folders
     tamper_check_legacy
     process_custom_services_legacy
diff --git a/root/etc/cont-init.d/01-envfile b/root/etc/cont-init.d/01-envfile
deleted file mode 100755
index 32e2450..0000000
--- a/root/etc/cont-init.d/01-envfile
+++ /dev/null
@@ -1,16 +0,0 @@
-#! /bin/bash
-
-if [[ "$(ls /var/run/s6/container_environment/ | xargs)" == *"FILE__"* ]]; then
-  for FILENAME in /var/run/s6/container_environment/*; do
-    if [[ "${FILENAME##*/}" == "FILE__"* ]]; then
-      SECRETFILE=$(cat ${FILENAME})
-      if [[ -f ${SECRETFILE} ]]; then
-        FILESTRIP=${FILENAME//FILE__/}
-        cat ${SECRETFILE} > ${FILESTRIP}
-        echo "[env-init] ${FILESTRIP##*/} set from ${FILENAME##*/}"
-      else
-        echo "[env-init] cannot find secret in ${FILENAME##*/}"
-      fi
-    fi
-  done
-fi
diff --git a/root/etc/cont-init.d/01-migrations b/root/etc/cont-init.d/01-migrations
deleted file mode 100755
index aaf084a..0000000
--- a/root/etc/cont-init.d/01-migrations
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/bin/bash
-
-MIGRATIONS_DIR="/migrations"
-MIGRATIONS_HISTORY="/config/.migrations"
-
-echo "[migrations] started"
-
-if [[ ! -d ${MIGRATIONS_DIR} ]]; then
-  echo "[migrations] no migrations found"
-  exit
-fi
-
-for MIGRATION in $(find ${MIGRATIONS_DIR}/* | sort -n); do
-  NAME="$(basename "${MIGRATION}")"
-  if [[ -f ${MIGRATIONS_HISTORY} ]] && grep -Fxq "${NAME}" ${MIGRATIONS_HISTORY}; then
-    echo "[migrations] ${NAME}: skipped"
-    continue
-  fi
-  echo "[migrations] ${NAME}: executing..."
-  chmod +x "${MIGRATION}"
-  EXIT_CODE=$(/bin/bash "${MIGRATION}"; echo $?)
-  if [[ ${EXIT_CODE} -ne 0 ]]; then
-    echo "[migrations] ${NAME}: failed with exit code ${EXIT_CODE}, contact support"
-    exit "${EXIT_CODE}"
-  fi
-  echo "${NAME}" >> ${MIGRATIONS_HISTORY}
-  echo "[migrations] ${NAME}: succeeded"
-done
-
-echo "[migrations] done"
diff --git a/ci-check/99-ci-service-check b/root/etc/s6-overlay/s6-rc.d/init-adduser/dependencies.d/init-migrations
similarity index 100%
rename from ci-check/99-ci-service-check
rename to root/etc/s6-overlay/s6-rc.d/init-adduser/dependencies.d/init-migrations
diff --git a/root/etc/s6-overlay/s6-rc.d/99-ci-service-check/dependencies.d/base b/root/etc/s6-overlay/s6-rc.d/init-adduser/dependencies.d/init-script-check
similarity index 100%
rename from root/etc/s6-overlay/s6-rc.d/99-ci-service-check/dependencies.d/base
rename to root/etc/s6-overlay/s6-rc.d/init-adduser/dependencies.d/init-script-check
diff --git a/root/etc/cont-init.d/10-adduser b/root/etc/s6-overlay/s6-rc.d/init-adduser/run
similarity index 95%
rename from root/etc/cont-init.d/10-adduser
rename to root/etc/s6-overlay/s6-rc.d/init-adduser/run
index 1cbae76..a619c4f 100755
--- a/root/etc/cont-init.d/10-adduser
+++ b/root/etc/s6-overlay/s6-rc.d/init-adduser/run
@@ -1,4 +1,5 @@
 #!/usr/bin/with-contenv bash
+# shellcheck shell=bash
 
 PUID=${PUID:-911}
 PGID=${PGID:-911}
@@ -37,7 +38,7 @@ User gid:    $(id -g abc)
 time32="$(date +%Y)"
 
 if [[ "${time32}" == "1970" || "${time32}" == "1969" ]] && [ "$(uname -m)" == "armv7l" ]; then
-  echo '
+    echo '
 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 
 Your DockerHost is running an outdated version of libseccomp
@@ -48,7 +49,7 @@ Apps will not behave correctly without this
 
 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 '
-sleep infinity
+    sleep infinity
 fi
 
 chown abc:abc /app
diff --git a/root/etc/s6-overlay/s6-rc.d/init-adduser/type b/root/etc/s6-overlay/s6-rc.d/init-adduser/type
new file mode 100644
index 0000000..bdd22a1
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-adduser/type
@@ -0,0 +1 @@
+oneshot
diff --git a/root/etc/s6-overlay/s6-rc.d/init-adduser/up b/root/etc/s6-overlay/s6-rc.d/init-adduser/up
new file mode 100644
index 0000000..b8522da
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-adduser/up
@@ -0,0 +1 @@
+/etc/s6-overlay/s6-rc.d/init-adduser/run
diff --git a/root/etc/s6-overlay/s6-rc.d/99-ci-service-check/dependencies.d/user b/root/etc/s6-overlay/s6-rc.d/init-config-end/dependencies.d/init-config
similarity index 100%
rename from root/etc/s6-overlay/s6-rc.d/99-ci-service-check/dependencies.d/user
rename to root/etc/s6-overlay/s6-rc.d/init-config-end/dependencies.d/init-config
diff --git a/root/etc/s6-overlay/s6-rc.d/init-config-end/type b/root/etc/s6-overlay/s6-rc.d/init-config-end/type
new file mode 100644
index 0000000..bdd22a1
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-config-end/type
@@ -0,0 +1 @@
+oneshot
diff --git a/root/etc/s6-overlay/s6-rc.d/init-config-end/up b/root/etc/s6-overlay/s6-rc.d/init-config-end/up
new file mode 100644
index 0000000..c329423
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-config-end/up
@@ -0,0 +1 @@
+# This file doesn't do anything, it's just the end of the downstream image init process
diff --git a/root/etc/s6-overlay/s6-rc.d/init-config/dependencies.d/init-os-end b/root/etc/s6-overlay/s6-rc.d/init-config/dependencies.d/init-os-end
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-config/type b/root/etc/s6-overlay/s6-rc.d/init-config/type
new file mode 100644
index 0000000..bdd22a1
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-config/type
@@ -0,0 +1 @@
+oneshot
diff --git a/root/etc/s6-overlay/s6-rc.d/init-config/up b/root/etc/s6-overlay/s6-rc.d/init-config/up
new file mode 100644
index 0000000..e80acfe
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-config/up
@@ -0,0 +1 @@
+# This file doesn't do anything, it's just the start of the downstream image init process
diff --git a/root/etc/s6-overlay/s6-rc.d/init-custom-files/dependencies.d/init-mods-end b/root/etc/s6-overlay/s6-rc.d/init-custom-files/dependencies.d/init-mods-end
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/cont-init.d/99-custom-files b/root/etc/s6-overlay/s6-rc.d/init-custom-files/run
similarity index 66%
rename from root/etc/cont-init.d/99-custom-files
rename to root/etc/s6-overlay/s6-rc.d/init-custom-files/run
index 6ebe2d2..86ca303 100755
--- a/root/etc/cont-init.d/99-custom-files
+++ b/root/etc/s6-overlay/s6-rc.d/init-custom-files/run
@@ -4,8 +4,8 @@
 # Directories
 SCRIPTS_DIR_OLD="/config/custom-cont-init.d"
 SCRIPTS_DIR="/custom-cont-init.d"
+
 SERVICES_DIR_OLD="/config/custom-services.d"
-SERVICES_DIR="/custom-services.d"
 
 # chown legacy folders if they exist
 if [[ -e "${SCRIPTS_DIR_OLD}" ]]; then
@@ -35,7 +35,7 @@ if [[ -e "${SCRIPTS_DIR}" ]] && [[ -n "$(/bin/ls -A ${SCRIPTS_DIR} 2>/dev/null)"
     if [[ -e "${SCRIPTS_DIR_OLD}" ]] && [[ -z "$(/bin/ls -A ${SCRIPTS_DIR_OLD} 2>/dev/null)" ]]; then
         echo "[custom-init] Legacy files folder ${SCRIPTS_DIR_OLD} is empty, deleting..."
         rm -rf "${SCRIPTS_DIR_OLD}"
-    fi     
+    fi 
 elif [[ -e "${SCRIPTS_DIR_OLD}" ]] && [[ -n "$(/bin/ls -A ${SCRIPTS_DIR_OLD} 2>/dev/null)" ]]; then
     echo "[custom-init] Files found, executing"
     for SCRIPT in "${SCRIPTS_DIR_OLD}"/*; do
@@ -54,24 +54,3 @@ elif [[ -e "${SCRIPTS_DIR_OLD}" ]] && [[ -z "$(/bin/ls -A ${SCRIPTS_DIR_OLD} 2>/
 else
     echo "[custom-init] No custom files found, skipping..."
 fi
-
-if [[ -n "$(/bin/ls -A "${SCRIPTS_DIR_OLD}" 2>/dev/null)" ]] ||
-    [[ -n "$(/bin/ls -A "${SERVICES_DIR_OLD}" 2>/dev/null)" ]]; then
-    cat << EOF | tee ${SCRIPTS_DIR_OLD}/README.txt 2>/dev/null
-********************************************************
-********************************************************
-*                                                      *
-*                         !!!!                         *
-* Custom scripts or services found in legacy locations *
-*                         !!!!                         *
-*    Please move your custom scripts and services      *
-*    to ${SCRIPTS_DIR} and ${SERVICES_DIR}     *
-*    respectively to ensure they continue working.     *
-*                                                      *
-*  Visit https://linuxserver.io/custom for more info.  *
-*                                                      *
-********************************************************
-********************************************************
-EOF
-fi
-exit 0
diff --git a/root/etc/s6-overlay/s6-rc.d/init-custom-files/type b/root/etc/s6-overlay/s6-rc.d/init-custom-files/type
new file mode 100644
index 0000000..bdd22a1
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-custom-files/type
@@ -0,0 +1 @@
+oneshot
diff --git a/root/etc/s6-overlay/s6-rc.d/init-custom-files/up b/root/etc/s6-overlay/s6-rc.d/init-custom-files/up
new file mode 100644
index 0000000..28bf318
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-custom-files/up
@@ -0,0 +1 @@
+/etc/s6-overlay/s6-rc.d/init-custom-files/run
diff --git a/root/etc/s6-overlay/s6-rc.d/init-envfile/dependencies.d/00-legacy b/root/etc/s6-overlay/s6-rc.d/init-envfile/dependencies.d/00-legacy
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-envfile/run b/root/etc/s6-overlay/s6-rc.d/init-envfile/run
new file mode 100755
index 0000000..3040a92
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-envfile/run
@@ -0,0 +1,17 @@
+#!/usr/bin/with-contenv bash
+# shellcheck shell=bash
+
+if find /var/run/s6/container_environment/*"FILE__"* -maxdepth 1 > /dev/null 2>&1; then
+    for FILENAME in /var/run/s6/container_environment/*; do
+        if [[ "${FILENAME##*/}" == "FILE__"* ]]; then
+            SECRETFILE=$(cat "${FILENAME}")
+            if [[ -f ${SECRETFILE} ]]; then
+                FILESTRIP=${FILENAME//FILE__/}
+                cat "${SECRETFILE}" >"${FILESTRIP}"
+                echo "[env-init] ${FILESTRIP##*/} set from ${FILENAME##*/}"
+            else
+                echo "[env-init] cannot find secret in ${FILENAME##*/}"
+            fi
+        fi
+    done
+fi
diff --git a/root/etc/s6-overlay/s6-rc.d/init-envfile/type b/root/etc/s6-overlay/s6-rc.d/init-envfile/type
new file mode 100644
index 0000000..bdd22a1
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-envfile/type
@@ -0,0 +1 @@
+oneshot
diff --git a/root/etc/s6-overlay/s6-rc.d/init-envfile/up b/root/etc/s6-overlay/s6-rc.d/init-envfile/up
new file mode 100644
index 0000000..b2b4fb8
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-envfile/up
@@ -0,0 +1 @@
+/etc/s6-overlay/s6-rc.d/init-envfile/run
diff --git a/root/etc/s6-overlay/s6-rc.d/init-migrations/dependencies.d/00-legacy b/root/etc/s6-overlay/s6-rc.d/init-migrations/dependencies.d/00-legacy
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-migrations/run b/root/etc/s6-overlay/s6-rc.d/init-migrations/run
new file mode 100755
index 0000000..ff0874b
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-migrations/run
@@ -0,0 +1,34 @@
+#!/usr/bin/with-contenv bash
+# shellcheck shell=bash
+
+MIGRATIONS_DIR="/migrations"
+MIGRATIONS_HISTORY="/config/.migrations"
+
+echo "[migrations] started"
+
+if [[ ! -d ${MIGRATIONS_DIR} ]]; then
+    echo "[migrations] no migrations found"
+    exit
+fi
+
+for MIGRATION in $(find ${MIGRATIONS_DIR}/* | sort -n); do
+    NAME="$(basename "${MIGRATION}")"
+    if [[ -f ${MIGRATIONS_HISTORY} ]] && grep -Fxq "${NAME}" ${MIGRATIONS_HISTORY}; then
+        echo "[migrations] ${NAME}: skipped"
+        continue
+    fi
+    echo "[migrations] ${NAME}: executing..."
+    chmod +x "${MIGRATION}"
+    EXIT_CODE=$(
+        /bin/bash "${MIGRATION}"
+        echo $?
+    )
+    if [[ ${EXIT_CODE} -ne 0 ]]; then
+        echo "[migrations] ${NAME}: failed with exit code ${EXIT_CODE}, contact support"
+        exit "${EXIT_CODE}"
+    fi
+    echo "${NAME}" >>${MIGRATIONS_HISTORY}
+    echo "[migrations] ${NAME}: succeeded"
+done
+
+echo "[migrations] done"
diff --git a/root/etc/s6-overlay/s6-rc.d/init-migrations/type b/root/etc/s6-overlay/s6-rc.d/init-migrations/type
new file mode 100644
index 0000000..bdd22a1
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-migrations/type
@@ -0,0 +1 @@
+oneshot
diff --git a/root/etc/s6-overlay/s6-rc.d/init-migrations/up b/root/etc/s6-overlay/s6-rc.d/init-migrations/up
new file mode 100644
index 0000000..7c4cbcf
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-migrations/up
@@ -0,0 +1 @@
+/etc/s6-overlay/s6-rc.d/init-migrations/run
diff --git a/root/etc/s6-overlay/s6-rc.d/init-mods-end/dependencies.d/init-mods b/root/etc/s6-overlay/s6-rc.d/init-mods-end/dependencies.d/init-mods
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-mods-package-install/run b/root/etc/s6-overlay/s6-rc.d/init-mods-package-install/run
index 81987dc..90b4b2e 100755
--- a/root/etc/s6-overlay/s6-rc.d/init-mods-package-install/run
+++ b/root/etc/s6-overlay/s6-rc.d/init-mods-package-install/run
@@ -4,7 +4,7 @@
 if [[ -f "/mod-repo-packages-to-install.list" ]]; then
     IFS=' ' read -ra REPO_PACKAGES <<< "$(tr '\n' ' ' < /mod-repo-packages-to-install.list)"
     if [[ ${#REPO_PACKAGES[@]} -ne 0 ]] && [[ ${REPO_PACKAGES[*]} != "" ]]; then
-        echo "**** Installing all mod packages ****"
+        echo "[mod-init] **** Installing all mod packages ****"
         if [[ -f /usr/bin/apt ]]; then
             export DEBIAN_FRONTEND="noninteractive"
             apt-get update
@@ -20,7 +20,7 @@ fi
 if [[ -f "/mod-pip-packages-to-install.list" ]]; then
     IFS=' ' read -ra PIP_PACKAGES <<< "$(tr '\n' ' ' < /mod-pip-packages-to-install.list)"
     if [[ ${#PIP_PACKAGES[@]} -ne 0 ]] && [[ ${PIP_PACKAGES[*]} != "" ]]; then
-        echo "**** Installing all pip packages ****"
+        echo "[mod-init] **** Installing all pip packages ****"
         python3 -m pip install -U pip wheel setuptools
         PIP_ARGS=()
         if [[ -f /usr/bin/apt ]]; then
diff --git a/root/etc/s6-overlay/s6-rc.d/init-mods/dependencies.d/init-config-end b/root/etc/s6-overlay/s6-rc.d/init-mods/dependencies.d/init-config-end
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-os-end/dependencies.d/base b/root/etc/s6-overlay/s6-rc.d/init-os-end/dependencies.d/base
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-os-end/dependencies.d/init-adduser b/root/etc/s6-overlay/s6-rc.d/init-os-end/dependencies.d/init-adduser
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-os-end/dependencies.d/init-envfile b/root/etc/s6-overlay/s6-rc.d/init-os-end/dependencies.d/init-envfile
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-os-end/dependencies.d/init-migrations b/root/etc/s6-overlay/s6-rc.d/init-os-end/dependencies.d/init-migrations
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-os-end/dependencies.d/init-script-check b/root/etc/s6-overlay/s6-rc.d/init-os-end/dependencies.d/init-script-check
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-os-end/type b/root/etc/s6-overlay/s6-rc.d/init-os-end/type
new file mode 100644
index 0000000..bdd22a1
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-os-end/type
@@ -0,0 +1 @@
+oneshot
diff --git a/root/etc/s6-overlay/s6-rc.d/init-os-end/up b/root/etc/s6-overlay/s6-rc.d/init-os-end/up
new file mode 100644
index 0000000..092149d
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-os-end/up
@@ -0,0 +1 @@
+# This file doesn't do anything, it's just the end of the mod init process
diff --git a/root/etc/s6-overlay/s6-rc.d/init-script-check/dependencies.d/00-legacy b/root/etc/s6-overlay/s6-rc.d/init-script-check/dependencies.d/00-legacy
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-script-check/run b/root/etc/s6-overlay/s6-rc.d/init-script-check/run
new file mode 100755
index 0000000..20c2c43
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-script-check/run
@@ -0,0 +1,23 @@
+#!/usr/bin/with-contenv bash
+# shellcheck shell=bash
+
+if [[ -n "$(/bin/ls -A "/config/custom-cont-init.d" 2>/dev/null)" ]] ||
+    [[ -n "$(/bin/ls -A "/config/custom-services.d" 2>/dev/null)" ]]; then
+    cat << EOF | tee /config/custom-cont-init.d/README.txt 2>/dev/null
+********************************************************
+********************************************************
+*                                                      *
+*                         !!!!                         *
+* Custom scripts or services found in legacy locations *
+*                         !!!!                         *
+*    Please move your custom scripts and services      *
+*    to /custom-cont-init.d and /custom-services.d     *
+*    respectively to ensure they continue working.     *
+*                                                      *
+*  Visit https://linuxserver.io/custom for more info.  *
+*                                                      *
+********************************************************
+********************************************************
+EOF
+fi
+exit 0
diff --git a/root/etc/s6-overlay/s6-rc.d/init-script-check/type b/root/etc/s6-overlay/s6-rc.d/init-script-check/type
new file mode 100644
index 0000000..bdd22a1
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-script-check/type
@@ -0,0 +1 @@
+oneshot
diff --git a/root/etc/s6-overlay/s6-rc.d/init-script-check/up b/root/etc/s6-overlay/s6-rc.d/init-script-check/up
new file mode 100644
index 0000000..a7c155a
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-script-check/up
@@ -0,0 +1 @@
+/etc/s6-overlay/s6-rc.d/init-script-check/run
diff --git a/root/etc/s6-overlay/s6-rc.d/init-services/dependencies.d/init-custom-files b/root/etc/s6-overlay/s6-rc.d/init-services/dependencies.d/init-custom-files
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-services/up b/root/etc/s6-overlay/s6-rc.d/init-services/up
index cd262c7..a7c3905 100644
--- a/root/etc/s6-overlay/s6-rc.d/init-services/up
+++ b/root/etc/s6-overlay/s6-rc.d/init-services/up
@@ -1 +1 @@
-# This file doesn't do anything, it's just the start of the service init process
+# This file doesn't do anything, it just signals that services can start
diff --git a/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-adduser b/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-adduser
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-config b/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-config
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-config-end b/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-config-end
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-custom-files b/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-custom-files
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-envfile b/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-envfile
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-migrations b/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-migrations
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-os-end b/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-os-end
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-script-check b/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-script-check
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/user2/contents.d/99-ci-service-check b/root/etc/s6-overlay/s6-rc.d/user2/contents.d/99-ci-service-check
new file mode 100644
index 0000000..e69de29
diff --git a/root/usr/bin/with-contenv b/root/usr/bin/with-contenv
index 212d908..e47468c 100755
--- a/root/usr/bin/with-contenv
+++ b/root/usr/bin/with-contenv
@@ -1,9 +1,9 @@
-#! /bin/bash
+#!/bin/bash
 
-if [[ -f /var/run/s6/container_environment/UMASK ]] && \
-    { [[ "$(pwdx $$)" =~ "/run/s6/legacy-services/" ]] || \
-    [[ "$(pwdx $$)" =~ "/run/s6/services/" ]] || \
-    [[ "$(pwdx $$)" =~ "/servicedirs/svc-" ]]; }; then
-    umask $(cat /var/run/s6/container_environment/UMASK)
+if [[ -f /var/run/s6/container_environment/UMASK ]] &&
+    { [[ "$(pwdx $$)" =~ "/run/s6/legacy-services/" ]] ||
+        [[ "$(pwdx $$)" =~ "/run/s6/services/" ]] ||
+        [[ "$(pwdx $$)" =~ "/servicedirs/svc-" ]]; }; then
+    umask "$(cat /var/run/s6/container_environment/UMASK)"
 fi
 exec /command/with-contenv "$@"