diff --git a/root/etc/cont-init.d/02-tamper-check b/root/etc/cont-init.d/02-tamper-check
deleted file mode 100755
index 6699a27..0000000
--- a/root/etc/cont-init.d/02-tamper-check
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/with-contenv bash
-
-if ([ -d "/config/custom-cont-init.d" ] && [ -n "$(find /config/custom-cont-init.d ! -user root)" ]) || ([ -d "/config/custom-services.d" ] && [ -n "$(find /config/custom-services.d ! -user root)" ]); then
-    echo "**** Potential tampering with custom scripts/services detected ****"
-    randstr=$(< /dev/urandom tr -dc _A-Z-a-z-0-9 | head -c${1:-8};echo;)
-    for folder in "/config/custom-cont-init.d" "/config/custom-services.d"; do
-        if [ -d "${folder}" ]; then
-            mv "${folder}" "${folder}.${randstr}"
-            echo "**** Folder ${folder} is moved to ${folder}.${randstr} ****"
-        fi
-    done
-    echo "**** The folders '/config/custom-cont-init.d' and '/config/custom-services.d'; and their contents need to all be owned by root to prevent root escalation inside the container!!! ****"
-    mkdir -p /config/custom-cont-init.d /config/custom-services.d
-    chown 0:0 /config/custom-cont-init.d /config/custom-services.d
-elif ([ -d "/config/custom-cont-init.d" ] && [ -n "$(find /config/custom-cont-init.d -perm -o+w)" ]) || ([ -d "/config/custom-services.d" ] && [ -n "$(find /config/custom-services.d -perm -o+w)" ]); then
-    echo "**** The folders '/config/custom-cont-init.d' or '/config/custom-services.d'; or some of their contents have write permissions for others, which is a security risk. ****"
-    echo "**** Please review the permissions of these two folders and their contents to make sure they are owned by root, and can only be modified by root. ****"
-fi
diff --git a/root/etc/cont-init.d/90-custom-folders b/root/etc/cont-init.d/90-custom-folders
deleted file mode 100755
index 14b7914..0000000
--- a/root/etc/cont-init.d/90-custom-folders
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/usr/bin/with-contenv bash
-
-# create custom folders and secure permissions
-mkdir -p /config/{custom-cont-init.d,custom-services.d}
-chown -R 0:0 /config/{custom-cont-init.d,custom-services.d}
diff --git a/root/etc/cont-init.d/99-custom-files b/root/etc/cont-init.d/99-custom-files
deleted file mode 100755
index 2195641..0000000
--- a/root/etc/cont-init.d/99-custom-files
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/usr/bin/with-contenv bash
-
-# Directories
-SCRIPTS_DIR="/config/custom-cont-init.d"
-SERVICES_DIR="/config/custom-services.d"
-
-# Remove all existing custom services before continuing to ensure
-# we aren't running anything the user may have removed
-if [ -n "$(/bin/ls -A /etc/services.d/custom-service-* 2>/dev/null)" ]; then
-  echo "[custom-init] removing existing custom services..."
-  rm -rf /etc/services.d/custom-service-*
-fi
-
-# Make sure custom init directory exists and has files in it
-if ([ -e "${SCRIPTS_DIR}" ] && \
-   [ -n "$(/bin/ls -A ${SCRIPTS_DIR} 2>/dev/null)" ]) || \
-   ([ -e "${SERVICES_DIR}" ] && \
-   [ -n "$(/bin/ls -A ${SERVICES_DIR} 2>/dev/null)" ]); then
-    if [ -n "$(/bin/ls -A ${SCRIPTS_DIR} 2>/dev/null)" ]; then
-      echo "[custom-init] files found in ${SCRIPTS_DIR} executing"
-      for SCRIPT in ${SCRIPTS_DIR}/*; do
-        NAME="$(basename "${SCRIPT}")"
-        if [ -f "${SCRIPT}" ]; then
-          echo "[custom-init] ${NAME}: executing..."
-          /bin/bash ${SCRIPT}
-          echo "[custom-init] ${NAME}: exited $?"
-        elif [ ! -f "${SCRIPT}" ]; then
-          echo "[custom-init] ${NAME}: is not a file"
-        fi
-      done
-    fi
-    if [ -n "$(/bin/ls -A ${SERVICES_DIR} 2>/dev/null)" ]; then
-      echo "[custom-init] service files found in ${SERVICES_DIR}"
-      for SERVICE in ${SERVICES_DIR}/*; do
-        NAME="$(basename "${SERVICE}")"
-        if [ -f "${SERVICE}" ]; then
-          echo "[custom-init] ${NAME}: service detected, copying..."
-          mkdir -p /etc/services.d/custom-service-${NAME}/
-          cp ${SERVICE} /etc/services.d/custom-service-${NAME}/run
-          chmod +x /etc/services.d/custom-service-${NAME}/run
-          echo "[custom-init] ${NAME}: copied"
-        elif [ ! -f "${SERVICE}" ]; then
-          echo "[custom-init] ${NAME}: is not a file"
-        fi
-      done
-    fi
-else
-  echo "[custom-init] no custom files found exiting..."
-fi
diff --git a/root/etc/s6-overlay/s6-rc.d/init-adduser/dependencies.d/init-migrations b/root/etc/s6-overlay/s6-rc.d/init-adduser/dependencies.d/init-migrations
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-adduser/dependencies.d/init-script-check b/root/etc/s6-overlay/s6-rc.d/init-adduser/dependencies.d/init-script-check
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/cont-init.d/10-adduser b/root/etc/s6-overlay/s6-rc.d/init-adduser/run
similarity index 100%
rename from root/etc/cont-init.d/10-adduser
rename to root/etc/s6-overlay/s6-rc.d/init-adduser/run
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/init-base/dependencies.d/init-adduser b/root/etc/s6-overlay/s6-rc.d/init-base/dependencies.d/init-adduser
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-base/dependencies.d/init-envfile b/root/etc/s6-overlay/s6-rc.d/init-base/dependencies.d/init-envfile
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-base/dependencies.d/init-migrations b/root/etc/s6-overlay/s6-rc.d/init-base/dependencies.d/init-migrations
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-base/dependencies.d/init-script-check b/root/etc/s6-overlay/s6-rc.d/init-base/dependencies.d/init-script-check
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-base/type b/root/etc/s6-overlay/s6-rc.d/init-base/type
new file mode 100644
index 0000000..bdd22a1
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-base/type
@@ -0,0 +1 @@
+oneshot
diff --git a/root/etc/s6-overlay/s6-rc.d/init-base/up b/root/etc/s6-overlay/s6-rc.d/init-base/up
new file mode 100644
index 0000000..0738317
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-base/up
@@ -0,0 +1 @@
+# This file doesn't do anything, it's just the end of the base image init process
diff --git a/root/etc/s6-overlay/s6-rc.d/init-custom-files/dependencies.d/init-downstream b/root/etc/s6-overlay/s6-rc.d/init-custom-files/dependencies.d/init-downstream
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-custom-files/run b/root/etc/s6-overlay/s6-rc.d/init-custom-files/run
new file mode 100755
index 0000000..9cded7f
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-custom-files/run
@@ -0,0 +1,87 @@
+#!/usr/bin/with-contenv bash
+
+# Directories
+SCRIPTS_DIR_OLD="/config/custom-cont-init.d"
+SERVICES_DIR_OLD="/config/custom-services.d"
+SCRIPTS_DIR="/custom-cont-init.d"
+SERVICES_DIR="/custom-services.d"
+
+# Remove all existing custom services before continuing to ensure
+# we aren't running anything the user may have removed
+if [ -n "$(/bin/ls -A /etc/services.d/custom-service-* 2>/dev/null)" ]; then
+  echo "[custom-init] removing existing custom services..."
+  rm -rf /etc/services.d/custom-service-*
+fi
+
+if { [ -z "$(/bin/ls -A ${SCRIPTS_DIR} 2>/dev/null)" ]; } && \
+    { [ -z "$(/bin/ls -A ${SERVICES_DIR} 2>/dev/null)" ]; } && \
+    { [ -z "$(/bin/ls -A ${SCRIPTS_DIR_OLD} 2>/dev/null)" ]; } && \
+    { [ -z "$(/bin/ls -A ${SERVICES_DIR_OLD} 2>/dev/null)" ]; }; then    
+    echo "[custom-init] no custom files found, exiting..."
+    exit 0
+fi
+
+# Make sure custom init directory exists and has files in it
+if { [ -e "${SCRIPTS_DIR}" ] && [ -n "$(/bin/ls -A ${SCRIPTS_DIR} 2>/dev/null)" ]; } || \
+    { [ -e "${SERVICES_DIR}" ] && [ -n "$(/bin/ls -A ${SERVICES_DIR} 2>/dev/null)" ]; }; then
+    if [ -n "$(/bin/ls -A ${SCRIPTS_DIR} 2>/dev/null)" ]; then
+      echo "[custom-init] files found, executing"
+      for SCRIPT in ${SCRIPTS_DIR}/*; do
+        NAME="$(basename "${SCRIPT}")"
+        if [ -f "${SCRIPT}" ]; then
+          echo "[custom-init] ${NAME}: executing..."
+          /bin/bash "${SCRIPT}"
+          echo "[custom-init] ${NAME}: exited $?"
+        elif [ ! -f "${SCRIPT}" ]; then
+          echo "[custom-init] ${NAME}: is not a file"
+        fi
+      done
+    fi
+    if [ -n "$(/bin/ls -A ${SERVICES_DIR} 2>/dev/null)" ]; then
+      echo "[custom-init] service files found in ${SERVICES_DIR}"
+      for SERVICE in ${SERVICES_DIR}/*; do
+        NAME="$(basename "${SERVICE}")"
+        if [ -f "${SERVICE}" ]; then
+          echo "[custom-init] ${NAME}: service detected, copying..."
+          mkdir -p /etc/services.d/custom-service-"${NAME}"/
+          cp "${SERVICE}" /etc/services.d/custom-service-"${NAME}"/run
+          chmod +x /etc/services.d/custom-service-"${NAME}"/run
+          echo "[custom-init] ${NAME}: copied"
+        elif [ ! -f "${SERVICE}" ]; then
+          echo "[custom-init] ${NAME}: is not a file"
+        fi
+      done
+    fi
+fi
+
+if { [ -e "${SCRIPTS_DIR_OLD}" ] && [ -n "$(/bin/ls -A ${SCRIPTS_DIR_OLD} 2>/dev/null)" ]; } || \
+    { [ -e "${SERVICES_DIR_OLD}" ] && [ -n "$(/bin/ls -A ${SERVICES_DIR_OLD} 2>/dev/null)" ]; }; then
+    if [ -n "$(/bin/ls -A ${SCRIPTS_DIR_OLD} 2>/dev/null)" ]; then
+      echo "[custom-init] files found, executing"
+      for SCRIPT in ${SCRIPTS_DIR_OLD}/*; do
+        NAME="$(basename "${SCRIPT}")"
+        if [ -f "${SCRIPT}" ]; then
+          echo "[custom-init] ${NAME}: executing..."
+          /bin/bash "${SCRIPT}"
+          echo "[custom-init] ${NAME}: exited $?"
+        elif [ ! -f "${SCRIPT}" ]; then
+          echo "[custom-init] ${NAME}: is not a file"
+        fi
+      done
+    fi
+    if [ -n "$(/bin/ls -A ${SERVICES_DIR_OLD} 2>/dev/null)" ]; then
+      echo "[custom-init] service files found in ${SERVICES_DIR_OLD}"
+      for SERVICE in ${SERVICES_DIR_OLD}/*; do
+        NAME="$(basename "${SERVICE}")"
+        if [ -f "${SERVICE}" ]; then
+          echo "[custom-init] ${NAME}: service detected, copying..."
+          mkdir -p /etc/services.d/custom-service-"${NAME}"/
+          cp "${SERVICE}" /etc/services.d/custom-service-"${NAME}"/run
+          chmod +x /etc/services.d/custom-service-"${NAME}"/run
+          echo "[custom-init] ${NAME}: copied"
+        elif [ ! -f "${SERVICE}" ]; then
+          echo "[custom-init] ${NAME}: is not a file"
+        fi
+      done
+    fi 
+fi
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-downstream/dependencies.d/init-base b/root/etc/s6-overlay/s6-rc.d/init-downstream/dependencies.d/init-base
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-downstream/type b/root/etc/s6-overlay/s6-rc.d/init-downstream/type
new file mode 100644
index 0000000..bdd22a1
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-downstream/type
@@ -0,0 +1 @@
+oneshot
diff --git a/root/etc/s6-overlay/s6-rc.d/init-downstream/up b/root/etc/s6-overlay/s6-rc.d/init-downstream/up
new file mode 100644
index 0000000..c329423
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-downstream/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-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/cont-init.d/01-envfile b/root/etc/s6-overlay/s6-rc.d/init-envfile/run
similarity index 100%
rename from root/etc/cont-init.d/01-envfile
rename to root/etc/s6-overlay/s6-rc.d/init-envfile/run
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/cont-init.d/01-migrations b/root/etc/s6-overlay/s6-rc.d/init-migrations/run
similarity index 98%
rename from root/etc/cont-init.d/01-migrations
rename to root/etc/s6-overlay/s6-rc.d/init-migrations/run
index 4ab4464..5eef083 100755
--- a/root/etc/cont-init.d/01-migrations
+++ b/root/etc/s6-overlay/s6-rc.d/init-migrations/run
@@ -7,7 +7,7 @@ echo "[migrations] started"
 
 if [ ! -d $MIGRATIONS_DIR ]; then
   echo "[migrations] no migrations found"
-  exit
+  exit 0
 fi
 
 for MIGRATION in $(ls -1 ${MIGRATIONS_DIR}/* | sort -n); do
diff --git a/root/etc/s6-overlay/s6-rc.d/init-migrations/type b/root/etc/s6-overlay/s6-rc.d/init-migrations/type
new file mode 100644
index 0000000..bdd22a1
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-migrations/type
@@ -0,0 +1 @@
+oneshot
diff --git a/root/etc/s6-overlay/s6-rc.d/init-migrations/up b/root/etc/s6-overlay/s6-rc.d/init-migrations/up
new file mode 100644
index 0000000..7c4cbcf
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-migrations/up
@@ -0,0 +1 @@
+/etc/s6-overlay/s6-rc.d/init-migrations/run
diff --git a/root/etc/s6-overlay/s6-rc.d/init-script-check/dependencies.d/00-legacy b/root/etc/s6-overlay/s6-rc.d/init-script-check/dependencies.d/00-legacy
new file mode 100644
index 0000000..e69de29
diff --git a/root/etc/s6-overlay/s6-rc.d/init-script-check/run b/root/etc/s6-overlay/s6-rc.d/init-script-check/run
new file mode 100755
index 0000000..05355ad
--- /dev/null
+++ b/root/etc/s6-overlay/s6-rc.d/init-script-check/run
@@ -0,0 +1,19 @@
+#!/usr/bin/with-contenv bash
+
+if { [ -n "$(/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,/config/custom-services.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.     *
+    *                                                      *
+    ********************************************************
+    ********************************************************
+EOF
+fi
\ No newline at end of file
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/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-base b/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-base
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-script-check b/root/etc/s6-overlay/s6-rc.d/user/contents.d/init-script-check
new file mode 100644
index 0000000..e69de29