diff --git a/.github/scripts/autoupdate-scripts-sha.sh b/.github/scripts/autoupdate-scripts-sha.sh
index 0759582b..0a56d891 100755
--- a/.github/scripts/autoupdate-scripts-sha.sh
+++ b/.github/scripts/autoupdate-scripts-sha.sh
@@ -35,7 +35,7 @@ for base in "${changed[@]}"; do
   fi
   sha=$(sha256sum "$docf" | awk '{print $1}')
   echo "$sha  $docf" > "$DOCS_DIR/$base.sha256"
-  echo "$sha  $docf" > "$SITE_DIR/$base.sha256"
+  echo "$sha  $docf" > "$sitef.sha256"
   modified=1
   echo "Updated sha for $base -> $sha"
   # Replace line in scripts.sha256
diff --git a/.github/scripts/verify-site-scripts.sh b/.github/scripts/verify-site-scripts.sh
index ddf26295..3e623c30 100755
--- a/.github/scripts/verify-site-scripts.sh
+++ b/.github/scripts/verify-site-scripts.sh
@@ -1,4 +1,3 @@
-
 #!/usr/bin/env bash
 set -euo pipefail
 
@@ -45,10 +44,19 @@ for f in "${files_to_check[@]}"; do
   fi
 
   sitef="$SITE_DIR/$base"
-  if [[ ! -f "$sitef" ]]; then
-    echo "MISSING site copy for $base"
-    EXIT_CODE=1
-    continue
+  if [[ ! -d "$SITE_DIR" ]]; then
+    echo "NOTE: site directory not found; skipping docs->site diff checks for $base"
+  else
+    if [[ ! -f "$sitef" ]]; then
+      echo "MISSING site copy for $base"
+      EXIT_CODE=1
+      continue
+    fi
+    # Compare content with site copy
+    if ! cmp -s "$docf" "$sitef"; then
+      echo "DIFF: $base differs between docs and site"
+      EXIT_CODE=1
+    fi
   fi
   if [[ ! -f "$docf" ]]; then
     echo "MISSING docs copy for $base"
diff --git a/docs/perfsonar/tools_scripts/check-deps.sh b/docs/perfsonar/tools_scripts/check-deps.sh
index 07445fe0..9ce728d3 100755
--- a/docs/perfsonar/tools_scripts/check-deps.sh
+++ b/docs/perfsonar/tools_scripts/check-deps.sh
@@ -38,6 +38,7 @@ fi
 # PKG_DNF and PKG_APT are kept for documentation and future use; they may not be referenced directly
 # shellcheck disable=SC2034
 PKG_DNF=(bash coreutils iproute NetworkManager rsync curl openssl)
+# shellcheck disable=SC2034
 PKG_APT=(bash coreutils iproute2 network-manager rsync curl openssl)
 
 declare -A CMD_TO_PKG_DNF=(
diff --git a/docs/perfsonar/tools_scripts/fasterdata-tuning.sh b/docs/perfsonar/tools_scripts/fasterdata-tuning.sh
index 37390039..975d0942 100755
--- a/docs/perfsonar/tools_scripts/fasterdata-tuning.sh
+++ b/docs/perfsonar/tools_scripts/fasterdata-tuning.sh
@@ -1084,7 +1084,7 @@ iface_audit() {
   local qdisc_val qdisc_rest qdisc_display
   if [[ -n "$qdisc" ]]; then
     qdisc_val="${qdisc%% *}"
-    qdisc_rest="${qdisc#${qdisc_val}}"
+    qdisc_rest="${qdisc#"${qdisc_val}"}"
   else
     qdisc_val="?"
     qdisc_rest=""
diff --git a/docs/perfsonar/tools_scripts/perfSONAR-auto-enroll-psconfig.sh b/docs/perfsonar/tools_scripts/perfSONAR-auto-enroll-psconfig.sh
index 9bba529d..92ec236f 100755
--- a/docs/perfsonar/tools_scripts/perfSONAR-auto-enroll-psconfig.sh
+++ b/docs/perfsonar/tools_scripts/perfSONAR-auto-enroll-psconfig.sh
@@ -42,7 +42,7 @@ USE_DOCKER=0
 
 log() { echo "[INFO] $*"; }
 err() { echo "[ERROR] $*" >&2; }
-dbg() { [ "$VERBOSE" -eq 1 ] && echo "[DEBUG] $*" >&2 || true; }
+dbg() { if [[ "$VERBOSE" -eq 1 ]]; then echo "[DEBUG] $*" >&2; fi; }
 
 # Persistent logging: try to write to /var/log, fall back to /tmp
 LOGFILE="/var/log/perfsonar-auto-enroll-psconfig.log"
diff --git a/docs/perfsonar/tools_scripts/perfSONAR-orchestrator.sh b/docs/perfsonar/tools_scripts/perfSONAR-orchestrator.sh
index 4da7dd7e..365fdcee 100755
--- a/docs/perfsonar/tools_scripts/perfSONAR-orchestrator.sh
+++ b/docs/perfsonar/tools_scripts/perfSONAR-orchestrator.sh
@@ -30,6 +30,7 @@ LOG_FILE="/var/log/perfsonar-orchestrator.log"
 DRY_RUN=false
 AUTO_YES=false
 NON_INTERACTIVE=false
+# shellcheck disable=SC2034
 AUTO_UPDATE=false
 DEPLOY_OPTION="A"         # A or B
 LE_FQDN=""
@@ -45,7 +46,7 @@ RECOMMENDED_PACKAGES=(
 
 log() {
   local ts; ts="$(date +'%Y-%m-%d %H:%M:%S')"
-  echo "$ts $*" | tee -a "$LOG_FILE"
+    echo "$ts $*" | tee -a "$LOG_FILE" # Ensure consistent use of LOG_FILE
 }
 
 confirm() {
@@ -90,7 +91,7 @@ parse_cli() {
       --help|-h)
         sed -n '1,80p' "$0" | sed -n '1,80p'
         exit 0;;
-      --auto-update) AUTO_UPDATE=true; shift;;  # shellcheck disable=SC2034
+      --auto-update) AUTO_UPDATE=true; shift;;
       *) echo "Unknown arg: $1" >&2; exit 2;;
     esac
   done
@@ -193,14 +194,15 @@ step_security() {
   fi
 }
 
+# shellcheck disable=SC2120
 step_auto_update_compose() {
   # Create update script, systemd service and timer to run daily
-  # shellcheck disable=SC2120
   if ! confirm "Create /usr/local/bin/perfsonar-auto-update.sh and enable systemd timer?"; then
     log "User skipped creating auto-update artifacts."
     return
   fi
 
+    # shellcheck disable=SC2153
   run bash -c "cat > /usr/local/bin/perfsonar-auto-update.sh <<'EOF'
 #!/bin/bash
 set -e
@@ -405,6 +407,11 @@ main() {
   need_root
   parse_cli "$@"
   preflight
+  if [ "$AUTO_UPDATE" = true ]; then
+    log "AUTO_UPDATE flag detected: enabling auto-update setup."
+    AUTO_YES=true
+    step_auto_update_compose
+  fi
   step_packages
   step_disable_conflicts
   step_bootstrap_tools
diff --git a/docs/perfsonar/tools_scripts/perfSONAR-pbr-nm.sh b/docs/perfsonar/tools_scripts/perfSONAR-pbr-nm.sh
index 63999c24..24df11f8 100755
--- a/docs/perfsonar/tools_scripts/perfSONAR-pbr-nm.sh
+++ b/docs/perfsonar/tools_scripts/perfSONAR-pbr-nm.sh
@@ -1,4 +1,6 @@
-#!/bin/bash
+#!/usr/bin/env bash
+# shellcheck disable=SC2004
+
 #
 # Multi-NIC perfSONAR NetworkManager Configuration Script
 # ------------------------------------------------------
@@ -1293,6 +1295,7 @@ configure_nic() {
             echo "  - ${nic} adding static route to table $table_id for $ipv4_addroute" | tee -a "$LOG_FILE"
             if ! run_cmd nmcli con mod "$conn" +ipv4.routes "$ipv4_addroute table=$table_id"; then
                 log "nmcli failed to add custom IPv4 route for $conn; falling back to ip route"
+                # shellcheck disable=SC2086
                 run_cmd ip route replace $ipv4_addroute table "$table_id" || log "Fallback: failed to add custom IPv4 route for $nic (may need manual intervention)"
             fi
         fi