diff --git a/scripts/lib/manifest.ps1 b/scripts/lib/manifest.ps1
index 78b7bf2..6bf7d23 100644
--- a/scripts/lib/manifest.ps1
+++ b/scripts/lib/manifest.ps1
@@ -86,6 +86,17 @@ function Sync-ManagedDestination {
         if ($relative -eq 'config.toml' -and (Test-Path -LiteralPath $target)) {
             $localConfig = [System.IO.File]::ReadAllText($target)
             $pluginTables = [regex]::Matches($localConfig, '(?m)^[ \t]*\[(?:plugins|marketplaces)(?:\.|\])[\s\S]*?(?=^[ \t]*\[|\z)')
+            $rootConfig = [regex]::Split($localConfig, '(?m)^[ \t]*\[', 2)[0]
+            $localSettings = [regex]::Matches($rootConfig, '(?m)^[ \t]*(?:model|reasoning_effort)[ \t]*=.*$')
+            if ($localSettings.Count -gt 0) {
+                $content = [System.Text.Encoding]::UTF8.GetString($newBytes).TrimEnd([char[]]"`r`n")
+                foreach ($setting in $localSettings) {
+                    $name = ([regex]::Match($setting.Value, '^[ \t]*([^ \t=]+)')).Groups[1].Value
+                    $content = [regex]::Replace($content, "(?m)^[ \t]*$([regex]::Escape($name))[ \t]*=.*(?:\r?\n|$)", '')
+                }
+                $preservedSettings = ($localSettings | ForEach-Object { $_.Value.TrimEnd([char[]]"`r`n") }) -join "`n"
+                $newBytes = [System.Text.Encoding]::UTF8.GetBytes("$content`n$preservedSettings`n")
+            }
             if ($pluginTables.Count -gt 0) {
                 $content = [System.Text.Encoding]::UTF8.GetString($newBytes).TrimEnd([char[]]"`r`n")
                 if ($content -match '(?m)^[ \t]*\[(?:plugins|marketplaces)(?:\.|\])') {
diff --git a/scripts/lib/manifest.sh b/scripts/lib/manifest.sh
index 458cec5..ca395cf 100755
--- a/scripts/lib/manifest.sh
+++ b/scripts/lib/manifest.sh
@@ -84,7 +84,21 @@ sync_managed_destination() {
       new_hash=$(sha256_of_file "$source_file")
     fi
     if [ "$relative" = config.toml ] && [ -f "$target" ]; then
-      local plugin_tables
+      local plugin_tables local_settings setting_name
+      local_settings=$(awk '
+        /^[ \t]*\[/ { exit }
+        /^[ \t]*(model|reasoning_effort)[ \t]*=/ { print }
+      ' "$target")
+      if [ -n "$local_settings" ]; then
+        while IFS= read -r setting; do
+          setting_name=${setting%%=*}
+          setting_name=${setting_name//[[:space:]]/}
+          content=$(printf '%s\n' "$content" | sed "/^[[:space:]]*$setting_name[[:space:]]*=/d")
+        done <<< "$local_settings"
+        content="$content"$'\n'"$local_settings"$'\n'
+        needs_sub=true
+        new_hash=$(sha256_of_string "$content")
+      fi
       plugin_tables=$(awk '
         /^[ \t]*\[/ { preserve = ($0 ~ /^[ \t]*\[(plugins|marketplaces)(\.|\])/) }
         preserve { print }
diff --git a/scripts/test-managed-install.ps1 b/scripts/test-managed-install.ps1
index 1712805..0c4dd79 100644
--- a/scripts/test-managed-install.ps1
+++ b/scripts/test-managed-install.ps1
@@ -54,15 +54,15 @@ try {
   [plugins."disabled@market"]
     enabled = false
 '@
-    [System.IO.File]::WriteAllText((Join-Path $source 'config.toml'), "model = 'new'`n")
-    [System.IO.File]::WriteAllText($configPath, "model = 'old'`n$pluginState`n[other]`nvalue = true`n")
+    [System.IO.File]::WriteAllText((Join-Path $source 'config.toml'), "model = 'new'`nreasoning_effort = 'low'`n")
+    [System.IO.File]::WriteAllText($configPath, "model = 'old'`nreasoning_effort = 'high'`n$pluginState`n[other]`nvalue = true`n")
     $originalConfig = [System.IO.File]::ReadAllText($configPath)
     $null = Sync-ManagedDestination -Source $source -Destination $destination -Stamp 'plugins-dry' -DryRun
     if ([System.IO.File]::ReadAllText($configPath) -ne $originalConfig) { throw 'Dry run must preserve plugin configuration.' }
     $null = Sync-ManagedDestination -Source $source -Destination $destination -Stamp 'plugins'
     $mergedConfig = [System.IO.File]::ReadAllText($configPath)
-    if (-not $mergedConfig.Contains($pluginState)) { throw 'Updating config.toml must preserve local marketplace and plugin tables, including disabled plugins.' }
-    if (-not $mergedConfig.Contains("model = 'new'") -or $mergedConfig.Contains('[other]')) { throw 'Managed configuration must still be updated.' }
+    if (-not ($mergedConfig -replace "`r`n", "`n").Contains(($pluginState -replace "`r`n", "`n"))) { throw 'Updating config.toml must preserve local marketplace and plugin tables, including disabled plugins.' }
+    if (-not $mergedConfig.Contains("model = 'old'") -or -not $mergedConfig.Contains("reasoning_effort = 'high'") -or $mergedConfig.Contains("model = 'new'") -or $mergedConfig.Contains("reasoning_effort = 'low'") -or $mergedConfig.Contains('[other]')) { throw 'Updating config.toml must preserve local model and reasoning effort while updating managed configuration.' }
     if ([System.IO.File]::ReadAllText((Join-Path $destination 'backups/plugins/config.toml')) -ne $originalConfig) { throw 'Original plugin configuration must be backed up.' }
     $null = Sync-ManagedDestination -Source $source -Destination $destination -Stamp 'plugins-repeat'
     if ([System.IO.File]::ReadAllText($configPath) -ne $mergedConfig -or (Test-Path (Join-Path $destination 'backups/plugins-repeat'))) { throw 'Preserving plugin configuration must be idempotent.' }
diff --git a/scripts/test-managed-install.sh b/scripts/test-managed-install.sh
index 8aea35e..a3bcbd1 100755
--- a/scripts/test-managed-install.sh
+++ b/scripts/test-managed-install.sh
@@ -58,15 +58,17 @@ plugin_state='  [marketplaces.ponytail]
     enabled = true
   [plugins."disabled@market"]
     enabled = false'
-printf "model = 'new'\n" > "$source_dir/config.toml"
-printf "model = 'old'\n%s\n[other]\nvalue = true\n" "$plugin_state" > "$destination/config.toml"
+printf "model = 'new'\nreasoning_effort = 'low'\n" > "$source_dir/config.toml"
+printf "model = 'old'\nreasoning_effort = 'high'\n%s\n[other]\nvalue = true\n" "$plugin_state" > "$destination/config.toml"
 original_config=$(cat "$destination/config.toml")
 sync_managed_destination "$source_dir" "$destination" plugins-dry "" "" "" true > /dev/null
 [ "$(cat "$destination/config.toml")" = "$original_config" ] || { printf 'Dry run changed plugin configuration.\n' >&2; exit 1; }
 sync_managed_destination "$source_dir" "$destination" plugins "" "" "" false > /dev/null
 merged_config=$(cat "$destination/config.toml")
-[[ "$merged_config" == *"$plugin_state"* ]] || { printf 'Updating config.toml must preserve local marketplace and plugin tables, including disabled plugins.\n' >&2; exit 1; }
-[[ "$merged_config" == *"model = 'new'"* && "$merged_config" != *'[other]'* ]] || { printf 'Managed configuration must still be updated.\n' >&2; exit 1; }
+merged_config_normalized=${merged_config//$'\r'/}
+plugin_state_normalized=${plugin_state//$'\r'/}
+[[ "$merged_config_normalized" == *"$plugin_state_normalized"* ]] || { printf 'Updating config.toml must preserve local marketplace and plugin tables, including disabled plugins.\n' >&2; exit 1; }
+[[ "$merged_config" == *"model = 'old'"* && "$merged_config" == *"reasoning_effort = 'high'"* && "$merged_config" != *"model = 'new'"* && "$merged_config" != *"reasoning_effort = 'low'"* && "$merged_config" != *'[other]'* ]] || { printf 'Updating config.toml must preserve local model and reasoning effort while updating managed configuration.\n' >&2; exit 1; }
 [ "$(cat "$destination/backups/plugins/config.toml")" = "$original_config" ] || { printf 'Original plugin configuration must be backed up.\n' >&2; exit 1; }
 sync_managed_destination "$source_dir" "$destination" plugins-repeat "" "" "" false > /dev/null
 [ "$(cat "$destination/config.toml")" = "$merged_config" ] && [ ! -d "$destination/backups/plugins-repeat" ] || { printf 'Preserving plugin configuration must be idempotent.\n' >&2; exit 1; }