diff --git a/app/RSpade/Core/Manifest/_Manifest_Builder_Helper.php b/app/RSpade/Core/Manifest/_Manifest_Builder_Helper.php
index aa7db12fa..99d321057 100755
--- a/app/RSpade/Core/Manifest/_Manifest_Builder_Helper.php
+++ b/app/RSpade/Core/Manifest/_Manifest_Builder_Helper.php
@@ -83,7 +83,7 @@ class _Manifest_Builder_Helper
             // This creates a map of className => filename (not full metadata to save space)
             // NOTE: Class override detection (rsx/ vs app/RSpade/) happens earlier in _check_unique_base_class_names()
             foreach (Manifest::$data['data']['files'] as $file => $filedata) {
-                if ($filedata['extension'] == $ext && !empty($filedata['class'])) {
+                if (isset($filedata['extension']) && $filedata['extension'] == $ext && !empty($filedata['class'])) {
                     $class_name = $filedata['class'];
 
                     // Duplicates should have been caught by _check_unique_base_class_names()
diff --git a/app/RSpade/Core/Manifest/_Manifest_Quality_Helper.php b/app/RSpade/Core/Manifest/_Manifest_Quality_Helper.php
index f1d64757f..c9f6c6f1e 100755
--- a/app/RSpade/Core/Manifest/_Manifest_Quality_Helper.php
+++ b/app/RSpade/Core/Manifest/_Manifest_Quality_Helper.php
@@ -310,21 +310,32 @@ class _Manifest_Quality_Helper
 
                     // Valid override: exactly one file in rsx/, rest in app/RSpade/
                     if (count($rsx_files) === 1 && count($framework_files) >= 1) {
+                        $did_change = false;
                         // Rename framework files to .upstream and remove from manifest
                         foreach ($framework_files as $framework_file) {
                             $full_framework_path = base_path($framework_file);
                             $upstream_path = $full_framework_path . '.upstream';
 
                             if (file_exists($full_framework_path) && !file_exists($upstream_path)) {
+                                // Normal case: rename to .upstream
                                 rename($full_framework_path, $upstream_path);
                                 console_debug('MANIFEST', "Class override: {$class_name} - moved {$framework_file} to .upstream");
+                                $did_change = true;
+                            } elseif (file_exists($full_framework_path) && file_exists($upstream_path)) {
+                                // Self-healing: both .php and .php.upstream exist (e.g., after framework update)
+                                // Remove the .php file since .upstream is the correct archived version
+                                unlink($full_framework_path);
+                                console_debug('MANIFEST', "Class override: {$class_name} - removed duplicate {$framework_file} (upstream already exists)");
+                                $did_change = true;
                             }
 
                             // Remove from manifest data so it won't be indexed
                             unset(Manifest::$data['data']['files'][$framework_file]);
                         }
 
-                        Manifest::$_needs_manifest_restart = true;
+                        if ($did_change) {
+                            Manifest::$_needs_manifest_restart = true;
+                        }
                         continue;
                     }
 
diff --git a/app/RSpade/Core/Manifest/_Manifest_Scanner_Helper.php b/app/RSpade/Core/Manifest/_Manifest_Scanner_Helper.php
index 8b5e31ccf..6c5218166 100755
--- a/app/RSpade/Core/Manifest/_Manifest_Scanner_Helper.php
+++ b/app/RSpade/Core/Manifest/_Manifest_Scanner_Helper.php
@@ -168,8 +168,8 @@ class _Manifest_Scanner_Helper
 
         $current_size = filesize($absolute_path);
 
-        // Stage 1: Size check
-        if ($old['size'] != $current_size) {
+        // Stage 1: Size check (guard for incomplete manifest entries)
+        if (!isset($old['size']) || $old['size'] != $current_size) {
             // Only show the message once per page load
             if (!Manifest::$__shown_rescan_message) {
                 console_debug('MANIFEST', '* File ' . $file . ' has changed size, triggering manifest rescan *');
@@ -180,9 +180,9 @@ class _Manifest_Scanner_Helper
             return true;
         }
 
-        // Stage 2: mtime check
+        // Stage 2: mtime check (guard for incomplete manifest entries)
         $current_mtime = filemtime($absolute_path);
-        if ($old['mtime'] != $current_mtime) {
+        if (!isset($old['mtime']) || $old['mtime'] != $current_mtime) {
             // Only show the message once per page load
             if (!Manifest::$__shown_rescan_message) {
                 console_debug('MANIFEST', '* File ' . $file . ' has changed mtime, triggering manifest rescan *');