fix to updating deleting plugins and replacing all files

flares.py

@@ -311,7 +311,6 @@ script_dir = os.path.dirname(os.path.abspath(__file__))
 os.chdir(script_dir)
 
 
-
 # Configure logging with rotation to prevent indefinite growth
 if PLATFORM_NAME == 'darwin':
     log_path = os.path.abspath(os.path.join(os.path.dirname(sys.executable), "../../../fnirs_analysis.log"))

updater.py

@@ -462,6 +462,88 @@ def _remove_readonly(func: Callable[[str], Any], path: str, exc: Any) -> None:
     func(path)
 
 
+def files_are_identical(src_path: str, dst_path: str) -> bool:
+    """
+    Check if two files are identical by comparing size and modification time.
+
+    This is much faster than hashing and catches all real changes for update purposes.
+
+    Args:
+        src_path (str): Path to source file.
+        dst_path (str): Path to destination file.
+
+    Returns:
+        bool: True if files are identical, False otherwise.
+    """
+    try:
+        if not os.path.exists(src_path) or not os.path.exists(dst_path):
+            return False
+
+        src_stat = os.stat(src_path)
+        dst_stat = os.stat(dst_path)
+
+        # Compare size first
+        if src_stat.st_size != dst_stat.st_size:
+            return False
+
+        # Compare modification time (rounded to 1 second to handle cross-platform differences)
+        src_mtime = int(src_stat.st_mtime)
+        dst_mtime = int(dst_stat.st_mtime)
+
+        return src_mtime == dst_mtime
+    except Exception:
+        return False
+
+
+def smart_replace_folder(source_dir: str, dest_dir: str) -> Tuple[int, int]:
+    """
+    Replace files in dest_dir with files from source_dir, but only if they differ.
+
+    Args:
+        source_dir (str): Source directory containing new files.
+        dest_dir (str): Destination directory to update.
+
+    Returns:
+        Tuple[int, int]: (files_updated, files_skipped) counts.
+    """
+    files_updated = 0
+    files_skipped = 0
+
+    for root, dirs, files in os.walk(source_dir):
+        relative_path = os.path.relpath(root, source_dir)
+        dest_root = os.path.join(dest_dir, relative_path)
+
+        # Create directory if it doesn't exist
+        if not os.path.exists(dest_root):
+            os.makedirs(dest_root)
+
+        for filename in files:
+            src_file = os.path.join(root, filename)
+            dst_file = os.path.join(dest_root, filename)
+
+            try:
+                # Skip if file is identical
+                if files_are_identical(src_file, dst_file):
+                    files_skipped += 1
+                    continue
+
+                # Remove destination if it exists (handles locked files on some systems)
+                if os.path.exists(dst_file):
+                    if os.path.isdir(dst_file):
+                        shutil.rmtree(dst_file, onexc=_remove_readonly)
+                    else:
+                        os.remove(dst_file)
+
+                # Copy the file
+                shutil.copy2(src_file, dst_file)
+                files_updated += 1
+
+            except Exception as e:
+                print(f"    Warning: Failed to update {filename}: {e}")
+
+    return files_updated, files_skipped
+
+
 def finish_update_if_needed(platform_name: str, app_name: str, cfg_path: str, finish_update: bool) -> None:
     """
     Completes a pending application update if '--finish-update' is present in the command-line arguments.
@@ -565,7 +647,14 @@ def finish_update_if_needed(platform_name: str, app_name: str, cfg_path: str, fi
         except Exception as e:
             print(f"Failed to replace {app_name}_updater: {e}")
 
-    # 5. Clean up all temporary update folders (with retries for Windows file locks)
+    # 5. Use smart replacement - only update files that have changed
+    print("Using smart update: only replacing files that have changed...")
+    files_updated, files_skipped = smart_replace_folder(target_updater_folder, target_base)
+    print(f"\nUpdate summary:")
+    print(f"  Files updated: {files_updated}")
+    print(f"  Files skipped (unchanged): {files_skipped}")
+
+    # 6. Clean up all temporary update folders (with retries for Windows file locks)
     for folder in update_folders:
         for attempt in range(3):
             try: