Sync from development - prepare for v0.1.5

CHANGELOG.md

@@ -1,5 +1,39 @@
 # Jackify Changelog
 
+## v0.1.5 - Winetricks Integration & Enhanced Compatibility
+**Release Date:** September 26, 2025
+
+### Major Improvements
+- **Winetricks Integration**: Replaced protontricks with bundled winetricks for faster, more reliable wine component installation
+- **Enhanced SD Card Detection**: Dynamic detection of SD card mount points supports both `/run/media/mmcblk0p1` and `/run/media/deck/UUID` patterns
+- **Smart Proton Detection**: Comprehensive GE-Proton support with detection in both steamapps/common and compatibilitytools.d directories
+- **Steam Deck SD Card Support**: Fixed path handling for SD card installations on Steam Deck
+
+### User Experience
+- **No Focus Stealing**: Wine component installation runs in background without disrupting user workflow
+- **Popup Suppression**: Eliminated wine GUI popups while maintaining functionality
+- **GUI Navigation**: Fixed navigation issues after Tuxborn workflow removal
+
+### Bug Fixes
+- **CLI Configure Existing**: Fixed AppID detection with signed-to-unsigned conversion, removing protontricks dependency
+- **GE-Proton Validation**: Fixed validation to support both Valve Proton and GE-Proton directory structures
+- **Resolution Override**: Eliminated hardcoded 2560x1600 fallbacks that overrode user Steam Deck settings
+- **VDF Case-Sensitivity**: Added case-insensitive parsing for Steam shortcuts fields
+- **Cabextract Bundling**: Bundled cabextract binary to resolve winetricks dependency issues
+- **ModOrganizer.ini Path Format**: Fixed missing backslash in gamePath format for proper Windows path structure
+- **SD Card Binary Paths**: Corrected binary paths to use D: drive mapping instead of raw Linux paths for SD card installs
+- **Proton Fallback Logic**: Enhanced fallback when user-selected Proton version is missing or invalid
+- **Settings Persistence**: Improved configuration saving with verification and logging
+- **System Wine Elimination**: Comprehensive audit ensures Jackify never uses system wine installations
+- **Winetricks Reliability**: Fixed vcrun2022 installation failures and wine app crashes
+- **Enderal Registry Injection**: Switched from launch options to registry injection approach
+- **Proton Path Detection**: Uses actual Steam libraries from libraryfolders.vdf instead of hardcoded paths
+
+### Technical Improvements
+- **Self-contained Cache**: Relocated winetricks cache to jackify_data_dir for better isolation
+
+---
+
 ## v0.1.4 - GE-Proton Support and Performance Optimization
 **Release Date:** September 22, 2025
 

jackify/__init__.py

@@ -5,4 +5,4 @@ This package provides both CLI and GUI interfaces for managing
 Wabbajack modlists natively on Linux systems.
 """
 
-__version__ = "0.1.4"
+__version__ = "0.1.5"

jackify/backend/core/modlist_operations.py

@@ -730,6 +730,14 @@ class ModlistInstallCLI:
                 cmd += ['-m', self.context['machineid']]
             cmd += ['-o', install_dir_str, '-d', download_dir_str]
 
+            # Add debug flag if debug mode is enabled
+            from jackify.backend.handlers.config_handler import ConfigHandler
+            config_handler = ConfigHandler()
+            debug_mode = config_handler.get('debug_mode', False)
+            if debug_mode:
+                cmd.append('--debug')
+                self.logger.info("Adding --debug flag to jackify-engine")
+
             # Store original environment values to restore later
             original_env_values = {
                 'NEXUS_API_KEY': os.environ.get('NEXUS_API_KEY'),

jackify/backend/handlers/modlist_handler.py

@@ -159,6 +159,9 @@ class ModlistHandler:
         
         # Initialize Handlers (should happen regardless of how paths were provided)
         self.protontricks_handler = ProtontricksHandler(steamdeck=self.steamdeck, logger=self.logger)
+        # Initialize winetricks handler for wine component installation
+        from .winetricks_handler import WinetricksHandler
+        self.winetricks_handler = WinetricksHandler(logger=self.logger)
         self.shortcut_handler = ShortcutHandler(steamdeck=self.steamdeck, verbose=self.verbose)
         self.filesystem_handler = filesystem_handler if filesystem_handler else FileSystemHandler()
         self.resolution_handler = ResolutionHandler()
@@ -224,44 +227,41 @@ class ModlistHandler:
         discovered_modlists_info = [] 
 
         try:
-            # 1. Get ALL non-Steam shortcuts from Protontricks
+            # Get shortcuts pointing to the executable from shortcuts.vdf
-            # Now calls the renamed method without filtering
-            protontricks_shortcuts = self.protontricks_handler.list_non_steam_shortcuts()
-            if not protontricks_shortcuts:
-                self.logger.warning("Protontricks did not list any non-Steam shortcuts.")
-                return []
-            self.logger.debug(f"Protontricks non-Steam shortcuts found: {protontricks_shortcuts}")
-
-            # 2. Get shortcuts pointing to the executable from shortcuts.vdf
             matching_vdf_shortcuts = self.shortcut_handler.find_shortcuts_by_exe(executable_name)
             if not matching_vdf_shortcuts:
                 self.logger.debug(f"No shortcuts found pointing to '{executable_name}' in shortcuts.vdf.")
                 return []
             self.logger.debug(f"Shortcuts matching executable '{executable_name}' in VDF: {matching_vdf_shortcuts}")
 
-            # 3. Correlate the two lists and extract required info
+            # Process each matching shortcut and convert signed AppID to unsigned
             for vdf_shortcut in matching_vdf_shortcuts:
                 app_name = vdf_shortcut.get('AppName')
                 start_dir = vdf_shortcut.get('StartDir')
+                signed_appid = vdf_shortcut.get('appid')
 
                 if not app_name or not start_dir:
                     self.logger.warning(f"Skipping VDF shortcut due to missing AppName or StartDir: {vdf_shortcut}")
                     continue
 
-                if app_name in protontricks_shortcuts:
+                if signed_appid is None:
-                    app_id = protontricks_shortcuts[app_name]
+                    self.logger.warning(f"Skipping VDF shortcut due to missing appid: {vdf_shortcut}")
+                    continue
 
-                    # Append dictionary with all necessary info
+                # Convert signed AppID to unsigned AppID (the format used by Steam prefixes)
+                if signed_appid < 0:
+                    unsigned_appid = signed_appid + (2**32)
+                else:
+                    unsigned_appid = signed_appid
+
+                # Append dictionary with all necessary info using unsigned AppID
                 modlist_info = {
                     'name': app_name,
-                        'appid': app_id,
+                    'appid': unsigned_appid,
                     'path': start_dir
                 }
                 discovered_modlists_info.append(modlist_info)
-                    self.logger.info(f"Validated shortcut: '{app_name}' (AppID: {app_id}, Path: {start_dir})")
+                self.logger.info(f"Discovered shortcut: '{app_name}' (Signed: {signed_appid} → Unsigned: {unsigned_appid}, Path: {start_dir})")
-                else:
-                    # Downgraded from WARNING to INFO
-                    self.logger.info(f"Shortcut '{app_name}' found in VDF but not listed by protontricks. Skipping.")
 
         except Exception as e:
             self.logger.error(f"Error discovering executable shortcuts: {e}", exc_info=True)
@@ -685,7 +685,14 @@ class ModlistHandler:
         # All modlists now use their own AppID for wine components
         target_appid = self.appid
         
-        if not self.protontricks_handler.install_wine_components(target_appid, self.game_var_full, specific_components=components):
+        # Use winetricks for wine component installation (faster than protontricks)
+        wineprefix = self.protontricks_handler.get_wine_prefix_path(target_appid)
+        if not wineprefix:
+            self.logger.error("Failed to get WINEPREFIX path for winetricks.")
+            print("Error: Could not determine wine prefix location.")
+            return False
+
+        if not self.winetricks_handler.install_wine_components(wineprefix, self.game_var_full, specific_components=components):
             self.logger.error("Failed to install Wine components. Configuration aborted.")
             print("Error: Failed to install necessary Wine components.")
             return False # Abort on failure
@@ -760,7 +767,8 @@ class ModlistHandler:
         
         # Conditionally update binary and working directory paths
         # Skip for jackify-engine workflows since paths are already correct
-        if not getattr(self, 'engine_installed', False):
+        # Exception: Always run for SD card installs to fix Z:/run/media/... to D:/... paths
+        if not getattr(self, 'engine_installed', False) or self.modlist_sdcard:
             # Convert steamapps/common path to library root path
             steam_libraries = None
             if self.steam_library:
@@ -863,7 +871,7 @@ class ModlistHandler:
         prefix_path_str = self.path_handler.find_compat_data(str(self.appid))
         if prefix_path_str:
             prefix_path = Path(prefix_path_str)
-            fonts_dir = prefix_path / "drive_c" / "windows" / "Fonts"
+            fonts_dir = prefix_path / "pfx" / "drive_c" / "windows" / "Fonts"
             font_url = "https://github.com/mrbvrz/segoe-ui-linux/raw/refs/heads/master/font/seguisym.ttf"
             font_dest_path = fonts_dir / "seguisym.ttf"
             

jackify/backend/handlers/path_handler.py

@@ -32,14 +32,21 @@ class PathHandler:
     @staticmethod
     def _strip_sdcard_path_prefix(path_obj: Path) -> str:
         """
-        Removes the '/run/media/mmcblk0p1/' prefix if present.
+        Removes any detected SD card mount prefix dynamically.
+        Handles both /run/media/mmcblk0p1 and /run/media/deck/UUID patterns.
         Returns the path as a POSIX-style string (using /).
         """
+        from .wine_utils import WineUtils
+
         path_str = path_obj.as_posix()  # Work with consistent forward slashes
-        if path_str.lower().startswith(SDCARD_PREFIX.lower()):
+
-            # Return the part *after* the prefix, ensuring no leading slash remains unless root
+        # Use dynamic SD card detection from WineUtils
-            relative_part = path_str[len(SDCARD_PREFIX):]
+        stripped_path = WineUtils._strip_sdcard_path(path_str)
-            return relative_part if relative_part else "." # Return '.' if it was exactly the prefix
+
+        if stripped_path != path_str:
+            # Path was stripped, remove leading slash for relative path
+            return stripped_path.lstrip('/') if stripped_path != '/' else '.'
+
         return path_str
 
     @staticmethod
@@ -737,7 +744,7 @@ class PathHandler:
         try:
             with open(modlist_ini_path, 'r', encoding='utf-8', errors='ignore') as f:
                 lines = f.readlines()
-            drive_letter = "D:" if modlist_sdcard else "Z:"
+            drive_letter = "D:\\\\" if modlist_sdcard else "Z:\\\\"
             processed_path = self._strip_sdcard_path_prefix(new_game_path)
             windows_style = processed_path.replace('/', '\\')
             windows_style_double = windows_style.replace('\\', '\\\\')
@@ -876,9 +883,10 @@ class PathHandler:
                             rel_path = value_part[idx:].lstrip('/')
                         else:
                             rel_path = exe_name
-                    new_binary_path = f"{drive_prefix}/{modlist_dir_path}/{rel_path}".replace('\\', '/').replace('//', '/')
+                    processed_modlist_path = PathHandler._strip_sdcard_path_prefix(modlist_dir_path) if modlist_sdcard else str(modlist_dir_path)
+                    new_binary_path = f"{drive_prefix}/{processed_modlist_path}/{rel_path}".replace('\\', '/').replace('//', '/')
                 formatted_binary_path = PathHandler._format_binary_for_mo2(new_binary_path)
-                new_binary_line = f"{index}{backslash_style}binary={formatted_binary_path}"
+                new_binary_line = f"{index}{backslash_style}binary = {formatted_binary_path}"
                 logger.debug(f"Updating binary path: {line.strip()} -> {new_binary_line}")
                 lines[i] = new_binary_line + "\n"
                 binary_paths_updated += 1
@@ -893,7 +901,7 @@ class PathHandler:
                     wd_path = drive_prefix + wd_path
                     formatted_wd_path = PathHandler._format_workingdir_for_mo2(wd_path)
                     key_part = f"{index}{backslash_style}workingDirectory"
-                    new_wd_line = f"{key_part}={formatted_wd_path}"
+                    new_wd_line = f"{key_part} = {formatted_wd_path}"
                     logger.debug(f"Updating working directory: {wd_line.strip()} -> {new_wd_line}")
                     lines[j] = new_wd_line + "\n"
                     working_dirs_updated += 1

jackify/backend/handlers/protontricks_handler.py

@@ -21,6 +21,9 @@ logger = logging.getLogger(__name__)
 class ProtontricksHandler:
     """
     Handles operations related to Protontricks detection and usage
+
+    This handler now supports native Steam operations as a fallback/replacement
+    for protontricks functionality.
     """
 
     def __init__(self, steamdeck: bool, logger=None):
@@ -29,6 +32,8 @@ class ProtontricksHandler:
         self.protontricks_version = None
         self.protontricks_path = None
         self.steamdeck = steamdeck # Store steamdeck status
+        self._native_steam_service = None
+        self.use_native_operations = True  # Enable native Steam operations by default
     
     def _get_clean_subprocess_env(self):
         """
@@ -70,6 +75,13 @@ class ProtontricksHandler:
         
         return env
 
+    def _get_native_steam_service(self):
+        """Get native Steam operations service instance"""
+        if self._native_steam_service is None:
+            from ..services.native_steam_operations_service import NativeSteamOperationsService
+            self._native_steam_service = NativeSteamOperationsService(steamdeck=self.steamdeck)
+        return self._native_steam_service
+
     def detect_protontricks(self):
         """
         Detect if protontricks is installed and whether it's flatpak or native.
@@ -255,9 +267,19 @@ class ProtontricksHandler:
     
     def set_protontricks_permissions(self, modlist_dir, steamdeck=False):
         """
-        Set permissions for Protontricks to access the modlist directory
+        Set permissions for Steam operations to access the modlist directory.
+
+        Uses native operations when enabled, falls back to protontricks permissions.
         Returns True on success, False on failure
         """
+        # Use native operations if enabled
+        if self.use_native_operations:
+            logger.debug("Using native Steam operations, permissions handled natively")
+            try:
+                return self._get_native_steam_service().set_steam_permissions(modlist_dir, steamdeck)
+            except Exception as e:
+                logger.warning(f"Native permissions failed, falling back to protontricks: {e}")
+
         if self.which_protontricks != 'flatpak':
             logger.debug("Using Native protontricks, skip setting permissions")
             return True
@@ -338,15 +360,22 @@ class ProtontricksHandler:
     
     # Renamed from list_non_steam_games for clarity and purpose
     def list_non_steam_shortcuts(self) -> Dict[str, str]:
-        """List ALL non-Steam shortcuts recognized by Protontricks.
+        """List ALL non-Steam shortcuts.
 
-        Runs 'protontricks -l' and parses the output for lines matching
+        Uses native VDF parsing when enabled, falls back to protontricks -l parsing.
-        "Non-Steam shortcut: [Name] ([AppID])".
 
         Returns:
             A dictionary mapping the shortcut name (AppName) to its AppID.
             Returns an empty dictionary if none are found or an error occurs.
         """
+        # Use native operations if enabled
+        if self.use_native_operations:
+            logger.info("Listing non-Steam shortcuts via native VDF parsing...")
+            try:
+                return self._get_native_steam_service().list_non_steam_shortcuts()
+            except Exception as e:
+                logger.warning(f"Native shortcut listing failed, falling back to protontricks: {e}")
+
         logger.info("Listing ALL non-Steam shortcuts via protontricks...")
         non_steam_shortcuts = {}
         # --- Ensure protontricks is detected before proceeding ---
@@ -577,12 +606,22 @@ class ProtontricksHandler:
     def get_wine_prefix_path(self, appid) -> Optional[str]:
         """Gets the WINEPREFIX path for a given AppID.
 
+        Uses native path discovery when enabled, falls back to protontricks detection.
+
         Args:
             appid (str): The Steam AppID.
 
         Returns:
             The WINEPREFIX path as a string, or None if detection fails.
         """
+        # Use native operations if enabled
+        if self.use_native_operations:
+            logger.debug(f"Getting WINEPREFIX for AppID {appid} via native path discovery")
+            try:
+                return self._get_native_steam_service().get_wine_prefix_path(appid)
+            except Exception as e:
+                logger.warning(f"Native WINEPREFIX detection failed, falling back to protontricks: {e}")
+
         logger.debug(f"Getting WINEPREFIX for AppID {appid}")
         result = self.run_protontricks("-c", "echo $WINEPREFIX", appid)
         if result and result.returncode == 0 and result.stdout.strip():

jackify/backend/handlers/shortcut_handler.py

@@ -1180,18 +1180,21 @@ class ShortcutHandler:
                     self.logger.warning(f"Skipping invalid shortcut entry at index {index} in {vdf_path}")
                     continue
 
-                exe_path = shortcut_details.get('Exe', '').strip('"') # Get Exe path, remove quotes
+                exe_path = shortcut_details.get('Exe', shortcut_details.get('exe', '')).strip('"') # Get Exe path, remove quotes
-                app_name = shortcut_details.get('AppName', 'Unknown Shortcut')
+                app_name = shortcut_details.get('AppName', shortcut_details.get('appname', 'Unknown Shortcut'))
 
                 # Check if the executable_name is present in the Exe path
                 if executable_name in os.path.basename(exe_path):
                     self.logger.info(f"Found matching shortcut '{app_name}' in {vdf_path}")
-                    # Extract relevant details
+                    # Extract relevant details with case-insensitive fallbacks
+                    app_id = shortcut_details.get('appid', shortcut_details.get('AppID', shortcut_details.get('appId', None)))
+                    start_dir = shortcut_details.get('StartDir', shortcut_details.get('startdir', '')).strip('"')
+
                     match = {
                         'AppName': app_name,
                         'Exe': exe_path, # Store unquoted path
-                        'StartDir': shortcut_details.get('StartDir', '').strip('"') # Unquoted
+                        'StartDir': start_dir,
-                        # Add other useful fields if needed, e.g., 'ShortcutPath'
+                        'appid': app_id  # Include the AppID for conversion to unsigned
                     }
                     matching_shortcuts.append(match)
                 else:

jackify/backend/handlers/wine_utils.py

@@ -197,16 +197,43 @@ class WineUtils:
             logger.error(f"Error editing binary working paths: {e}")
             return False
     
+    @staticmethod
+    def _get_sd_card_mounts():
+        """
+        Dynamically detect all current SD card mount points
+        Returns list of mount point paths
+        """
+        try:
+            import subprocess
+            result = subprocess.run(['df', '-h'], capture_output=True, text=True, timeout=5)
+            sd_mounts = []
+            for line in result.stdout.split('\n'):
+                # Look for common SD card mount patterns
+                if '/run/media' in line or ('/mnt' in line and 'sdcard' in line.lower()):
+                    parts = line.split()
+                    if len(parts) >= 6:  # df output has 6+ columns
+                        mount_point = parts[-1]  # Last column is mount point
+                        if mount_point.startswith(('/run/media', '/mnt')):
+                            sd_mounts.append(mount_point)
+            return sd_mounts
+        except Exception:
+            # Fallback to common patterns if df fails
+            return ['/run/media/mmcblk0p1', '/run/media/deck']
+
     @staticmethod
     def _strip_sdcard_path(path):
         """
-        Strip /run/media/deck/UUID from SD card paths
+        Strip any detected SD card mount prefix from paths
-        Internal helper method
+        Handles both /run/media/mmcblk0p1 and /run/media/deck/UUID patterns
         """
-        if path.startswith("/run/media/deck/"):
+        sd_mounts = WineUtils._get_sd_card_mounts()
-            parts = path.split("/", 5)
+
-            if len(parts) >= 6:
+        for mount in sd_mounts:
-                return "/" + parts[5]
+            if path.startswith(mount):
+                # Strip the mount prefix and ensure proper leading slash
+                relative_path = path[len(mount):].lstrip('/')
+                return "/" + relative_path if relative_path else "/"
+
         return path
     
     @staticmethod
@@ -609,12 +636,46 @@ class WineUtils:
         """
         # Clean up the version string for directory matching
         version_patterns = [proton_version, proton_version.replace(' ', '_'), proton_version.replace(' ', '')]
-        # Standard Steam library locations
+
+        # Get actual Steam library paths from libraryfolders.vdf (smart detection)
+        steam_common_paths = []
+        compatibility_paths = []
+
+        try:
+            from .path_handler import PathHandler
+            # Get root Steam library paths (without /steamapps/common suffix)
+            root_steam_libs = PathHandler.get_all_steam_library_paths()
+            for lib_path in root_steam_libs:
+                lib = Path(lib_path)
+                if lib.exists():
+                    # Valve Proton: {library}/steamapps/common
+                    common_path = lib / "steamapps/common"
+                    if common_path.exists():
+                        steam_common_paths.append(common_path)
+                    # GE-Proton: same Steam installation root + compatibilitytools.d
+                    compatibility_paths.append(lib / "compatibilitytools.d")
+        except Exception as e:
+            logger.warning(f"Could not detect Steam libraries from libraryfolders.vdf: {e}")
+
+        # Fallback locations if dynamic detection fails
+        if not steam_common_paths:
             steam_common_paths = [
                 Path.home() / ".steam/steam/steamapps/common",
                 Path.home() / ".local/share/Steam/steamapps/common",
                 Path.home() / ".steam/root/steamapps/common"
             ]
+
+        if not compatibility_paths:
+            compatibility_paths = [
+                Path.home() / ".steam/steam/compatibilitytools.d",
+                Path.home() / ".local/share/Steam/compatibilitytools.d"
+            ]
+
+        # Add standard compatibility tool locations (covers edge cases like Flatpak)
+        compatibility_paths.extend([
+            Path.home() / ".steam/root/compatibilitytools.d",
+            Path.home() / ".var/app/com.valvesoftware.Steam/.local/share/Steam/compatibilitytools.d"
+        ])
         # Special handling for Proton 9: try all possible directory names
         if proton_version.strip().startswith("Proton 9"):
             proton9_candidates = ["Proton 9.0", "Proton 9.0 (Beta)"]
@@ -628,8 +689,9 @@ class WineUtils:
                     wine_bin = subdir / "files/bin/wine"
                     if wine_bin.is_file():
                         return str(wine_bin)
-        # General case: try version patterns
+        # General case: try version patterns in both steamapps and compatibilitytools.d
-        for base_path in steam_common_paths:
+        all_paths = steam_common_paths + compatibility_paths
+        for base_path in all_paths:
             if not base_path.is_dir():
                 continue
             for pattern in version_patterns:
@@ -716,19 +778,32 @@ class WineUtils:
     @staticmethod
     def get_steam_library_paths() -> List[Path]:
         """
-        Get all Steam library paths including standard locations.
+        Get all Steam library paths from libraryfolders.vdf (handles Flatpak, custom locations, etc.).
 
         Returns:
             List of Path objects for Steam library directories
         """
-        steam_paths = [
+        try:
+            from .path_handler import PathHandler
+            # Use existing PathHandler that reads libraryfolders.vdf
+            library_paths = PathHandler.get_all_steam_library_paths()
+            # Convert to steamapps/common paths for Proton scanning
+            steam_common_paths = []
+            for lib_path in library_paths:
+                common_path = lib_path / "steamapps" / "common"
+                if common_path.exists():
+                    steam_common_paths.append(common_path)
+            logger.debug(f"Found Steam library paths: {steam_common_paths}")
+            return steam_common_paths
+        except Exception as e:
+            logger.warning(f"Failed to get Steam library paths from libraryfolders.vdf: {e}")
+            # Fallback to hardcoded paths if PathHandler fails
+            fallback_paths = [
                 Path.home() / ".steam/steam/steamapps/common",
                 Path.home() / ".local/share/Steam/steamapps/common",
                 Path.home() / ".steam/root/steamapps/common"
             ]
-
+            return [path for path in fallback_paths if path.exists()]
-        # Return only existing paths
-        return [path for path in steam_paths if path.exists()]
 
     @staticmethod
     def get_compatibility_tool_paths() -> List[Path]:

jackify/backend/handlers/winetricks_handler.py

@@ -0,0 +1,263 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Winetricks Handler Module
+Handles wine component installation using bundled winetricks
+"""
+
+import os
+import subprocess
+import logging
+from pathlib import Path
+from typing import Optional, List
+
+logger = logging.getLogger(__name__)
+
+
+class WinetricksHandler:
+    """
+    Handles wine component installation using bundled winetricks
+    """
+
+    def __init__(self, logger=None):
+        self.logger = logger or logging.getLogger(__name__)
+        self.winetricks_path = self._get_bundled_winetricks_path()
+
+    def _get_bundled_winetricks_path(self) -> Optional[str]:
+        """
+        Get the path to the bundled winetricks script following AppImage best practices
+        """
+        possible_paths = []
+
+        # AppImage environment - use APPDIR (standard AppImage best practice)
+        if os.environ.get('APPDIR'):
+            appdir_path = os.path.join(os.environ['APPDIR'], 'opt', 'jackify', 'tools', 'winetricks')
+            possible_paths.append(appdir_path)
+
+        # Development environment - relative to module location
+        module_dir = Path(__file__).parent.parent.parent  # Go from handlers/ up to jackify/
+        dev_path = module_dir / 'tools' / 'winetricks'
+        possible_paths.append(str(dev_path))
+
+        # Try each path until we find one that works
+        for path in possible_paths:
+            if os.path.exists(path) and os.access(path, os.X_OK):
+                self.logger.debug(f"Found bundled winetricks at: {path}")
+                return str(path)
+
+        self.logger.error(f"Bundled winetricks not found. Tried paths: {possible_paths}")
+        return None
+
+    def _get_bundled_cabextract(self) -> Optional[str]:
+        """
+        Get the path to the bundled cabextract binary, checking same locations as winetricks
+        """
+        possible_paths = []
+
+        # AppImage environment - same pattern as winetricks detection
+        if os.environ.get('APPDIR'):
+            appdir_path = os.path.join(os.environ['APPDIR'], 'opt', 'jackify', 'tools', 'cabextract')
+            possible_paths.append(appdir_path)
+
+        # Development environment - relative to module location, same as winetricks
+        module_dir = Path(__file__).parent.parent.parent  # Go from handlers/ up to jackify/
+        dev_path = module_dir / 'tools' / 'cabextract'
+        possible_paths.append(str(dev_path))
+
+        # Try each path until we find one that works
+        for path in possible_paths:
+            if os.path.exists(path) and os.access(path, os.X_OK):
+                self.logger.debug(f"Found bundled cabextract at: {path}")
+                return str(path)
+
+        # Fallback to system PATH
+        try:
+            import shutil
+            system_cabextract = shutil.which('cabextract')
+            if system_cabextract:
+                self.logger.debug(f"Using system cabextract: {system_cabextract}")
+                return system_cabextract
+        except Exception:
+            pass
+
+        self.logger.warning("Bundled cabextract not found in tools directory")
+        return None
+
+    def is_available(self) -> bool:
+        """
+        Check if winetricks is available and ready to use
+        """
+        if not self.winetricks_path:
+            self.logger.error("Bundled winetricks not found")
+            return False
+
+        try:
+            env = os.environ.copy()
+            result = subprocess.run(
+                [self.winetricks_path, '--version'],
+                capture_output=True,
+                text=True,
+                env=env,
+                timeout=10
+            )
+            if result.returncode == 0:
+                self.logger.debug(f"Winetricks version: {result.stdout.strip()}")
+                return True
+            else:
+                self.logger.error(f"Winetricks --version failed: {result.stderr}")
+                return False
+        except Exception as e:
+            self.logger.error(f"Error testing winetricks: {e}")
+            return False
+
+    def install_wine_components(self, wineprefix: str, game_var: str, specific_components: Optional[List[str]] = None) -> bool:
+        """
+        Install the specified Wine components into the given prefix using winetricks.
+        If specific_components is None, use the default set (fontsmooth=rgb, xact, xact_x64, vcrun2022).
+        """
+        if not self.is_available():
+            self.logger.error("Winetricks is not available")
+            return False
+
+        env = os.environ.copy()
+        env['WINEDEBUG'] = '-all'  # Suppress Wine debug output
+        env['WINEPREFIX'] = wineprefix
+        env['WINETRICKS_GUI'] = 'none'  # Suppress GUI popups
+        # Less aggressive popup suppression - don't completely disable display
+        if 'DISPLAY' in env:
+            # Keep DISPLAY but add window manager hints to prevent focus stealing
+            env['WINEDLLOVERRIDES'] = 'winemenubuilder.exe=d'  # Disable Wine menu integration
+        else:
+            # No display available anyway
+            env['DISPLAY'] = ''
+
+        # Force winetricks to use Proton wine binary - NEVER fall back to system wine
+        try:
+            from ..handlers.config_handler import ConfigHandler
+            from ..handlers.wine_utils import WineUtils
+
+            config = ConfigHandler()
+            user_proton_path = config.get('proton_path', 'auto')
+
+            # If user selected a specific Proton, try that first
+            wine_binary = None
+            if user_proton_path != 'auto':
+                # Check if user-selected Proton still exists
+                if os.path.exists(user_proton_path):
+                    # Resolve symlinks to handle ~/.steam/steam -> ~/.local/share/Steam
+                    resolved_proton_path = os.path.realpath(user_proton_path)
+
+                    # Check for wine binary in different Proton structures
+                    valve_proton_wine = os.path.join(resolved_proton_path, 'dist', 'bin', 'wine')
+                    ge_proton_wine = os.path.join(resolved_proton_path, 'files', 'bin', 'wine')
+
+                    if os.path.exists(valve_proton_wine):
+                        wine_binary = valve_proton_wine
+                        self.logger.info(f"Using user-selected Proton: {user_proton_path}")
+                    elif os.path.exists(ge_proton_wine):
+                        wine_binary = ge_proton_wine
+                        self.logger.info(f"Using user-selected GE-Proton: {user_proton_path}")
+                    else:
+                        self.logger.warning(f"User-selected Proton path invalid: {user_proton_path}")
+                else:
+                    self.logger.warning(f"User-selected Proton no longer exists: {user_proton_path}")
+
+            # Fall back to auto-detection if user selection failed or is 'auto'
+            if not wine_binary:
+                self.logger.info("Falling back to automatic Proton detection")
+                best_proton = WineUtils.select_best_proton()
+                if best_proton:
+                    wine_binary = WineUtils.find_proton_binary(best_proton['name'])
+                    self.logger.info(f"Auto-selected Proton: {best_proton['name']} at {best_proton['path']}")
+
+            if not wine_binary:
+                self.logger.error("Cannot run winetricks: No compatible Proton version found")
+                return False
+
+            if not (os.path.exists(wine_binary) and os.access(wine_binary, os.X_OK)):
+                self.logger.error(f"Cannot run winetricks: Wine binary not found or not executable: {wine_binary}")
+                return False
+
+            env['WINE'] = str(wine_binary)
+            self.logger.info(f"Using Proton wine binary for winetricks: {wine_binary}")
+
+        except Exception as e:
+            self.logger.error(f"Cannot run winetricks: Failed to get Proton wine binary: {e}")
+            return False
+
+        # Set up bundled cabextract for winetricks
+        bundled_cabextract = self._get_bundled_cabextract()
+        if bundled_cabextract:
+            env['PATH'] = f"{os.path.dirname(bundled_cabextract)}:{env.get('PATH', '')}"
+            self.logger.info(f"Using bundled cabextract: {bundled_cabextract}")
+        else:
+            self.logger.warning("Bundled cabextract not found, relying on system PATH")
+
+        # Set winetricks cache to jackify_data_dir for self-containment
+        from jackify.shared.paths import get_jackify_data_dir
+        jackify_cache_dir = get_jackify_data_dir() / 'winetricks_cache'
+        jackify_cache_dir.mkdir(parents=True, exist_ok=True)
+        env['WINETRICKS_CACHE'] = str(jackify_cache_dir)
+
+        if specific_components is not None:
+            components_to_install = specific_components
+            self.logger.info(f"Installing specific components: {components_to_install}")
+        else:
+            components_to_install = ["fontsmooth=rgb", "xact", "xact_x64", "vcrun2022"]
+            self.logger.info(f"Installing default components: {components_to_install}")
+
+        if not components_to_install:
+            self.logger.info("No Wine components to install.")
+            return True
+
+        self.logger.info(f"WINEPREFIX: {wineprefix}, Game: {game_var}, Components: {components_to_install}")
+
+        max_attempts = 3
+        for attempt in range(1, max_attempts + 1):
+            if attempt > 1:
+                self.logger.warning(f"Retrying component installation (attempt {attempt}/{max_attempts})...")
+                self._cleanup_wine_processes()
+
+            try:
+                # Build winetricks command - using --unattended for silent installation
+                cmd = [self.winetricks_path, '--unattended'] + components_to_install
+
+                self.logger.debug(f"Running: {' '.join(cmd)}")
+                self.logger.debug(f"Environment WINE={env.get('WINE', 'NOT SET')}")
+                self.logger.debug(f"Environment DISPLAY={env.get('DISPLAY', 'NOT SET')}")
+                self.logger.debug(f"Environment WINEPREFIX={env.get('WINEPREFIX', 'NOT SET')}")
+                result = subprocess.run(
+                    cmd,
+                    env=env,
+                    stdout=subprocess.PIPE,
+                    stderr=subprocess.PIPE,
+                    text=True,
+                    timeout=600
+                )
+
+                self.logger.debug(f"Winetricks output: {result.stdout}")
+                if result.returncode == 0:
+                    self.logger.info("Wine Component installation command completed successfully.")
+                    return True
+                else:
+                    self.logger.error(f"Winetricks command failed (Attempt {attempt}/{max_attempts}). Return Code: {result.returncode}")
+                    self.logger.error(f"Stdout: {result.stdout.strip()}")
+                    self.logger.error(f"Stderr: {result.stderr.strip()}")
+
+            except Exception as e:
+                self.logger.error(f"Error during winetricks run (Attempt {attempt}/{max_attempts}): {e}", exc_info=True)
+
+        self.logger.error(f"Failed to install Wine components after {max_attempts} attempts.")
+        return False
+
+    def _cleanup_wine_processes(self):
+        """
+        Internal method to clean up wine processes during component installation
+        Only cleanup winetricks processes - NEVER kill all wine processes
+        """
+        try:
+            # Only cleanup winetricks processes - do NOT kill other wine apps
+            subprocess.run("pkill -f winetricks", shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+            self.logger.debug("Cleaned up winetricks processes only")
+        except Exception as e:
+            self.logger.error(f"Error cleaning up winetricks processes: {e}")

jackify/backend/services/automated_prefix_service.py

@@ -448,7 +448,7 @@ exit"""
                 
                 if shortcut_name in name:
                     appid = shortcut.get('appid')
-                    exe_path = shortcut.get('Exe', '')
+                    exe_path = shortcut.get('Exe', '').strip('"')
                     
                     logger.info(f"Found shortcut: {name}")
                     logger.info(f"  AppID: {appid}")
@@ -1759,21 +1759,15 @@ echo Prefix creation complete.
             progress_callback("=== Steam Integration ===")
             progress_callback(f"{self._get_progress_timestamp()} Creating Steam shortcut with native service")
         
-        # Dual approach: Registry injection for FNV, launch options for Enderal
+        # Registry injection approach for both FNV and Enderal
         from ..handlers.modlist_handler import ModlistHandler
         modlist_handler = ModlistHandler()
         special_game_type = modlist_handler.detect_special_game_type(modlist_install_dir)
 
-        # Generate launch options only for Enderal (FNV uses registry injection)
+        # No launch options needed - both FNV and Enderal use registry injection
         custom_launch_options = None
-        if special_game_type == "enderal":
+        if special_game_type in ["fnv", "enderal"]:
-            custom_launch_options = self._generate_special_game_launch_options(special_game_type, modlist_install_dir)
+            logger.info(f"Using registry injection approach for {special_game_type.upper()} modlist")
-            if not custom_launch_options:
-                logger.error(f"Failed to generate launch options for Enderal modlist")
-                return False, None, None, None
-            logger.info("Using launch options approach for Enderal modlist")
-        elif special_game_type == "fnv":
-            logger.info("Using registry injection approach for FNV modlist")
         else:
             logger.debug("Standard modlist - no special game handling needed")
         
@@ -1849,23 +1843,19 @@ echo Prefix creation complete.
             if progress_callback:
                 progress_callback(f"{self._get_progress_timestamp()} Setup verification completed")
             
-            # Step 5: Inject game registry entries for FNV modlists (Enderal uses launch options)
+            # Step 5: Inject game registry entries for FNV and Enderal modlists
             # Get prefix path (needed for logging regardless of game type)
             prefix_path = self.get_prefix_path(appid)
 
-            if special_game_type == "fnv":
+            if special_game_type in ["fnv", "enderal"]:
-                logger.info("Step 5: Injecting FNV game registry entries")
+                logger.info(f"Step 5: Injecting {special_game_type.upper()} game registry entries")
                 if progress_callback:
-                    progress_callback(f"{self._get_progress_timestamp()} Injecting FNV game registry entries...")
+                    progress_callback(f"{self._get_progress_timestamp()} Injecting {special_game_type.upper()} game registry entries...")
 
                 if prefix_path:
                     self._inject_game_registry_entries(str(prefix_path))
                 else:
                     logger.warning("Could not find prefix path for registry injection")
-            elif special_game_type == "enderal":
-                logger.info("Step 5: Skipping registry injection for Enderal (using launch options)")
-                if progress_callback:
-                    progress_callback(f"{self._get_progress_timestamp()} Skipping registry injection for Enderal")
             else:
                 logger.info("Step 5: Skipping registry injection for standard modlist")
                 if progress_callback:
@@ -2690,7 +2680,36 @@ echo Prefix creation complete.
             return False
     
     def _find_proton_binary(self, proton_common_dir: Path) -> Optional[Path]:
-        """Locate a Proton wrapper script to use (prefer Experimental)."""
+        """Locate a Proton wrapper script to use, respecting user's configuration."""
+        try:
+            from jackify.backend.handlers.config_handler import ConfigHandler
+            from jackify.backend.handlers.wine_utils import WineUtils
+
+            config = ConfigHandler()
+            user_proton_path = config.get('proton_path', 'auto')
+
+            # If user selected a specific Proton, try that first
+            if user_proton_path != 'auto':
+                # Resolve symlinks to handle ~/.steam/steam -> ~/.local/share/Steam
+                resolved_proton_path = os.path.realpath(user_proton_path)
+
+                # Check for wine binary in different Proton structures
+                valve_proton_wine = Path(resolved_proton_path) / "dist" / "bin" / "wine"
+                ge_proton_wine = Path(resolved_proton_path) / "files" / "bin" / "wine"
+
+                if valve_proton_wine.exists() or ge_proton_wine.exists():
+                    # Found user's Proton, now find the proton wrapper script
+                    proton_wrapper = Path(resolved_proton_path) / "proton"
+                    if proton_wrapper.exists():
+                        logger.info(f"Using user-selected Proton wrapper: {proton_wrapper}")
+                        return proton_wrapper
+                    else:
+                        logger.warning(f"User-selected Proton missing wrapper script: {proton_wrapper}")
+                else:
+                    logger.warning(f"User-selected Proton path invalid: {user_proton_path}")
+
+            # Fall back to auto-detection
+            logger.info("Falling back to automatic Proton detection")
             candidates = []
             preferred = [
                 "Proton - Experimental",
@@ -2713,9 +2732,13 @@ echo Prefix creation complete.
                 logger.error("No Proton wrapper found under steamapps/common")
                 return None
 
-        logger.info(f"Using Proton wrapper: {candidates[0]}")
+            logger.info(f"Using auto-detected Proton wrapper: {candidates[0]}")
             return candidates[0]
 
+        except Exception as e:
+            logger.error(f"Error finding Proton binary: {e}")
+            return None
+    
     def replace_existing_shortcut(self, shortcut_name: str, exe_path: str, modlist_install_dir: str) -> Tuple[bool, Optional[int]]:
         """
         Replace an existing shortcut with a new one using STL.
@@ -2948,6 +2971,15 @@ echo Prefix creation complete.
                 )
                 if success:
                     logger.info(f"Updated registry entry for {config['name']}")
+
+                    # Special handling for Enderal: Create required user directory
+                    if app_id == "976620":  # Enderal Special Edition
+                        try:
+                            enderal_docs_path = os.path.join(modlist_compatdata_path, "pfx", "drive_c", "users", "steamuser", "Documents", "My Games", "Enderal Special Edition")
+                            os.makedirs(enderal_docs_path, exist_ok=True)
+                            logger.info(f"Created Enderal user directory: {enderal_docs_path}")
+                        except Exception as e:
+                            logger.warning(f"Failed to create Enderal user directory: {e}")
                 else:
                     logger.warning(f"Failed to update registry entry for {config['name']}")
             else:

jackify/backend/services/modlist_service.py

@@ -294,14 +294,6 @@ class ModlistService:
                 cmd += ['-m', context['machineid']]
             cmd += ['-o', install_dir_str, '-d', download_dir_str]
 
-            # Check for debug mode and add --debug flag
-            from ..handlers.config_handler import ConfigHandler
-            config_handler = ConfigHandler()
-            debug_mode = config_handler.get('debug_mode', False)
-            if debug_mode:
-                cmd.append('--debug')
-                logger.debug("DEBUG: Added --debug flag to jackify-engine command")
-            
             # NOTE: API key is passed via environment variable only, not as command line argument
             
             # Store original environment values (copied from working code)

jackify/backend/services/native_steam_operations_service.py

@@ -0,0 +1,185 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Native Steam Operations Service
+
+This service provides direct Steam operations using VDF parsing and path discovery.
+Replaces protontricks dependencies with native Steam functionality.
+"""
+
+import os
+import logging
+import vdf
+from pathlib import Path
+from typing import Dict, Optional, List
+import subprocess
+import shutil
+
+logger = logging.getLogger(__name__)
+
+
+class NativeSteamOperationsService:
+    """
+    Service providing native Steam operations for shortcut discovery and prefix management.
+
+    Replaces protontricks functionality with:
+    - Direct VDF parsing for shortcut discovery
+    - Native compatdata path construction
+    - Direct Steam library detection
+    """
+
+    def __init__(self, steamdeck: bool = False):
+        self.steamdeck = steamdeck
+        self.logger = logger
+
+    def list_non_steam_shortcuts(self) -> Dict[str, str]:
+        """
+        List non-Steam shortcuts via direct VDF parsing.
+
+        Returns:
+            Dict mapping shortcut name to AppID string
+        """
+        logger.info("Listing non-Steam shortcuts via native VDF parsing...")
+        shortcuts = {}
+
+        try:
+            # Find all possible shortcuts.vdf locations
+            shortcuts_paths = self._find_shortcuts_vdf_paths()
+
+            for shortcuts_path in shortcuts_paths:
+                logger.debug(f"Checking shortcuts.vdf at: {shortcuts_path}")
+
+                if not shortcuts_path.exists():
+                    continue
+
+                try:
+                    with open(shortcuts_path, 'rb') as f:
+                        data = vdf.binary_load(f)
+
+                    shortcuts_data = data.get('shortcuts', {})
+                    for shortcut_key, shortcut_data in shortcuts_data.items():
+                        if isinstance(shortcut_data, dict):
+                            app_name = shortcut_data.get('AppName', '').strip()
+                            app_id = shortcut_data.get('appid', '')
+
+                            if app_name and app_id:
+                                # Convert to positive AppID string (compatible format)
+                                positive_appid = str(abs(int(app_id)))
+                                shortcuts[app_name] = positive_appid
+                                logger.debug(f"Found non-Steam shortcut: '{app_name}' with AppID {positive_appid}")
+
+                except Exception as e:
+                    logger.warning(f"Error reading shortcuts.vdf at {shortcuts_path}: {e}")
+                    continue
+
+            if not shortcuts:
+                logger.warning("No non-Steam shortcuts found in any shortcuts.vdf")
+
+        except Exception as e:
+            logger.error(f"Error listing non-Steam shortcuts: {e}")
+
+        return shortcuts
+
+    def set_steam_permissions(self, modlist_dir: str, steamdeck: bool = False) -> bool:
+        """
+        Handle Steam access permissions for native operations.
+
+        Since we're using direct file access, no special permissions needed.
+
+        Args:
+            modlist_dir: Modlist directory path (for future use)
+            steamdeck: Steam Deck flag (for future use)
+
+        Returns:
+            Always True (no permissions needed for native operations)
+        """
+        logger.debug("Using native Steam operations, no permission setting needed")
+        return True
+
+    def get_wine_prefix_path(self, appid: str) -> Optional[str]:
+        """
+        Get WINEPREFIX path via direct compatdata discovery.
+
+        Args:
+            appid: Steam AppID string
+
+        Returns:
+            WINEPREFIX path string or None if not found
+        """
+        logger.debug(f"Getting WINEPREFIX for AppID {appid} using native path discovery")
+
+        try:
+            # Find all possible compatdata locations
+            compatdata_paths = self._find_compatdata_paths()
+
+            for compatdata_base in compatdata_paths:
+                prefix_path = compatdata_base / appid / "pfx"
+                logger.debug(f"Checking prefix path: {prefix_path}")
+
+                if prefix_path.exists():
+                    logger.debug(f"Found WINEPREFIX: {prefix_path}")
+                    return str(prefix_path)
+
+            logger.error(f"WINEPREFIX not found for AppID {appid} in any compatdata location")
+            return None
+
+        except Exception as e:
+            logger.error(f"Error getting WINEPREFIX for AppID {appid}: {e}")
+            return None
+
+    def _find_shortcuts_vdf_paths(self) -> List[Path]:
+        """Find all possible shortcuts.vdf file locations"""
+        paths = []
+
+        # Standard Steam locations
+        steam_locations = [
+            Path.home() / ".steam/steam",
+            Path.home() / ".local/share/Steam",
+            Path.home() / ".var/app/com.valvesoftware.Steam/home/.steam/steam",
+            Path.home() / ".var/app/com.valvesoftware.Steam/home/.local/share/Steam"
+        ]
+
+        for steam_root in steam_locations:
+            if not steam_root.exists():
+                continue
+
+            # Find userdata directories
+            userdata_path = steam_root / "userdata"
+            if userdata_path.exists():
+                for user_dir in userdata_path.iterdir():
+                    if user_dir.is_dir() and user_dir.name.isdigit():
+                        shortcuts_path = user_dir / "config" / "shortcuts.vdf"
+                        paths.append(shortcuts_path)
+
+        return paths
+
+    def _find_compatdata_paths(self) -> List[Path]:
+        """Find all possible compatdata directory locations"""
+        paths = []
+
+        # Standard compatdata locations
+        standard_locations = [
+            Path.home() / ".steam/steam/steamapps/compatdata",
+            Path.home() / ".local/share/Steam/steamapps/compatdata",
+            Path.home() / ".var/app/com.valvesoftware.Steam/home/.steam/steam/steamapps/compatdata",
+            Path.home() / ".var/app/com.valvesoftware.Steam/home/.local/share/Steam/steamapps/compatdata"
+        ]
+
+        for path in standard_locations:
+            if path.exists():
+                paths.append(path)
+
+        # Also check additional Steam libraries via libraryfolders.vdf
+        try:
+            from jackify.shared.paths import PathHandler
+            all_steam_libs = PathHandler.get_all_steam_library_paths()
+
+            for lib_path in all_steam_libs:
+                compatdata_path = lib_path / "steamapps" / "compatdata"
+                if compatdata_path.exists():
+                    paths.append(compatdata_path)
+
+        except Exception as e:
+            logger.debug(f"Could not get additional Steam library paths: {e}")
+
+        return paths

jackify/frontends/cli/commands/tuxborn.py

@@ -1,247 +0,0 @@
-"""
-Tuxborn Command
-
-CLI command for the Tuxborn Automatic Installer.
-Extracted from the original jackify-cli.py.
-"""
-
-import os
-import sys
-import logging
-from pathlib import Path
-from typing import Optional
-
-# Import the backend services we'll need
-from jackify.backend.models.modlist import ModlistContext
-from jackify.shared.colors import COLOR_INFO, COLOR_ERROR, COLOR_RESET
-
-logger = logging.getLogger(__name__)
-
-
-class TuxbornCommand:
-    """Handler for the tuxborn-auto CLI command."""
-    
-    def __init__(self, backend_services, system_info):
-        """Initialize with backend services.
-        
-        Args:
-            backend_services: Dictionary of backend service instances
-            system_info: System information (steamdeck flag, etc.)
-        """
-        self.backend_services = backend_services
-        self.system_info = system_info
-    
-    def add_args(self, parser):
-        """Add tuxborn-auto arguments to the main parser.
-        
-        Args:
-            parser: The main ArgumentParser
-        """
-        parser.add_argument(
-            "--tuxborn-auto", 
-            action="store_true", 
-            help="Run the Tuxborn Automatic Installer non-interactively (for GUI integration)"
-        )
-        parser.add_argument(
-            "--install-dir", 
-            type=str, 
-            help="Install directory for Tuxborn (required with --tuxborn-auto)"
-        )
-        parser.add_argument(
-            "--download-dir", 
-            type=str, 
-            help="Downloads directory for Tuxborn (required with --tuxborn-auto)"
-        )
-        parser.add_argument(
-            "--modlist-name", 
-            type=str, 
-            default="Tuxborn", 
-            help="Modlist name (optional, defaults to 'Tuxborn')"
-        )
-    
-    def execute(self, args) -> int:
-        """Execute the tuxborn-auto command.
-        
-        Args:
-            args: Parsed command-line arguments
-            
-        Returns:
-            Exit code (0 for success, 1 for failure)
-        """
-        logger.info("Starting Tuxborn Automatic Installer (GUI integration mode)")
-        
-        try:
-            # Set up logging redirection (copied from original)
-            self._setup_tee_logging()
-            
-            # Build context from args
-            context = self._build_context_from_args(args)
-            
-            # Validate required fields
-            if not self._validate_context(context):
-                return 1
-            
-            # Use legacy implementation for now - will migrate to backend services later
-            result = self._execute_legacy_tuxborn(context)
-            
-            logger.info("Finished Tuxborn Automatic Installer")
-            return result
-            
-        except Exception as e:
-            logger.error(f"Failed to run Tuxborn installer: {e}")
-            print(f"{COLOR_ERROR}Tuxborn installation failed: {e}{COLOR_RESET}")
-            return 1
-        finally:
-            # Restore stdout/stderr
-            self._restore_stdout_stderr()
-    
-    def _build_context_from_args(self, args) -> dict:
-        """Build context dictionary from command arguments.
-        
-        Args:
-            args: Parsed command-line arguments
-            
-        Returns:
-            Context dictionary
-        """
-        install_dir = getattr(args, 'install_dir', None)
-        download_dir = getattr(args, 'download_dir', None)
-        modlist_name = getattr(args, 'modlist_name', 'Tuxborn')
-        machineid = 'Tuxborn/Tuxborn'
-        
-        # Try to get API key from saved config first, then environment variable
-        from jackify.backend.services.api_key_service import APIKeyService
-        api_key_service = APIKeyService()
-        api_key = api_key_service.get_saved_api_key()
-        if not api_key:
-            api_key = os.environ.get('NEXUS_API_KEY')
-        
-        resolution = getattr(args, 'resolution', None)
-        mo2_exe_path = getattr(args, 'mo2_exe_path', None)
-        skip_confirmation = True  # Always true in GUI mode
-        
-        context = {
-            'machineid': machineid,
-            'modlist_name': modlist_name,
-            'install_dir': install_dir,
-            'download_dir': download_dir,
-            'nexus_api_key': api_key,
-            'skip_confirmation': skip_confirmation,
-            'resolution': resolution,
-            'mo2_exe_path': mo2_exe_path,
-        }
-        
-        # PATCH: Always set modlist_value and modlist_source for Tuxborn workflow
-        context['modlist_value'] = 'Tuxborn/Tuxborn'
-        context['modlist_source'] = 'identifier'
-        
-        return context
-    
-    def _validate_context(self, context: dict) -> bool:
-        """Validate Tuxborn context.
-        
-        Args:
-            context: Tuxborn context dictionary
-            
-        Returns:
-            True if valid, False otherwise
-        """
-        required_keys = ['modlist_name', 'install_dir', 'download_dir', 'nexus_api_key']
-        missing = [k for k in required_keys if not context.get(k)]
-        
-        if missing:
-            print(f"{COLOR_ERROR}Missing required arguments for --tuxborn-auto.\\n"
-                  f"--install-dir, --download-dir, and NEXUS_API_KEY (env, 32+ chars) are required.{COLOR_RESET}")
-            return False
-        
-        return True
-    
-    def _setup_tee_logging(self):
-        """Set up TEE logging (copied from original implementation)."""
-        import shutil
-        
-        # TEE logging setup & log rotation (copied from original)
-        class TeeStdout:
-            def __init__(self, *files):
-                self.files = files
-            def write(self, data):
-                for f in self.files:
-                    f.write(data)
-                    f.flush()
-            def flush(self):
-                for f in self.files:
-                    f.flush()
-        
-        log_dir = Path.home() / "Jackify" / "logs"
-        log_dir.mkdir(parents=True, exist_ok=True)
-        workflow_log_path = log_dir / "tuxborn_workflow.log"
-        
-        # Log rotation: keep last 3 logs, 1KB each (for testing)
-        max_logs = 3
-        max_size = 1024  # 1KB for testing
-        if workflow_log_path.exists() and workflow_log_path.stat().st_size > max_size:
-            for i in range(max_logs, 0, -1):
-                prev = log_dir / f"tuxborn_workflow.log.{i-1}" if i > 1 else workflow_log_path
-                dest = log_dir / f"tuxborn_workflow.log.{i}"
-                if prev.exists():
-                    if dest.exists():
-                        dest.unlink()
-                    prev.rename(dest)
-        
-        self.workflow_log = open(workflow_log_path, 'a')
-        self.orig_stdout, self.orig_stderr = sys.stdout, sys.stderr
-        sys.stdout = TeeStdout(sys.stdout, self.workflow_log)
-        sys.stderr = TeeStdout(sys.stderr, self.workflow_log)
-    
-    def _restore_stdout_stderr(self):
-        """Restore original stdout/stderr."""
-        if hasattr(self, 'orig_stdout'):
-            sys.stdout = self.orig_stdout
-            sys.stderr = self.orig_stderr
-        if hasattr(self, 'workflow_log'):
-            self.workflow_log.close()
-    
-    def _execute_legacy_tuxborn(self, context: dict) -> int:
-        """Execute Tuxborn using legacy implementation.
-        
-        Args:
-            context: Tuxborn context dictionary
-            
-        Returns:
-            Exit code
-        """
-        # Import backend services
-        from jackify.backend.core.modlist_operations import ModlistInstallCLI
-        from jackify.backend.handlers.menu_handler import MenuHandler
-        
-        # Create legacy handler instances
-        menu_handler = MenuHandler()
-        modlist_cli = ModlistInstallCLI(
-            menu_handler=menu_handler, 
-            steamdeck=self.system_info.get('is_steamdeck', False)
-        )
-        
-        confirmed_context = modlist_cli.run_discovery_phase(context_override=context)
-        if confirmed_context:
-            menu_handler.logger.info("Tuxborn discovery confirmed by GUI. Proceeding to configuration/installation.")
-            modlist_cli.configuration_phase()
-            
-            # Handle GUI integration prompts (copied from original)
-            print('[PROMPT:RESTART_STEAM]')
-            if os.environ.get('JACKIFY_GUI_MODE'):
-                input()  # Wait for GUI to send confirmation, no CLI prompt
-            else:
-                answer = input('Restart Steam automatically now? (Y/n): ')
-                # ... handle answer as before ...
-            
-            print('[PROMPT:MANUAL_STEPS]')
-            if os.environ.get('JACKIFY_GUI_MODE'):
-                input()  # Wait for GUI to send confirmation, no CLI prompt
-            else:
-                input('Once you have completed ALL the steps above, press Enter to continue...')
-            
-            return 0
-        else:
-            menu_handler.logger.info("Tuxborn discovery/confirmation cancelled or failed (GUI mode).")
-            print(f"{COLOR_INFO}Tuxborn installation cancelled or not confirmed.{COLOR_RESET}")
-            return 1 

jackify/frontends/cli/main.py

@@ -21,11 +21,9 @@ from jackify import __version__ as jackify_version
 # Import our command handlers
 from .commands.configure_modlist import ConfigureModlistCommand
 from .commands.install_modlist import InstallModlistCommand
-from .commands.tuxborn import TuxbornCommand
 
 # Import our menu handlers
 from .menus.main_menu import MainMenuHandler
-from .menus.tuxborn_menu import TuxbornMenuHandler
 from .menus.wabbajack_menu import WabbajackMenuHandler
 from .menus.hoolamike_menu import HoolamikeMenuHandler
 from .menus.additional_menu import AdditionalMenuHandler
@@ -280,7 +278,6 @@ class JackifyCLI:
         commands = {
             'configure_modlist': ConfigureModlistCommand(self.backend_services),
             'install_modlist': InstallModlistCommand(self.backend_services, self.system_info),
-            'tuxborn': TuxbornCommand(self.backend_services, self.system_info)
         }
         return commands
 
@@ -292,7 +289,6 @@ class JackifyCLI:
         """
         menus = {
             'main': MainMenuHandler(dev_mode=getattr(self, 'dev_mode', False)),
-            'tuxborn': TuxbornMenuHandler(),
             'wabbajack': WabbajackMenuHandler(),
             'hoolamike': HoolamikeMenuHandler(),
             'additional': AdditionalMenuHandler()
@@ -371,10 +367,6 @@ class JackifyCLI:
             self._debug_print('Entering restart_steam workflow')
             return self._handle_restart_steam()
         
-        # Handle Tuxborn auto mode
-        if getattr(self.args, 'tuxborn_auto', False):
-            self._debug_print('Entering Tuxborn workflow')
-            return self.commands['tuxborn'].execute(self.args)
         
         # Handle install-modlist top-level functionality
         if getattr(self.args, 'install_modlist', False):
@@ -404,7 +396,6 @@ class JackifyCLI:
         parser.add_argument('--update', action='store_true', help='Check for and install updates')
         
         # Add command-specific arguments
-        self.commands['tuxborn'].add_args(parser)
         self.commands['install_modlist'].add_top_level_args(parser)
         
         # Add subcommands
@@ -459,8 +450,6 @@ class JackifyCLI:
                     return 0
                 elif choice == "wabbajack":
                     self.menus['wabbajack'].show_wabbajack_tasks_menu(self)
-                elif choice == "tuxborn":
-                    self.menus['tuxborn'].show_tuxborn_installer_menu(self)
                 # HIDDEN FOR FIRST RELEASE - UNCOMMENT WHEN READY
                 # elif choice == "hoolamike":
                 #     self.menus['hoolamike'].show_hoolamike_menu(self)

jackify/frontends/cli/menus/__init__.py

@@ -4,7 +4,6 @@ Extracted from the legacy monolithic CLI system
 """
 
 from .main_menu import MainMenuHandler
-from .tuxborn_menu import TuxbornMenuHandler  
 from .wabbajack_menu import WabbajackMenuHandler
 from .hoolamike_menu import HoolamikeMenuHandler
 from .additional_menu import AdditionalMenuHandler
@@ -12,7 +11,6 @@ from .recovery_menu import RecoveryMenuHandler
 
 __all__ = [
     'MainMenuHandler',
-    'TuxbornMenuHandler', 
     'WabbajackMenuHandler',
     'HoolamikeMenuHandler',
     'AdditionalMenuHandler',

jackify/frontends/cli/menus/tuxborn_menu.py

@@ -1,194 +0,0 @@
-"""
-Tuxborn Menu Handler for Jackify CLI Frontend  
-Extracted from src.modules.menu_handler.MenuHandler.show_tuxborn_installer_menu()
-"""
-
-from pathlib import Path
-from typing import Optional
-
-from jackify.shared.colors import (
-    COLOR_SELECTION, COLOR_RESET, COLOR_INFO, COLOR_PROMPT, COLOR_WARNING
-)
-from jackify.shared.ui_utils import print_jackify_banner
-from jackify.backend.handlers.config_handler import ConfigHandler
-
-class TuxbornMenuHandler:
-    """
-    Handles the Tuxborn Automatic Installer workflow
-    Extracted from legacy MenuHandler class
-    """
-    
-    def __init__(self):
-        self.logger = None  # Will be set by CLI when needed
-    
-    def show_tuxborn_installer_menu(self, cli_instance):
-        """
-        Implements the Tuxborn Automatic Installer workflow.
-        Prompts for install path, downloads path, and Nexus API key, then runs the one-shot install from start to finish
-        
-        Args:
-            cli_instance: Reference to main CLI instance for access to handlers
-        """
-        # Import backend service
-        from jackify.backend.core.modlist_operations import ModlistInstallCLI
-        
-        print_jackify_banner()
-        print(f"{COLOR_SELECTION}Tuxborn Automatic Installer{COLOR_RESET}")
-        print(f"{COLOR_SELECTION}{'-'*32}{COLOR_RESET}")
-        print(f"{COLOR_INFO}This will install the Tuxborn modlist using the custom Jackify Install Engine in one automated flow.{COLOR_RESET}")
-        print(f"{COLOR_INFO}You will be prompted for the install location, downloads directory, and your Nexus API key.{COLOR_RESET}\n")
-        
-        tuxborn_machineid = "Tuxborn/Tuxborn"
-        tuxborn_modlist_name = "Tuxborn"
-
-        # Prompt for install directory
-        print("----------------------------")
-        config_handler = ConfigHandler()
-        base_install_dir = Path(config_handler.get_modlist_install_base_dir())
-        default_install_dir = base_install_dir / "Skyrim" / "Tuxborn"
-        print(f"{COLOR_PROMPT}Please enter the directory you wish to use for Tuxborn installation.{COLOR_RESET}")
-        print(f"(Default: {default_install_dir})")
-        install_dir_result = self._get_directory_path_legacy(
-            cli_instance,
-            prompt_message=f"{COLOR_PROMPT}Install directory (Enter for default, 'q' to cancel): {COLOR_RESET}",
-            default_path=default_install_dir,
-            create_if_missing=True,
-            no_header=True
-        )
-        if not install_dir_result:
-            print(f"{COLOR_INFO}Cancelled by user.{COLOR_RESET}")
-            input("Press Enter to return to the main menu...")
-            return
-        if isinstance(install_dir_result, tuple):
-            install_dir, _ = install_dir_result  # We'll use the path, creation handled by engine or later
-        else:
-            install_dir = install_dir_result
-
-        # Prompt for download directory
-        print("----------------------------")
-        base_download_dir = Path(config_handler.get_modlist_downloads_base_dir())
-        default_download_dir = base_download_dir / "Tuxborn"
-        print(f"{COLOR_PROMPT}Please enter the directory you wish to use for Tuxborn downloads.{COLOR_RESET}")
-        print(f"(Default: {default_download_dir})")
-        download_dir_result = self._get_directory_path_legacy(
-            cli_instance,
-            prompt_message=f"{COLOR_PROMPT}Download directory (Enter for default, 'q' to cancel): {COLOR_RESET}",
-            default_path=default_download_dir,
-            create_if_missing=True,
-            no_header=True
-        )
-        if not download_dir_result:
-            print(f"{COLOR_INFO}Cancelled by user.{COLOR_RESET}")
-            input("Press Enter to return to the main menu...")
-            return
-        if isinstance(download_dir_result, tuple):
-            download_dir, _ = download_dir_result  # We'll use the path, creation handled by engine or later
-        else:
-            download_dir = download_dir_result
-
-        # Prompt for Nexus API key
-        print("----------------------------")
-        from jackify.backend.services.api_key_service import APIKeyService
-        api_key_service = APIKeyService()
-        saved_key = api_key_service.get_saved_api_key()
-        api_key = None
-        
-        if saved_key:
-            print(f"{COLOR_INFO}A Nexus API Key is already saved.{COLOR_RESET}")
-            use_saved = input(f"{COLOR_PROMPT}Use the saved API key? [Y/n]: {COLOR_RESET}").strip().lower()
-            if use_saved in ('', 'y', 'yes'):
-                api_key = saved_key
-            else:
-                new_key = input(f"{COLOR_PROMPT}Enter a new Nexus API Key (or press Enter to keep the saved one): {COLOR_RESET}").strip()
-                if new_key:
-                    api_key = new_key
-                    replace = input(f"{COLOR_PROMPT}Replace the saved key with this one? [y/N]: {COLOR_RESET}").strip().lower()
-                    if replace == 'y':
-                        if api_key_service.save_api_key(api_key):
-                            print(f"{COLOR_INFO}API key saved successfully.{COLOR_RESET}")
-                        else:
-                            print(f"{COLOR_WARNING}Failed to save API key. Using for this session only.{COLOR_RESET}")
-                    else:
-                        print(f"{COLOR_INFO}Using new key for this session only. Saved key unchanged.{COLOR_RESET}")
-                else:
-                    api_key = saved_key
-        else:
-            print(f"{COLOR_PROMPT}A Nexus Mods API key is required for downloading mods.{COLOR_RESET}")
-            print(f"{COLOR_INFO}You can get your personal key at: {COLOR_SELECTION}https://www.nexusmods.com/users/myaccount?tab=api{COLOR_RESET}")
-            print(f"{COLOR_WARNING}Your API Key is NOT saved locally. It is used only for this session unless you choose to save it.{COLOR_RESET}")
-            api_key = input(f"{COLOR_PROMPT}Enter Nexus API Key (or 'q' to cancel): {COLOR_RESET}").strip()
-            if not api_key or api_key.lower() == 'q':
-                print(f"{COLOR_INFO}Cancelled by user.{COLOR_RESET}")
-                input("Press Enter to return to the main menu...")
-                return
-            save = input(f"{COLOR_PROMPT}Would you like to save this API key for future use? [y/N]: {COLOR_RESET}").strip().lower()
-            if save == 'y':
-                if api_key_service.save_api_key(api_key):
-                    print(f"{COLOR_INFO}API key saved successfully.{COLOR_RESET}")
-                else:
-                    print(f"{COLOR_WARNING}Failed to save API key. Using for this session only.{COLOR_RESET}")
-            else:
-                print(f"{COLOR_INFO}Using API key for this session only. It will not be saved.{COLOR_RESET}")
-
-        # Context for ModlistInstallCLI
-        context = {
-            'machineid': tuxborn_machineid,
-            'modlist_name': tuxborn_modlist_name,  # Will be used for shortcut name
-            'install_dir': install_dir_result,  # Pass tuple (path, create_flag) or path
-            'download_dir': download_dir_result,  # Pass tuple (path, create_flag) or path
-            'nexus_api_key': api_key,
-            'resolution': None
-        }
-
-        modlist_cli = ModlistInstallCLI(self, getattr(cli_instance, 'steamdeck', False))
-        
-        # run_discovery_phase will use context_override, display summary, and ask for confirmation.
-        # If user confirms, it returns the context, otherwise None.
-        confirmed_context = modlist_cli.run_discovery_phase(context_override=context)
-
-        if confirmed_context:
-            if self.logger:
-                self.logger.info("Tuxborn discovery confirmed by user. Proceeding to configuration/installation.")
-            # The modlist_cli instance now holds the confirmed context.
-            # configuration_phase will use modlist_cli.context
-            modlist_cli.configuration_phase() 
-            # After configuration_phase, messages about success or next steps are handled within it or by _configure_new_modlist
-        else:
-            if self.logger:
-                self.logger.info("Tuxborn discovery/confirmation cancelled or failed.")
-            print(f"{COLOR_INFO}Tuxborn installation cancelled or not confirmed.{COLOR_RESET}")
-            input(f"{COLOR_PROMPT}Press Enter to return to the main menu...{COLOR_RESET}")
-            return
-
-    def _get_directory_path_legacy(self, cli_instance, prompt_message: str, default_path: Optional[Path], 
-                                  create_if_missing: bool = True, no_header: bool = False) -> Optional[Path]:
-        """
-        LEGACY BRIDGE: Delegate to legacy menu handler until full backend migration
-        
-        Args:
-            cli_instance: Reference to main CLI instance
-            prompt_message: The prompt to show user
-            default_path: Default path if user presses Enter
-            create_if_missing: Whether to create directory if it doesn't exist
-            no_header: Whether to skip header display
-            
-        Returns:
-            Path object or None if cancelled
-        """
-        # LEGACY BRIDGE: Use the original menu handler's method
-        if hasattr(cli_instance, 'menu') and hasattr(cli_instance.menu, 'get_directory_path'):
-            return cli_instance.menu.get_directory_path(
-                prompt_message=prompt_message,
-                default_path=default_path,
-                create_if_missing=create_if_missing,
-                no_header=no_header
-            )
-        else:
-            # Fallback: simple input for now (will be replaced in future phases)
-            response = input(prompt_message).strip()
-            if response.lower() == 'q':
-                return None
-            elif response == '':
-                return default_path
-            else:
-                return Path(response) 

jackify/frontends/gui/main.py

@@ -131,7 +131,6 @@ DISCLAIMER_TEXT = (
 
 MENU_ITEMS = [
     ("Modlist Tasks", "modlist_tasks"),
-    ("Tuxborn Automatic Installer", "tuxborn_installer"),
     ("Hoolamike Tasks", "hoolamike_tasks"),
     ("Additional Tasks", "additional_tasks"),
     ("Exit Jackify", "exit_jackify"),
@@ -162,6 +161,8 @@ class SettingsDialog(QDialog):
         try:
             super().__init__(parent)
             from jackify.backend.handlers.config_handler import ConfigHandler
+            import logging
+            self.logger = logging.getLogger(__name__)
             self.config_handler = ConfigHandler()
             self._original_debug_mode = self.config_handler.get('debug_mode', False)
             self.setWindowTitle("Settings")
@@ -627,7 +628,18 @@ class SettingsDialog(QDialog):
         self.config_handler.set("proton_path", resolved_path)
         self.config_handler.set("proton_version", resolved_version)
 
-        self.config_handler.save_config()
+        # Force immediate save and verify
+        save_result = self.config_handler.save_config()
+        if not save_result:
+            self.logger.error("Failed to save Proton configuration")
+        else:
+            self.logger.info(f"Saved Proton config: path={resolved_path}, version={resolved_version}")
+            # Verify the save worked by reading it back
+            saved_path = self.config_handler.get("proton_path")
+            if saved_path != resolved_path:
+                self.logger.error(f"Config save verification failed: expected {resolved_path}, got {saved_path}")
+            else:
+                self.logger.debug("Config save verified successfully")
         
         # Refresh cached paths in GUI screens if Jackify directory changed
         self._refresh_gui_paths()
@@ -664,7 +676,6 @@ class SettingsDialog(QDialog):
                 getattr(main_window, 'install_modlist_screen', None),
                 getattr(main_window, 'configure_new_modlist_screen', None),
                 getattr(main_window, 'configure_existing_modlist_screen', None),
-                getattr(main_window, 'tuxborn_screen', None),
             ]
             
             for screen in screens_to_refresh:
@@ -773,7 +784,7 @@ class JackifyMainWindow(QMainWindow):
         
         # Create screens using refactored codebase
         from jackify.frontends.gui.screens import (
-            MainMenu, TuxbornInstallerScreen, ModlistTasksScreen, 
+            MainMenu, ModlistTasksScreen,
             InstallModlistScreen, ConfigureNewModlistScreen, ConfigureExistingModlistScreen
         )
         
@@ -785,31 +796,26 @@ class JackifyMainWindow(QMainWindow):
             main_menu_index=0,
             dev_mode=dev_mode
         )
-        self.tuxborn_screen = TuxbornInstallerScreen(
+        self.install_modlist_screen = InstallModlistScreen(
             stacked_widget=self.stacked_widget,
             main_menu_index=0
         )
-        self.install_modlist_screen = InstallModlistScreen(
-            stacked_widget=self.stacked_widget, 
-            main_menu_index=3
-        )
         self.configure_new_modlist_screen = ConfigureNewModlistScreen(
             stacked_widget=self.stacked_widget,
-            main_menu_index=3
+            main_menu_index=0
         )
         self.configure_existing_modlist_screen = ConfigureExistingModlistScreen(
             stacked_widget=self.stacked_widget,
-            main_menu_index=3
+            main_menu_index=0
         )
         
         # Add screens to stacked widget
         self.stacked_widget.addWidget(self.main_menu)           # Index 0: Main Menu
-        self.stacked_widget.addWidget(self.tuxborn_screen)      # Index 1: Tuxborn Installer
+        self.stacked_widget.addWidget(self.feature_placeholder) # Index 1: Placeholder
-        self.stacked_widget.addWidget(self.feature_placeholder) # Index 2: Placeholder
+        self.stacked_widget.addWidget(self.modlist_tasks_screen)  # Index 2: Modlist Tasks
-        self.stacked_widget.addWidget(self.modlist_tasks_screen)  # Index 3: Modlist Tasks
+        self.stacked_widget.addWidget(self.install_modlist_screen)        # Index 3: Install Modlist
-        self.stacked_widget.addWidget(self.install_modlist_screen)        # Index 4: Install Modlist
+        self.stacked_widget.addWidget(self.configure_new_modlist_screen)  # Index 4: Configure New
-        self.stacked_widget.addWidget(self.configure_new_modlist_screen)  # Index 5: Configure New
+        self.stacked_widget.addWidget(self.configure_existing_modlist_screen)  # Index 5: Configure Existing
-        self.stacked_widget.addWidget(self.configure_existing_modlist_screen)  # Index 6: Configure Existing
         
         # Add debug tracking for screen changes
         self.stacked_widget.currentChanged.connect(self._debug_screen_change)
@@ -887,12 +893,11 @@ class JackifyMainWindow(QMainWindow):
             
         screen_names = {
             0: "Main Menu",
-            1: "Tuxborn Installer", 
+            1: "Feature Placeholder",
-            2: "Feature Placeholder",
+            2: "Modlist Tasks Menu",
-            3: "Modlist Tasks Menu",
+            3: "Install Modlist Screen",
-            4: "Install Modlist Screen",
+            4: "Configure New Modlist",
-            5: "Configure New Modlist",
+            5: "Configure Existing Modlist"
-            6: "Configure Existing Modlist"
         }
         screen_name = screen_names.get(index, f"Unknown Screen (Index {index})")
         widget = self.stacked_widget.widget(index)
@@ -1002,7 +1007,7 @@ class JackifyMainWindow(QMainWindow):
             
             # Clean up screen processes
             screens = [
-                self.modlist_tasks_screen, self.tuxborn_screen, self.install_modlist_screen,
+                self.modlist_tasks_screen, self.install_modlist_screen,
                 self.configure_new_modlist_screen, self.configure_existing_modlist_screen
             ]
             for screen in screens:
@@ -1072,7 +1077,18 @@ def main():
     # Command-line --debug always takes precedence
     if '--debug' in sys.argv or '-d' in sys.argv:
         debug_mode = True
+        # Temporarily save CLI debug flag to config so engine can see it
+        config_handler.set('debug_mode', True)
+        print("[DEBUG] CLI --debug flag detected, saved debug_mode=True to config")
     import logging
+
+    # Initialize file logging on root logger so all modules inherit it
+    from jackify.shared.logging import LoggingHandler
+    logging_handler = LoggingHandler()
+    # Rotate log file before setting up new logger
+    logging_handler.rotate_log_for_logger('jackify_gui', 'jackify-gui.log')
+    root_logger = logging_handler.setup_logger('', 'jackify-gui.log', is_general=True)  # Empty name = root logger
+
     if debug_mode:
         logging.getLogger().setLevel(logging.DEBUG)
         print("[Jackify] Debug mode enabled (from config or CLI)")

jackify/frontends/gui/screens/__init__.py

@@ -5,7 +5,6 @@ Contains all the GUI screen components for Jackify.
 """
 
 from .main_menu import MainMenu
-from .tuxborn_installer import TuxbornInstallerScreen
 from .modlist_tasks import ModlistTasksScreen
 from .install_modlist import InstallModlistScreen
 from .configure_new_modlist import ConfigureNewModlistScreen
@@ -13,7 +12,6 @@ from .configure_existing_modlist import ConfigureExistingModlistScreen
 
 __all__ = [
     'MainMenu',
-    'TuxbornInstallerScreen', 
     'ModlistTasksScreen',
     'InstallModlistScreen',
     'ConfigureNewModlistScreen',

jackify/frontends/gui/screens/configure_existing_modlist.py

@@ -119,7 +119,7 @@ class ConfigureExistingModlistScreen(QWidget):
         self.shortcut_combo.addItem("Please Select...")
         self.shortcut_map = []
         for shortcut in self.mo2_shortcuts:
-            display = f"{shortcut.get('AppName', 'Unknown')} ({shortcut.get('StartDir', '')})"
+            display = f"{shortcut.get('AppName', shortcut.get('appname', 'Unknown'))} ({shortcut.get('StartDir', shortcut.get('startdir', ''))})"
             self.shortcut_combo.addItem(display)
             self.shortcut_map.append(shortcut)
         
@@ -427,8 +427,8 @@ class ConfigureExistingModlistScreen(QWidget):
             self._enable_controls_after_operation()
             return
         shortcut = self.shortcut_map[idx]
-        modlist_name = shortcut.get('AppName', '')
+        modlist_name = shortcut.get('AppName', shortcut.get('appname', ''))
-        install_dir = shortcut.get('StartDir', '')
+        install_dir = shortcut.get('StartDir', shortcut.get('startdir', ''))
         if not modlist_name or not install_dir:
             MessageService.critical(self, "Invalid Shortcut", "The selected shortcut is missing required information.", safety_level="medium")
             self._enable_controls_after_operation()
@@ -710,7 +710,7 @@ class ConfigureExistingModlistScreen(QWidget):
             self.shortcut_map.clear()
             
             for shortcut in self.mo2_shortcuts:
-                display = f"{shortcut.get('AppName', 'Unknown')} ({shortcut.get('StartDir', '')})"
+                display = f"{shortcut.get('AppName', shortcut.get('appname', 'Unknown'))} ({shortcut.get('StartDir', shortcut.get('startdir', ''))})"
                 self.shortcut_combo.addItem(display)
                 self.shortcut_map.append(shortcut)
             

jackify/frontends/gui/screens/configure_new_modlist.py

@@ -481,7 +481,7 @@ class ConfigureNewModlistScreen(QWidget):
 
     def go_back(self):
         if self.stacked_widget:
-            self.stacked_widget.setCurrentIndex(3)  # Return to Modlist Tasks menu
+            self.stacked_widget.setCurrentIndex(self.main_menu_index)
 
     def update_top_panel(self):
         try:

jackify/frontends/gui/screens/install_modlist.py

@@ -1057,7 +1057,7 @@ class InstallModlistScreen(QWidget):
 
     def go_back(self):
         if self.stacked_widget:
-            self.stacked_widget.setCurrentIndex(3)  # Return to Modlist Tasks menu 
+            self.stacked_widget.setCurrentIndex(self.main_menu_index) 
 
     def update_top_panel(self):
         try:
@@ -1746,7 +1746,7 @@ class InstallModlistScreen(QWidget):
             
             # Save resolution for later use in configuration
             resolution = self.resolution_combo.currentText()
-            self._current_resolution = resolution.split()[0] if resolution != "Leave unchanged" else "2560x1600"
+            self._current_resolution = resolution.split()[0] if resolution != "Leave unchanged" else None
             
             # Use automated prefix creation instead of manual steps
             debug_print("DEBUG: Starting automated prefix creation workflow")
@@ -2321,7 +2321,7 @@ class InstallModlistScreen(QWidget):
                 'mo2_exe_path': self._get_mo2_path(install_dir, modlist_name),
                 'modlist_value': None,
                 'modlist_source': None,
-                'resolution': getattr(self, '_current_resolution', '2560x1600'),
+                'resolution': getattr(self, '_current_resolution', None),
                 'skip_confirmation': True,
                 'manual_steps_completed': True,  # Mark as completed since automated prefix is done
                 'appid': new_appid,  # Use the NEW AppID from automated prefix creation
@@ -2360,7 +2360,7 @@ class InstallModlistScreen(QWidget):
                             nexus_api_key='',  # Not needed for configuration
                             modlist_value=self.context.get('modlist_value'),
                             modlist_source=self.context.get('modlist_source', 'identifier'),
-                            resolution=self.context.get('resolution', '2560x1600'),
+                            resolution=self.context.get('resolution'),
                             skip_confirmation=True,
                             engine_installed=True  # Skip path manipulation for engine workflows
                         )
@@ -2419,7 +2419,7 @@ class InstallModlistScreen(QWidget):
                 'mo2_exe_path': self._get_mo2_path(install_dir, modlist_name),
                 'modlist_value': None,
                 'modlist_source': None,
-                'resolution': getattr(self, '_current_resolution', '2560x1600'),
+                'resolution': getattr(self, '_current_resolution', None),
                 'skip_confirmation': True,
                 'manual_steps_completed': True,  # Mark as completed
                 'appid': new_appid  # Use the NEW AppID from Steam

jackify/frontends/gui/screens/main_menu.py

@@ -120,7 +120,7 @@ class MainMenu(QWidget):
             msg.setIcon(QMessageBox.Information)
             msg.exec()
         elif action_id == "modlist_tasks" and self.stacked_widget:
-            self.stacked_widget.setCurrentIndex(3)
+            self.stacked_widget.setCurrentIndex(2)
         elif action_id == "return_main_menu":
             # This is the main menu, so do nothing
             pass

jackify/frontends/gui/screens/modlist_tasks.py

@@ -198,11 +198,11 @@ class ModlistTasksScreen(QWidget):
         if action_id == "return_main_menu":
             self.stacked_widget.setCurrentIndex(0)
         elif action_id == "install_modlist":
-            self.stacked_widget.setCurrentIndex(4)
+            self.stacked_widget.setCurrentIndex(3)
         elif action_id == "configure_new_modlist":
-            self.stacked_widget.setCurrentIndex(5)
+            self.stacked_widget.setCurrentIndex(4)
         elif action_id == "configure_existing_modlist":
-            self.stacked_widget.setCurrentIndex(6)
+            self.stacked_widget.setCurrentIndex(5)
     
     def go_back(self):
         """Return to main menu"""