[core, *] support bundled application program IDs

src/android/app/src/main/java/org/yuzu/yuzu_emu/features/settings/utils/SettingsFile.kt

@@ -1,3 +1,6 @@
+// SPDX-FileCopyrightText: Copyright 2026 Eden Emulator Project
+// SPDX-License-Identifier: GPL-3.0-or-later
+
 // SPDX-FileCopyrightText: 2023 yuzu Emulator Project
 // SPDX-License-Identifier: GPL-2.0-or-later
 
@@ -24,6 +27,6 @@ object SettingsFile {
 
     fun loadCustomConfig(game: Game) {
         val fileName = FileUtil.getFilename(Uri.parse(game.path))
-        NativeConfig.initializePerGameConfig(game.programId, fileName)
+        NativeConfig.initializePerGameConfig(game.applicationId, fileName)
     }
 }

src/android/app/src/main/java/org/yuzu/yuzu_emu/fragments/AddonsFragment.kt

@@ -189,7 +189,7 @@ class AddonsFragment : Fragment() {
                 fragmentManager = parentFragmentManager,
                 addonViewModel = addonViewModel,
                 documents = documents,
-                programId = args.game.programId
+                programId = args.game.applicationId
             )
         }
 

src/android/app/src/main/java/org/yuzu/yuzu_emu/fragments/EmulationFragment.kt

@@ -347,7 +347,7 @@ class EmulationFragment : Fragment(), SurfaceHolder.Callback {
         }
         try {
             if (GpuDriverHelper.isAdrenoGpu()) {
-                val programIdHex = game!!.programIdHex
+                val programIdHex = game!!.applicationIdHex
                 if (NativeFreedrenoConfig.loadPerGameConfigWithGlobalFallback(programIdHex)) {
                     Log.info("[EmulationFragment] Loaded per-game Freedreno config for $programIdHex")
                 } else {

src/android/app/src/main/java/org/yuzu/yuzu_emu/fragments/FreedrenoSettingsFragment.kt

@@ -59,7 +59,7 @@ class FreedrenoSettingsFragment : Fragment() {
         NativeFreedrenoConfig.initializeFreedrenoConfig()
 
         if (isPerGameConfig) {
-            NativeFreedrenoConfig.loadPerGameConfig(game!!.programIdHex)
+            NativeFreedrenoConfig.loadPerGameConfig(game!!.applicationIdHex)
         } else {
             NativeFreedrenoConfig.reloadFreedrenoConfig()
         }
@@ -157,7 +157,7 @@ class FreedrenoSettingsFragment : Fragment() {
 
         binding.buttonSave.setOnClickListener {
             if (isPerGameConfig) {
-                NativeFreedrenoConfig.savePerGameConfig(game!!.programIdHex)
+                NativeFreedrenoConfig.savePerGameConfig(game!!.applicationIdHex)
                 showSnackbar(getString(R.string.freedreno_per_game_saved))
             } else {
                 NativeFreedrenoConfig.saveFreedrenoConfig()

src/android/app/src/main/java/org/yuzu/yuzu_emu/fragments/GamePropertiesFragment.kt

@@ -455,7 +455,7 @@ class GamePropertiesFragment : Fragment() {
 
                 val shaderCacheDir = File(
                     DirectoryInitialization.userDirectory +
-                        "/cache/shader/" + args.game.settingsName.lowercase()
+                        "/cache/shader/" + args.game.shaderCacheName.lowercase()
                 )
                 if (shaderCacheDir.exists()) {
                     add(
@@ -600,7 +600,7 @@ class GamePropertiesFragment : Fragment() {
                     val files = cacheSaveDir.listFiles()
                     var savesFolderFile: File? = null
                     if (files != null) {
-                        val savesFolderName = args.game.programIdHex
+                        val savesFolderName = args.game.applicationIdHex
                         for (file in files) {
                             if (file.isDirectory && file.name == savesFolderName) {
                                 savesFolderFile = file

src/android/app/src/main/java/org/yuzu/yuzu_emu/fragments/InstallableFragment.kt

@@ -232,7 +232,7 @@ class InstallableFragment : Fragment() {
                 fragmentManager = parentFragmentManager,
                 addonViewModel = addonViewModel,
                 documents = documents,
-                programId = addonViewModel.game?.programId
+                programId = addonViewModel.game?.applicationId
             )
         }
 

src/android/app/src/main/java/org/yuzu/yuzu_emu/model/AddonViewModel.kt

@@ -142,10 +142,11 @@ class AddonViewModel : ViewModel() {
     }
 
     fun onDeleteAddon(patch: Patch) {
+        val currentGame = game ?: return
         when (PatchType.from(patch.type)) {
-            PatchType.Update -> NativeLibrary.removeUpdate(patch.programId)
-            PatchType.DLC -> NativeLibrary.removeDLC(patch.programId)
-            PatchType.Mod -> NativeLibrary.removeMod(patch.programId, patch.name)
+            PatchType.Update -> NativeLibrary.removeUpdate(currentGame.programId)
+            PatchType.DLC -> NativeLibrary.removeDLC(currentGame.applicationId)
+            PatchType.Mod -> NativeLibrary.removeMod(currentGame.programId, patch.name)
         }
         refreshAddons(force = true)
     }
@@ -165,7 +166,7 @@ class AddonViewModel : ViewModel() {
         }
 
         NativeConfig.setDisabledAddons(
-            currentGame.programId,
+            currentGame.applicationId,
             currentList.mapNotNull {
                 if (it.enabled) {
                     null
@@ -199,6 +200,6 @@ class AddonViewModel : ViewModel() {
     }
 
     private fun gameKey(game: Game): String {
-        return "${game.programId}|${game.path}"
+        return "${game.applicationId}|${game.path}"
     }
 }

src/android/app/src/main/java/org/yuzu/yuzu_emu/model/DriverViewModel.kt

@@ -150,7 +150,7 @@ class DriverViewModel : ViewModel() {
                     ?: return@withContext
                 val shaderDir = File(
                     externalFilesDir.absolutePath +
-                    "/shader/" + game.settingsName.lowercase()
+                    "/shader/" + game.shaderCacheName.lowercase()
                 )
                 if (shaderDir.exists()) {
                     shaderDir.deleteRecursively()

src/android/app/src/main/java/org/yuzu/yuzu_emu/model/Game.kt

@@ -1,4 +1,4 @@
-// SPDX-FileCopyrightText: Copyright 2025 Eden Emulator Project
+// SPDX-FileCopyrightText: Copyright 2026 Eden Emulator Project
 // SPDX-License-Identifier: GPL-3.0-or-later
 
 // SPDX-FileCopyrightText: 2023 yuzu Emulator Project
@@ -35,19 +35,26 @@ class Game(
     val keyAddedToLibraryTime get() = "${path}_AddedToLibraryTime"
     val keyLastPlayedTime get() = "${path}_LastPlayed"
 
+    private val programIdLong: Long
+        get() = programId.toLongOrNull() ?: 0L
+
+    private val applicationIdLong: Long
+        get() = programIdLong and -8192L
+
+    val applicationId: String
+        get() = applicationIdLong.toString()
+
     val settingsName: String
         get() {
-            val programIdLong = programId.toLong()
-            return if (programIdLong == 0L) {
+            return if (applicationIdLong == 0L) {
                 FileUtil.getFilename(Uri.parse(path))
             } else {
-                "0" + programIdLong.toString(16).uppercase()
+                "0" + applicationIdLong.toString(16).uppercase()
             }
         }
 
     val programIdHex: String
         get() {
-            val programIdLong = programId.toLong()
             return if (programIdLong == 0L) {
                 "0"
             } else {
@@ -55,16 +62,32 @@ class Game(
             }
         }
 
+    val shaderCacheName: String
+        get() = if (programIdLong == 0L) {
+            FileUtil.getFilename(Uri.parse(path))
+        } else {
+            "0" + programIdLong.toString(16).uppercase()
+        }
+
+    val applicationIdHex: String
+        get() {
+            return if (applicationIdLong == 0L) {
+                "0"
+            } else {
+                "0" + applicationIdLong.toString(16).uppercase()
+            }
+        }
+
     val saveZipName: String
         get() = "$title ${YuzuApplication.appContext.getString(R.string.save_data).lowercase()} - ${
         LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyy-MM-dd HH:mm"))
         }.zip"
 
     val saveDir: String
-        get() = NativeConfig.getSaveDir() + NativeLibrary.getSavePath(programId)
+        get() = NativeConfig.getSaveDir() + NativeLibrary.getSavePath(applicationId)
 
     val addonDir: String
-        get() = DirectoryInitialization.userDirectory + "/load/" + programIdHex + "/"
+        get() = DirectoryInitialization.userDirectory + "/load/" + applicationIdHex + "/"
 
     val launchIntent: Intent
         get() = Intent(YuzuApplication.appContext, EmulationActivity::class.java).apply {

src/android/app/src/main/java/org/yuzu/yuzu_emu/utils/CustomSettingsHandler.kt

@@ -1,4 +1,4 @@
-// SPDX-FileCopyrightText: Copyright 2025 Eden Emulator Project
+// SPDX-FileCopyrightText: Copyright 2026 Eden Emulator Project
 // SPDX-License-Identifier: GPL-3.0-or-later
 
 // SPDX-FileCopyrightText: 2023 yuzu Emulator Project
@@ -65,7 +65,7 @@ object CustomSettingsHandler {
         // Initialize per-game config
         try {
             val fileName = FileUtil.getFilename(Uri.parse(game.path))
-            NativeConfig.initializePerGameConfig(game.programId, fileName)
+            NativeConfig.initializePerGameConfig(game.applicationId, fileName)
             Log.info("[CustomSettingsHandler] Successfully applied custom settings")
             return game
         } catch (e: Exception) {
@@ -333,20 +333,20 @@ object CustomSettingsHandler {
      */
     fun findGameByTitleId(titleId: String, context: Context): Game? {
         Log.info("[CustomSettingsHandler] Searching for game with title ID: $titleId")
-        // Convert hex title ID to decimal for comparison with programId
-        val programIdDecimal = try {
-            titleId.toLong(16).toString()
+        // Convert the program ID to the application ID used by per-game settings.
+        val applicationIdLong = try {
+            titleId.toLong(16) and -8192L
         } catch (e: NumberFormatException) {
             Log.error("[CustomSettingsHandler] Invalid title ID format: $titleId")
             return null
         }
+        val applicationIdDecimal = applicationIdLong.toString()
 
         // Expected hex format with "0" prefix
-        val expectedHex = "0${titleId.uppercase()}"
+        val expectedHex = "0${applicationIdLong.toString(16).uppercase()}"
         // First check cached games for fast lookup
         GameHelper.cachedGameList.find { game ->
-            game.programId == programIdDecimal ||
-                game.programIdHex.equals(expectedHex, ignoreCase = true)
+            game.applicationId == applicationIdDecimal || game.applicationIdHex.equals(expectedHex, ignoreCase = true)
         }?.let { foundGame ->
             Log.info("[CustomSettingsHandler] Found game in cache: ${foundGame.title}")
             return foundGame
@@ -355,8 +355,7 @@ object CustomSettingsHandler {
         Log.info("[CustomSettingsHandler] Game not in cache, scanning full library...")
         val allGames = GameHelper.getGames()
         val foundGame = allGames.find { game ->
-            game.programId == programIdDecimal ||
-                game.programIdHex.equals(expectedHex, ignoreCase = true)
+            game.applicationId == applicationIdDecimal || game.applicationIdHex.equals(expectedHex, ignoreCase = true)
         }
         if (foundGame != null) {
             Log.info("[CustomSettingsHandler] Found game: ${foundGame.title} at ${foundGame.path}")

src/android/app/src/main/java/org/yuzu/yuzu_emu/utils/GameHelper.kt

@@ -170,12 +170,12 @@ object GameHelper {
                     val game = getGame(it.uri, true, false)
                     if (game != null) {
                         games.add(game)
-                        if (game.programId != "0") {
-                            gamesByProgramId[game.programId] = game
+                        if (game.applicationId != "0") {
+                            gamesByProgramId[game.applicationId] = game
                         }
                     } else if (mountedContainer) {
                         GameMetadata.getProgramId(filePath).toLongOrNull()?.let { programId ->
-                            gamesByProgramId[(programId and 0x800L.inv()).toString()]
+                            gamesByProgramId[(programId and -8192L).toString()]
                         }?.let { existingGame ->
                             NativeLibrary.getPatchesForFile(existingGame.path, existingGame.programId)
                             existingGame.version = GameMetadata.getVersion(

src/android/app/src/main/jni/native.cpp

@@ -788,7 +788,7 @@ int Java_org_yuzu_yuzu_1emu_NativeLibrary_installFileToNand(JNIEnv* env, jobject
 jboolean Java_org_yuzu_yuzu_1emu_NativeLibrary_doesUpdateMatchProgram(JNIEnv* env, jobject jobj,
                                                                       jstring jprogramId,
                                                                       jstring jupdatePath) {
-    u64 program_id = EmulationSession::GetProgramId(env, jprogramId);
+    const u64 program_id = FileSys::GetBaseTitleID(EmulationSession::GetProgramId(env, jprogramId));
     std::string updatePath = Common::Android::GetJString(env, jupdatePath);
     std::shared_ptr<FileSys::NSP> nsp = std::make_shared<FileSys::NSP>(
         EmulationSession::GetInstance().System().GetFilesystem()->OpenFile(
@@ -796,7 +796,7 @@ jboolean Java_org_yuzu_yuzu_1emu_NativeLibrary_doesUpdateMatchProgram(JNIEnv* en
     for (const auto& item : nsp->GetNCAs()) {
         for (const auto& nca_details : item.second) {
             if (nca_details.second->GetName().ends_with(".cnmt.nca")) {
-                auto update_id = nca_details.second->GetTitleId() & ~0xFFFULL;
+                const auto update_id = FileSys::GetBaseTitleID(nca_details.second->GetTitleId());
                 if (update_id == program_id) {
                     return true;
                 }
@@ -1491,7 +1491,7 @@ jstring Java_org_yuzu_yuzu_1emu_NativeLibrary_firmwareVersion(JNIEnv* env, jclas
 }
 
 jboolean Java_org_yuzu_yuzu_1emu_NativeLibrary_gameRequiresFirmware(JNIEnv* env, jclass clazz, jstring jprogramId) {
-    auto program_id = EmulationSession::GetProgramId(env, jprogramId);
+    const auto program_id = FileSys::GetBaseTitleID(EmulationSession::GetProgramId(env, jprogramId));
 
     return FirmwareManager::GameRequiresFirmware(program_id);
 }
@@ -1575,20 +1575,21 @@ jobjectArray Java_org_yuzu_yuzu_1emu_NativeLibrary_getPatchesForFile(JNIEnv* env
 
 void Java_org_yuzu_yuzu_1emu_NativeLibrary_removeUpdate(JNIEnv* env, jobject jobj,
                                                         jstring jprogramId) {
-    auto program_id = EmulationSession::GetProgramId(env, jprogramId);
+    const auto program_id = EmulationSession::GetProgramId(env, jprogramId);
     ContentManager::RemoveUpdate(EmulationSession::GetInstance().System().GetFileSystemController(),
                                  program_id);
 }
 
 void Java_org_yuzu_yuzu_1emu_NativeLibrary_removeDLC(JNIEnv* env, jobject jobj,
                                                      jstring jprogramId) {
-    auto program_id = EmulationSession::GetProgramId(env, jprogramId);
+    const auto program_id = FileSys::GetBaseTitleID(
+        EmulationSession::GetProgramId(env, jprogramId));
     ContentManager::RemoveAllDLC(EmulationSession::GetInstance().System(), program_id);
 }
 
 void Java_org_yuzu_yuzu_1emu_NativeLibrary_removeMod(JNIEnv* env, jobject jobj, jstring jprogramId,
                                                      jstring jname) {
-    auto program_id = EmulationSession::GetProgramId(env, jprogramId);
+    const auto program_id = EmulationSession::GetProgramId(env, jprogramId);
     ContentManager::RemoveMod(EmulationSession::GetInstance().System().GetFileSystemController(),
                               program_id, Common::Android::GetJString(env, jname));
 }
@@ -1635,7 +1636,7 @@ jint Java_org_yuzu_yuzu_1emu_NativeLibrary_verifyGameContents(JNIEnv* env, jobje
 
 jstring Java_org_yuzu_yuzu_1emu_NativeLibrary_getSavePath(JNIEnv* env, jobject jobj,
                                                           jstring jprogramId) {
-    auto program_id = EmulationSession::GetProgramId(env, jprogramId);
+    const auto program_id = FileSys::GetBaseTitleID(EmulationSession::GetProgramId(env, jprogramId));
     if (program_id == 0) {
         return Common::Android::ToJString(env, "");
     }

src/android/app/src/main/jni/native_config.cpp

@@ -12,6 +12,7 @@
 #include "common/fs/path_util.h"
 #include "common/logging.h"
 #include "common/settings.h"
+#include "core/file_sys/common_funcs.h"
 #include "frontend_common/config.h"
 #include "frontend_common/settings_generator.h"
 #include "native.h"
@@ -56,7 +57,7 @@ void Java_org_yuzu_yuzu_1emu_utils_NativeConfig_saveGlobalConfig(JNIEnv* env, jo
 void Java_org_yuzu_yuzu_1emu_utils_NativeConfig_initializePerGameConfig(JNIEnv* env, jobject obj,
                                                                         jstring jprogramId,
                                                                         jstring jfileName) {
-    auto program_id = EmulationSession::GetProgramId(env, jprogramId);
+    const auto program_id = FileSys::GetBaseTitleID(EmulationSession::GetProgramId(env, jprogramId));
     auto file_name = Common::Android::GetJString(env, jfileName);
     const auto config_file_name = program_id == 0 ? file_name : fmt::format("{:016X}", program_id);
     per_game_config =
@@ -322,7 +323,7 @@ void Java_org_yuzu_yuzu_1emu_utils_NativeConfig_addGameDir(JNIEnv* env, jobject
 
 jobjectArray Java_org_yuzu_yuzu_1emu_utils_NativeConfig_getDisabledAddons(JNIEnv* env, jobject obj,
                                                                           jstring jprogramId) {
-    auto program_id = EmulationSession::GetProgramId(env, jprogramId);
+    const auto program_id = FileSys::GetBaseTitleID(EmulationSession::GetProgramId(env, jprogramId));
     auto& disabledAddons = Settings::values.disabled_addons[program_id];
     jobjectArray jdisabledAddonsArray =
         env->NewObjectArray(disabledAddons.size(), Common::Android::GetStringClass(),
@@ -337,7 +338,7 @@ jobjectArray Java_org_yuzu_yuzu_1emu_utils_NativeConfig_getDisabledAddons(JNIEnv
 void Java_org_yuzu_yuzu_1emu_utils_NativeConfig_setDisabledAddons(JNIEnv* env, jobject obj,
                                                                   jstring jprogramId,
                                                                   jobjectArray jdisabledAddons) {
-    auto program_id = EmulationSession::GetProgramId(env, jprogramId);
+    const auto program_id = FileSys::GetBaseTitleID(EmulationSession::GetProgramId(env, jprogramId));
     Settings::values.disabled_addons[program_id].clear();
     std::vector<std::string> disabled_addons;
     const int size = env->GetArrayLength(jdisabledAddons);

src/core/core.cpp

@@ -17,6 +17,7 @@
 #include "common/string_util.h"
 #include "core/arm/exclusive_monitor.h"
 #include "core/core.h"
+#include "core/file_sys/common_funcs.h"
 
 #include "launch_timestamp_cache.h"
 #include "core/core_timing.h"
@@ -396,7 +397,7 @@ struct System::Impl {
             LOG_ERROR(Core, "Failed to find program id for ROM");
         }
 
-        GameSettings::LoadOverrides(program_id, gpu_core->Renderer());
+        GameSettings::LoadOverrides(FileSys::GetBaseTitleID(program_id), gpu_core->Renderer());
         if (auto room_member = Network::GetRoomMember().lock()) {
             Network::GameInfo game_info;
             game_info.name = name;

src/core/file_sys/patch_manager.cpp

@@ -161,7 +161,7 @@ std::string GetUpdateVersionStringFromSlot(const ContentProvider* provider, u64
 PatchManager::PatchManager(u64 title_id_,
                            const Service::FileSystem::FileSystemController& fs_controller_,
                            const ContentProvider& content_provider_)
-    : title_id{title_id_}, fs_controller{fs_controller_}, content_provider{content_provider_} {}
+    : title_id{title_id_}, application_id{GetBaseTitleID(title_id_)}, fs_controller{fs_controller_}, content_provider{content_provider_} {}
 
 PatchManager::~PatchManager() = default;
 
@@ -169,13 +169,41 @@ u64 PatchManager::GetTitleID() const {
     return title_id;
 }
 
+u64 PatchManager::GetUpdateTitleIDForContent() const {
+    const auto program_update_id = GetUpdateTitleID(title_id);
+    if (program_update_id == GetUpdateTitleID(application_id) || content_provider.HasEntry(program_update_id, ContentRecordType::Program)) {
+        return program_update_id;
+    }
+    return GetUpdateTitleID(application_id);
+}
+
+std::vector<VirtualDir> PatchManager::GetModificationLoadRoots() const {
+    std::vector<VirtualDir> roots;
+    roots.push_back(fs_controller.GetModificationLoadRoot(title_id));
+    if (application_id != title_id) {
+        roots.push_back(fs_controller.GetModificationLoadRoot(application_id));
+    }
+    std::erase(roots, nullptr);
+    return roots;
+}
+
+std::vector<VirtualDir> PatchManager::GetSDMCModificationLoadRoots() const {
+    std::vector<VirtualDir> roots;
+    roots.push_back(fs_controller.GetSDMCModificationLoadRoot(title_id));
+    if (application_id != title_id) {
+        roots.push_back(fs_controller.GetSDMCModificationLoadRoot(application_id));
+    }
+    std::erase(roots, nullptr);
+    return roots;
+}
+
 VirtualDir PatchManager::PatchExeFS(VirtualDir exefs) const {
     LOG_INFO(Loader, "Patching ExeFS for title_id={:016X}", title_id);
 
     if (exefs == nullptr)
         return exefs;
 
-    const auto& disabled = Settings::values.disabled_addons[title_id];
+    const auto& disabled = Settings::values.disabled_addons[application_id];
 
     bool update_disabled = true;
     std::optional<u32> enabled_version;
@@ -183,7 +211,7 @@ VirtualDir PatchManager::PatchExeFS(VirtualDir exefs) const {
     bool checked_manual = false;
 
     const auto* content_union = static_cast<const ContentProviderUnion*>(&content_provider);
-    const auto update_tid = GetUpdateTitleID(title_id);
+    const auto update_tid = GetUpdateTitleIDForContent();
 
     if (content_union) {
         // First, check ExternalContentProvider
@@ -303,17 +331,21 @@ VirtualDir PatchManager::PatchExeFS(VirtualDir exefs) const {
     }
 
     // LayeredExeFS
-    const auto load_dir = fs_controller.GetModificationLoadRoot(title_id);
-    const auto sdmc_load_dir = fs_controller.GetSDMCModificationLoadRoot(title_id);
+    const auto load_dirs = GetModificationLoadRoots();
+    const auto sdmc_load_dirs = GetSDMCModificationLoadRoots();
 
-    std::vector<VirtualDir> patch_dirs = {sdmc_load_dir};
-    if (load_dir != nullptr) {
+    std::vector<VirtualDir> patch_dirs;
+    for (const auto& sdmc_load_dir : sdmc_load_dirs) {
+        patch_dirs.push_back(sdmc_load_dir);
+    }
+    for (const auto& load_dir : load_dirs) {
         const auto load_patch_dirs = load_dir->GetSubdirectories();
         patch_dirs.insert(patch_dirs.end(), load_patch_dirs.begin(), load_patch_dirs.end());
     }
 
-    std::sort(patch_dirs.begin(), patch_dirs.end(),
-              [](const VirtualDir& l, const VirtualDir& r) { return l->GetName() < r->GetName(); });
+    std::stable_sort(patch_dirs.begin(), patch_dirs.end(), [](const VirtualDir& l, const VirtualDir& r) {
+        return l->GetName() < r->GetName();
+    });
 
     std::vector<VirtualDir> layers;
     layers.reserve(patch_dirs.size() + 1);
@@ -347,7 +379,7 @@ VirtualDir PatchManager::PatchExeFS(VirtualDir exefs) const {
 
 std::vector<VirtualFile> PatchManager::CollectPatches(const std::vector<VirtualDir>& patch_dirs,
                                                       const std::string& build_id) const {
-    const auto& disabled = Settings::values.disabled_addons[title_id];
+    const auto& disabled = Settings::values.disabled_addons[application_id];
     const auto nso_build_id = fmt::format("{:0<64}", build_id);
 
     std::vector<VirtualFile> out;
@@ -412,15 +444,20 @@ std::vector<u8> PatchManager::PatchNSO(const std::vector<u8>& nso, const std::st
 
     LOG_INFO(Loader, "Patching NSO for name={}, build_id={}", name, build_id);
 
-    const auto load_dir = fs_controller.GetModificationLoadRoot(title_id);
-    if (load_dir == nullptr) {
+    const auto load_dirs = GetModificationLoadRoots();
+    if (load_dirs.empty()) {
         LOG_ERROR(Loader, "Cannot load mods for invalid title_id={:016X}", title_id);
         return nso;
     }
 
-    auto patch_dirs = load_dir->GetSubdirectories();
-    std::sort(patch_dirs.begin(), patch_dirs.end(),
-              [](const VirtualDir& l, const VirtualDir& r) { return l->GetName() < r->GetName(); });
+    std::vector<VirtualDir> patch_dirs;
+    for (const auto& load_dir : load_dirs) {
+        const auto load_patch_dirs = load_dir->GetSubdirectories();
+        patch_dirs.insert(patch_dirs.end(), load_patch_dirs.begin(), load_patch_dirs.end());
+    }
+    std::stable_sort(patch_dirs.begin(), patch_dirs.end(), [](const VirtualDir& l, const VirtualDir& r) {
+        return l->GetName() < r->GetName();
+    });
     const auto patches = CollectPatches(patch_dirs, build_id);
 
     auto out = nso;
@@ -455,29 +492,39 @@ bool PatchManager::HasNSOPatch(const BuildID& build_id_, std::string_view name)
 
     LOG_INFO(Loader, "Querying NSO patch existence for build_id={}, name={}", build_id, name);
 
-    const auto load_dir = fs_controller.GetModificationLoadRoot(title_id);
-    if (load_dir == nullptr) {
+    const auto load_dirs = GetModificationLoadRoots();
+    if (load_dirs.empty()) {
         LOG_ERROR(Loader, "Cannot load mods for invalid title_id={:016X}", title_id);
         return false;
     }
 
-    auto patch_dirs = load_dir->GetSubdirectories();
-    std::sort(patch_dirs.begin(), patch_dirs.end(),
-              [](const VirtualDir& l, const VirtualDir& r) { return l->GetName() < r->GetName(); });
+    std::vector<VirtualDir> patch_dirs;
+    for (const auto& load_dir : load_dirs) {
+        const auto load_patch_dirs = load_dir->GetSubdirectories();
+        patch_dirs.insert(patch_dirs.end(), load_patch_dirs.begin(), load_patch_dirs.end());
+    }
+    std::stable_sort(patch_dirs.begin(), patch_dirs.end(), [](const VirtualDir& l, const VirtualDir& r) {
+        return l->GetName() < r->GetName();
+    });
 
     return !CollectPatches(patch_dirs, build_id).empty();
 }
 
 std::vector<Core::Memory::CheatEntry> PatchManager::CreateCheatList(const BuildID& build_id_) const {
-    const auto load_dir = fs_controller.GetModificationLoadRoot(title_id);
-    if (load_dir == nullptr) {
+    const auto load_dirs = GetModificationLoadRoots();
+    if (load_dirs.empty()) {
         LOG_ERROR(Loader, "Cannot load mods for invalid title_id={:016X}", title_id);
         return {};
     }
 
-    const auto& disabled = Settings::values.disabled_addons[title_id];
-    auto patch_dirs = load_dir->GetSubdirectories();
-    std::sort(patch_dirs.begin(), patch_dirs.end(), [](auto const& l, auto const& r) { return l->GetName() < r->GetName(); });
+    const auto& disabled = Settings::values.disabled_addons[application_id];
+    std::vector<VirtualDir> patch_dirs;
+    for (const auto& load_dir : load_dirs) {
+        const auto load_patch_dirs = load_dir->GetSubdirectories();
+        patch_dirs.insert(patch_dirs.end(), load_patch_dirs.begin(), load_patch_dirs.end());
+    }
+    std::stable_sort(patch_dirs.begin(), patch_dirs.end(),
+                     [](auto const& l, auto const& r) { return l->GetName() < r->GetName(); });
 
     // <mod dir> / <folder> / cheats / <build id>.txt
     std::vector<Core::Memory::CheatEntry> out;
@@ -493,39 +540,52 @@ std::vector<Core::Memory::CheatEntry> PatchManager::CreateCheatList(const BuildI
     }
     // Uncareless user-friendly loading of patches (must start with 'cheat_')
     // <mod dir> / <cheat file>.txt
-    for (auto const& f : load_dir->GetFiles()) {
-        auto const name = f->GetName();
-        if (name.starts_with("cheat_") && std::find(disabled.cbegin(), disabled.cend(), name) == disabled.cend()) {
-            std::vector<u8> data(f->GetSize());
-            if (f->Read(data.data(), data.size()) == data.size()) {
-                const Core::Memory::TextCheatParser parser;
-                auto const res = parser.Parse(std::string_view(reinterpret_cast<const char*>(data.data()), data.size()));
-                std::copy(res.begin(), res.end(), std::back_inserter(out));
-            } else {
-                LOG_INFO(Common_Filesystem, "Failed to read cheats file for title_id={:016X}", title_id);
+    for (const auto& load_dir : load_dirs) {
+        for (auto const& f : load_dir->GetFiles()) {
+            auto const name = f->GetName();
+            if (name.starts_with("cheat_") && std::find(disabled.cbegin(), disabled.cend(), name) == disabled.cend()) {
+                std::vector<u8> data(f->GetSize());
+                if (f->Read(data.data(), data.size()) == data.size()) {
+                    const Core::Memory::TextCheatParser parser;
+                    auto const res = parser.Parse(std::string_view(reinterpret_cast<const char*>(data.data()), data.size()));
+                    std::copy(res.begin(), res.end(), std::back_inserter(out));
+                } else {
+                    LOG_INFO(Common_Filesystem, "Failed to read cheats file for title_id={:016X}", title_id);
+                }
             }
         }
     }
     return out;
 }
 
-static void ApplyLayeredFS(VirtualFile& romfs, u64 title_id, ContentRecordType type,
+static void ApplyLayeredFS(VirtualFile& romfs, u64 title_id, u64 application_id, ContentRecordType type,
                            const Service::FileSystem::FileSystemController& fs_controller) {
-    const auto load_dir = fs_controller.GetModificationLoadRoot(title_id);
-    const auto sdmc_load_dir = fs_controller.GetSDMCModificationLoadRoot(title_id);
+    std::vector<VirtualDir> load_dirs{fs_controller.GetModificationLoadRoot(title_id)};
+    std::vector<VirtualDir> sdmc_load_dirs{fs_controller.GetSDMCModificationLoadRoot(title_id)};
+    if (application_id != title_id) {
+        load_dirs.push_back(fs_controller.GetModificationLoadRoot(application_id));
+        sdmc_load_dirs.push_back(fs_controller.GetSDMCModificationLoadRoot(application_id));
+    }
+    std::erase(load_dirs, nullptr);
+    std::erase(sdmc_load_dirs, nullptr);
     if ((type != ContentRecordType::Program && type != ContentRecordType::Data &&
          type != ContentRecordType::HtmlDocument) ||
-        (load_dir == nullptr && sdmc_load_dir == nullptr)) {
+        (load_dirs.empty() && sdmc_load_dirs.empty())) {
         return;
     }
 
-    const auto& disabled = Settings::values.disabled_addons[title_id];
-    std::vector<VirtualDir> patch_dirs = load_dir->GetSubdirectories();
-    if (std::find(disabled.cbegin(), disabled.cend(), "SDMC") == disabled.cend()) {
-        patch_dirs.push_back(sdmc_load_dir);
+    const auto& disabled = Settings::values.disabled_addons[application_id];
+    std::vector<VirtualDir> patch_dirs;
+    for (const auto& load_dir : load_dirs) {
+        const auto load_patch_dirs = load_dir->GetSubdirectories();
+        patch_dirs.insert(patch_dirs.end(), load_patch_dirs.begin(), load_patch_dirs.end());
     }
-    std::sort(patch_dirs.begin(), patch_dirs.end(),
-              [](const VirtualDir& l, const VirtualDir& r) { return l->GetName() < r->GetName(); });
+    if (std::find(disabled.cbegin(), disabled.cend(), "SDMC") == disabled.cend()) {
+        patch_dirs.insert(patch_dirs.end(), sdmc_load_dirs.begin(), sdmc_load_dirs.end());
+    }
+    std::stable_sort(patch_dirs.begin(), patch_dirs.end(), [](const VirtualDir& l, const VirtualDir& r) {
+        return l->GetName() < r->GetName();
+    });
 
     std::vector<VirtualDir> layers;
     std::vector<VirtualDir> layers_ext;
@@ -597,8 +657,8 @@ VirtualFile PatchManager::PatchRomFS(const NCA* base_nca, VirtualFile base_romfs
     auto romfs = base_romfs;
 
     // Game Updates
-    const auto update_tid = GetUpdateTitleID(title_id);
-    const auto& disabled = Settings::values.disabled_addons[title_id];
+    const auto update_tid = GetUpdateTitleIDForContent();
+    const auto& disabled = Settings::values.disabled_addons[application_id];
 
     bool update_disabled = true;
     std::optional<u32> enabled_version;
@@ -705,7 +765,7 @@ VirtualFile PatchManager::PatchRomFS(const NCA* base_nca, VirtualFile base_romfs
 
     // LayeredFS
     if (apply_layeredfs) {
-        ApplyLayeredFS(romfs, title_id, type, fs_controller);
+        ApplyLayeredFS(romfs, title_id, application_id, type, fs_controller);
     }
 
     return romfs;
@@ -717,10 +777,10 @@ std::vector<Patch> PatchManager::GetPatches(VirtualFile update_raw) const {
     }
 
     std::vector<Patch> out;
-    const auto& disabled = Settings::values.disabled_addons[title_id];
+    const auto& disabled = Settings::values.disabled_addons[application_id];
 
     // Game Updates
-    const auto update_tid = GetUpdateTitleID(title_id);
+    const auto update_tid = GetUpdateTitleIDForContent();
 
     std::vector<Patch> external_update_patches;
 
@@ -869,7 +929,7 @@ std::vector<Patch> PatchManager::GetPatches(VirtualFile update_raw) const {
                               .version = "",
                               .type = PatchType::Update,
                               .program_id = title_id,
-                              .title_id = title_id,
+                              .title_id = update_tid,
                               .source = PatchSource::Unknown,
                               .numeric_version = 0};
 
@@ -895,8 +955,7 @@ std::vector<Patch> PatchManager::GetPatches(VirtualFile update_raw) const {
     }
 
     // General Mods (LayeredFS and IPS)
-    const auto mod_dir = fs_controller.GetModificationLoadRoot(title_id);
-    if (mod_dir != nullptr) {
+    for (const auto& mod_dir : GetModificationLoadRoots()) {
         for (auto const& f : mod_dir->GetFiles())
             if (auto const name = f->GetName(); name.starts_with("cheat_")) {
                 auto const mod_disabled = std::find(disabled.begin(), disabled.end(), name) != disabled.end();
@@ -963,8 +1022,7 @@ std::vector<Patch> PatchManager::GetPatches(VirtualFile update_raw) const {
     }
 
     // SDMC mod directory (RomFS LayeredFS)
-    const auto sdmc_mod_dir = fs_controller.GetSDMCModificationLoadRoot(title_id);
-    if (sdmc_mod_dir != nullptr) {
+    for (const auto& sdmc_mod_dir : GetSDMCModificationLoadRoots()) {
         std::string types;
         if (IsDirValidAndNonEmpty(FindSubdirectoryCaseless(sdmc_mod_dir, "exefs")))
             AppendCommaIfNotEmpty(types, "LayeredExeFS");
@@ -999,10 +1057,10 @@ std::vector<Patch> PatchManager::GetPatches(VirtualFile update_raw) const {
     dlc_match.reserve(dlc_entries_with_origin.size());
     for (const auto& [slot, entry] : dlc_entries_with_origin) {
         const auto base_tid = GetBaseTitleID(entry.title_id);
-        const bool matches_base = base_tid == title_id;
+        const bool matches_base = base_tid == application_id;
         if (!matches_base) {
             LOG_DEBUG(Loader, "DLC {:016X} base {:016X} doesn't match title {:016X}",
-                      entry.title_id, base_tid, title_id);
+                      entry.title_id, base_tid, application_id);
             continue;
         }
 
@@ -1077,16 +1135,22 @@ std::vector<Patch> PatchManager::GetPatches(VirtualFile update_raw) const {
 }
 
 std::optional<u32> PatchManager::GetGameVersion() const {
-    const auto update_tid = GetUpdateTitleID(title_id);
+    const auto update_tid = GetUpdateTitleIDForContent();
     if (content_provider.HasEntry(update_tid, ContentRecordType::Program)) {
         return content_provider.GetEntryVersion(update_tid);
     }
 
-    return content_provider.GetEntryVersion(title_id);
+    if (const auto version = content_provider.GetEntryVersion(title_id); version.has_value()) {
+        return version;
+    }
+    return content_provider.GetEntryVersion(application_id);
 }
 
 PatchManager::Metadata PatchManager::GetControlMetadata() const {
-    const auto base_control_nca = content_provider.GetEntry(title_id, ContentRecordType::Control);
+    auto base_control_nca = content_provider.GetEntry(title_id, ContentRecordType::Control);
+    if (base_control_nca == nullptr && application_id != title_id) {
+        base_control_nca = content_provider.GetEntry(application_id, ContentRecordType::Control);
+    }
     if (base_control_nca == nullptr) {
         return {};
     }
@@ -1162,8 +1226,14 @@ PatchManager::Metadata PatchManager::ParseControlNCA(const NCA& nca) const {
     auto metadata = pm.GetControlMetadata();
     if (metadata.first != nullptr)
         return metadata;
-    const FileSys::PatchManager pm_update{FileSys::GetUpdateTitleID(application_id), system.GetFileSystemController(), system.GetContentProvider()};
-    return pm_update.GetControlMetadata();
+    const auto update_id = FileSys::GetUpdateTitleID(application_id);
+    const auto application_update_id = FileSys::GetUpdateTitleID(GetBaseTitleID(application_id));
+    const FileSys::PatchManager pm_update{update_id, system.GetFileSystemController(), system.GetContentProvider()};
+    metadata = pm_update.GetControlMetadata();
+    if (metadata.first != nullptr || update_id == application_update_id)
+        return metadata;
+    const FileSys::PatchManager pm_application_update{application_update_id, system.GetFileSystemController(), system.GetContentProvider()};
+    return pm_application_update.GetControlMetadata();
 }
 
 } // namespace FileSys

src/core/file_sys/patch_manager.h

@@ -10,6 +10,7 @@
 #include <memory>
 #include <optional>
 #include <string>
+#include <vector>
 #include "common/common_types.h"
 #include "core/file_sys/nca_metadata.h"
 #include "core/file_sys/vfs/vfs_types.h"
@@ -109,10 +110,14 @@ public:
     [[nodiscard]] static PatchManager::Metadata GetMetadataFromBaseOrUpdate(Core::System& system, u64 application_id) noexcept;
 
 private:
+    [[nodiscard]] u64 GetUpdateTitleIDForContent() const;
+    [[nodiscard]] std::vector<VirtualDir> GetModificationLoadRoots() const;
+    [[nodiscard]] std::vector<VirtualDir> GetSDMCModificationLoadRoots() const;
     [[nodiscard]] std::vector<VirtualFile> CollectPatches(const std::vector<VirtualDir>& patch_dirs,
                                                           const std::string& build_id) const;
 
     u64 title_id;
+    u64 application_id;
     const Service::FileSystem::FileSystemController& fs_controller;
     const ContentProvider& content_provider;
 };

src/core/hle/service/am/process_creation.cpp

@@ -6,6 +6,7 @@
 
 #include <optional>
 #include "core/core.h"
+#include "core/file_sys/common_funcs.h"
 #include "core/file_sys/content_archive.h"
 #include "core/file_sys/nca_metadata.h"
 #include "core/file_sys/patch_manager.h"
@@ -104,8 +105,16 @@ std::unique_ptr<Process> CreateApplicationProcess(std::vector<u8>& out_control,
 
         // TODO(DarkLordZach): When FSController/Game Card Support is added, if
         // current_process_game_card use correct StorageId
-        launch.base_game_storage_id = GetStorageIdForFrontendSlot(storage.GetSlotForEntry(launch.title_id, FileSys::ContentRecordType::Program));
-        launch.update_storage_id = GetStorageIdForFrontendSlot(storage.GetSlotForEntry(FileSys::GetUpdateTitleID(launch.title_id), FileSys::ContentRecordType::Program));
+        auto base_slot = storage.GetSlotForEntry(launch.title_id, FileSys::ContentRecordType::Program);
+        if (!base_slot) {
+            base_slot = storage.GetSlotForEntry(FileSys::GetBaseTitleID(launch.title_id), FileSys::ContentRecordType::Program);
+        }
+        launch.base_game_storage_id = GetStorageIdForFrontendSlot(base_slot);
+        auto update_slot = storage.GetSlotForEntry(FileSys::GetUpdateTitleID(launch.title_id), FileSys::ContentRecordType::Program);
+        if (!update_slot) {
+            update_slot = storage.GetSlotForEntry(FileSys::GetUpdateTitleID(FileSys::GetBaseTitleID(launch.title_id)), FileSys::ContentRecordType::Program);
+        }
+        launch.update_storage_id = GetStorageIdForFrontendSlot(update_slot);
 
         system.GetARPManager().Register(launch.title_id, launch, out_control);
         return process;

src/core/hle/service/am/service/application_functions.cpp

@@ -158,7 +158,7 @@ Result IApplicationFunctions::EnsureSaveData(Out<u64> out_size, Common::UUID use
     LOG_INFO(Service_AM, "called, uid={}", user_id.FormattedString());
 
     FileSys::SaveDataAttribute attribute{};
-    attribute.program_id = m_applet->program_id;
+    attribute.program_id = FileSys::GetBaseTitleID(m_applet->program_id);
     attribute.user_id = user_id.AsU128();
     attribute.type = FileSys::SaveDataType::Account;
 
@@ -238,7 +238,7 @@ Result IApplicationFunctions::ExtendSaveData(Out<u64> out_required_size, FileSys
               static_cast<u8>(type), user_id.FormattedString(), normal_size, journal_size);
 
     system.GetFileSystemController().OpenSaveDataController()->WriteSaveDataSize(
-        type, m_applet->program_id, user_id.AsU128(), {normal_size, journal_size});
+        type, FileSys::GetBaseTitleID(m_applet->program_id), user_id.AsU128(), {normal_size, journal_size});
 
     // The following value is used to indicate the amount of space remaining on failure
     // due to running out of space. Since we always succeed, this should be 0.
@@ -252,7 +252,7 @@ Result IApplicationFunctions::GetSaveDataSize(Out<u64> out_normal_size, Out<u64>
     LOG_DEBUG(Service_AM, "called with type={} user_id={}", type, user_id.FormattedString());
 
     const auto size = system.GetFileSystemController().OpenSaveDataController()->ReadSaveDataSize(
-        type, m_applet->program_id, user_id.AsU128());
+        type, FileSys::GetBaseTitleID(m_applet->program_id), user_id.AsU128());
 
     *out_normal_size = size.normal;
     *out_journal_size = size.journal;

src/core/hle/service/filesystem/filesystem.cpp

@@ -14,6 +14,7 @@
 #include "core/core.h"
 #include "core/file_sys/bis_factory.h"
 #include "core/file_sys/card_image.h"
+#include "core/file_sys/common_funcs.h"
 #include "core/file_sys/control_metadata.h"
 #include "core/file_sys/errors.h"
 #include "core/file_sys/patch_manager.h"
@@ -339,7 +340,7 @@ Result FileSystemController::RegisterProcess(
     registrations.emplace(process_id, Registration{
                                           .program_id = program_id,
                                           .romfs_factory = std::move(romfs_factory),
-                                          .save_data_factory = CreateSaveDataFactory(program_id),
+                                          .save_data_factory = CreateSaveDataFactory(FileSys::GetBaseTitleID(program_id)),
                                       });
 
     LOG_DEBUG(Service_FS, "Registered for process {}", process_id);

src/core/hle/service/filesystem/fsp/fsp_srv.cpp

@@ -18,6 +18,7 @@
 #include "common/settings.h"
 #include "common/string_util.h"
 #include "core/core.h"
+#include "core/file_sys/common_funcs.h"
 #include "core/file_sys/content_archive.h"
 #include "core/file_sys/errors.h"
 #include "core/file_sys/fs_directory.h"
@@ -313,7 +314,7 @@ Result FSP_SRV::OpenSaveDataFileSystemBySystemSaveDataId(OutInterface<IFileSyste
              FileSys::ResultInvalidArgument);
 
     if (attribute.program_id == 0) {
-        attribute.program_id = program_id;
+        attribute.program_id = FileSys::GetBaseTitleID(program_id);
     }
 
     FileSys::VirtualDir dir{};

src/core/loader/loader.cpp

@@ -70,6 +70,15 @@ std::optional<IndexedProgram> ResolveIndexedProgram(Core::System& system, u64 pr
         return IndexedProgram{std::move(update), target_id, true};
     }
 
+    const auto application_update_id =
+        FileSys::GetUpdateTitleID(FileSys::GetBaseTitleID(target_id));
+    if (application_update_id != update_id) {
+        if (auto update = provider.GetEntryRaw(application_update_id, FileSys::ContentRecordType::Program)) {
+            LOG_INFO(Loader, "Program index {} has no base program, loading it from application update {:016X}", program_index, application_update_id);
+            return IndexedProgram{std::move(update), target_id, true};
+        }
+    }
+
     LOG_WARNING(Loader, "No program NCA for {:016X} (index {}), falling back to the container",
                 target_id, program_index);
     return std::nullopt;

src/core/loader/nca.cpp

@@ -11,6 +11,7 @@
 #include "common/hex_util.h"
 #include "common/scope_exit.h"
 #include "core/core.h"
+#include "core/file_sys/common_funcs.h"
 #include "core/file_sys/content_archive.h"
 #include "core/file_sys/control_metadata.h"
 #include "core/file_sys/nca_metadata.h"
@@ -76,8 +77,13 @@ AppLoader_NCA::LoadResult AppLoader_NCA::Load(Kernel::KProcess& process, Core::S
         LOG_INFO(Loader, "No ExeFS found in NCA, looking for ExeFS from update");
 
         const auto& installed = system.GetContentProvider();
-        const auto update_nca = installed.GetEntry(FileSys::GetUpdateTitleID(nca->GetTitleId()),
-                                                   FileSys::ContentRecordType::Program);
+        const auto program_update_id = FileSys::GetUpdateTitleID(nca->GetTitleId());
+        auto update_nca = installed.GetEntry(program_update_id, FileSys::ContentRecordType::Program);
+        if (update_nca == nullptr) {
+            update_nca = installed.GetEntry(
+                FileSys::GetUpdateTitleID(FileSys::GetBaseTitleID(nca->GetTitleId())),
+                FileSys::ContentRecordType::Program);
+        }
 
         if (update_nca) {
             exefs = update_nca->GetExeFS();

src/core/loader/nsp.cpp

@@ -186,8 +186,13 @@ ResultStatus AppLoader_NSP::ReadUpdateRaw(FileSys::VirtualFile& out_file) {
         return ResultStatus::ErrorNoPackedUpdate;
     }
 
-    const auto read = nsp->GetNCAFile(FileSys::GetUpdateTitleID(nsp->GetProgramTitleID()),
-                                      FileSys::ContentRecordType::Program);
+    const auto program_update_id = FileSys::GetUpdateTitleID(nsp->GetProgramTitleID());
+    auto read = nsp->GetNCAFile(program_update_id, FileSys::ContentRecordType::Program);
+    if (read == nullptr) {
+        read = nsp->GetNCAFile(
+            FileSys::GetUpdateTitleID(FileSys::GetBaseTitleID(nsp->GetProgramTitleID())),
+            FileSys::ContentRecordType::Program);
+    }
 
     if (read == nullptr) {
         return ResultStatus::ErrorNoPackedUpdate;

src/core/loader/xci.cpp

@@ -9,6 +9,7 @@
 #include "common/common_types.h"
 #include "core/core.h"
 #include "core/file_sys/card_image.h"
+#include "core/file_sys/common_funcs.h"
 #include "core/file_sys/content_archive.h"
 #include "core/file_sys/control_metadata.h"
 #include "core/file_sys/patch_manager.h"
@@ -137,8 +138,13 @@ ResultStatus AppLoader_XCI::ReadUpdateRaw(FileSys::VirtualFile& out_file) {
         return ResultStatus::ErrorXCIMissingProgramNCA;
     }
 
-    const auto read = xci->GetSecurePartitionNSP()->GetNCAFile(
-        FileSys::GetUpdateTitleID(program_id), FileSys::ContentRecordType::Program);
+    const auto program_update_id = FileSys::GetUpdateTitleID(program_id);
+    auto read = xci->GetSecurePartitionNSP()->GetNCAFile(program_update_id, FileSys::ContentRecordType::Program);
+    if (read == nullptr) {
+        read = xci->GetSecurePartitionNSP()->GetNCAFile(
+            FileSys::GetUpdateTitleID(FileSys::GetBaseTitleID(program_id)),
+            FileSys::ContentRecordType::Program);
+    }
     if (read == nullptr) {
         return ResultStatus::ErrorNoPackedUpdate;
     }

src/frontend_common/content_manager.h

@@ -1,4 +1,4 @@
-// SPDX-FileCopyrightText: Copyright 2025 Eden Emulator Project
+// SPDX-FileCopyrightText: Copyright 2026 Eden Emulator Project
 // SPDX-License-Identifier: GPL-3.0-or-later
 
 // SPDX-FileCopyrightText: 2024 yuzu Emulator Project
@@ -56,13 +56,14 @@ inline bool RemoveDLC(const Service::FileSystem::FileSystemController& fs_contro
  */
 inline size_t RemoveAllDLC(Core::System& system, const u64 program_id) {
     size_t count{};
+    const auto application_id = FileSys::GetBaseTitleID(program_id);
     const auto& fs_controller = system.GetFileSystemController();
     const auto dlc_entries = system.GetContentProvider().ListEntriesFilter(
         FileSys::TitleType::AOC, FileSys::ContentRecordType::Data);
     std::vector<u64> program_dlc_entries;
 
     for (const auto& entry : dlc_entries) {
-        if (FileSys::GetBaseTitleID(entry.title_id) == program_id) {
+        if (FileSys::GetBaseTitleID(entry.title_id) == application_id) {
             program_dlc_entries.push_back(entry.title_id);
         }
     }
@@ -83,9 +84,17 @@ inline size_t RemoveAllDLC(Core::System& system, const u64 program_id) {
  */
 inline bool RemoveUpdate(const Service::FileSystem::FileSystemController& fs_controller,
                          const u64 program_id) {
-    const auto update_id = program_id | 0x800;
-    return fs_controller.GetUserNANDContents()->RemoveExistingEntry(update_id) ||
-           fs_controller.GetSDMCContents()->RemoveExistingEntry(update_id);
+    const auto remove_update = [&fs_controller](u64 update_id) {
+        return fs_controller.GetUserNANDContents()->RemoveExistingEntry(update_id) ||
+               fs_controller.GetSDMCContents()->RemoveExistingEntry(update_id);
+    };
+    const auto update_id = FileSys::GetUpdateTitleID(program_id);
+    const auto application_update_id =
+        FileSys::GetUpdateTitleID(FileSys::GetBaseTitleID(program_id));
+    if (update_id != application_update_id && remove_update(update_id)) {
+        return true;
+    }
+    return remove_update(application_update_id);
 }
 
 /**
@@ -111,15 +120,26 @@ inline bool RemoveBaseContent(const Service::FileSystem::FileSystemController& f
 inline bool RemoveMod(const Service::FileSystem::FileSystemController& fs_controller,
                       const u64 program_id, const std::string& mod_name) {
     // Check general Mods (LayeredFS and IPS)
-    const auto mod_dir = fs_controller.GetModificationLoadRoot(program_id);
-    if (mod_dir != nullptr) {
-        return mod_dir->DeleteSubdirectoryRecursive(mod_name);
+    const auto remove_from_root = [&mod_name](const auto& root) {
+        return root != nullptr && root->DeleteSubdirectoryRecursive(mod_name);
+    };
+    if (remove_from_root(fs_controller.GetModificationLoadRoot(program_id))) {
+        return true;
+    }
+    if (FileSys::GetBaseTitleID(program_id) != program_id &&
+        remove_from_root(
+            fs_controller.GetModificationLoadRoot(FileSys::GetBaseTitleID(program_id)))) {
+        return true;
     }
 
     // Check SDMC mod directory (RomFS LayeredFS)
-    const auto sdmc_mod_dir = fs_controller.GetSDMCModificationLoadRoot(program_id);
-    if (sdmc_mod_dir != nullptr) {
-        return sdmc_mod_dir->DeleteSubdirectoryRecursive(mod_name);
+    if (remove_from_root(fs_controller.GetSDMCModificationLoadRoot(program_id))) {
+        return true;
+    }
+    if (FileSys::GetBaseTitleID(program_id) != program_id &&
+        remove_from_root(
+            fs_controller.GetSDMCModificationLoadRoot(FileSys::GetBaseTitleID(program_id)))) {
+        return true;
     }
 
     return false;

src/frontend_common/mod_manager.cpp

@@ -7,6 +7,7 @@
 #include "common/fs/fs.h"
 #include "common/fs/fs_types.h"
 #include "common/logging.h"
+#include "core/file_sys/common_funcs.h"
 #include "frontend_common/data_manager.h"
 #include "mod_manager.h"
 
@@ -40,7 +41,7 @@ std::vector<std::filesystem::path> GetModFolder(const std::string& root) {
 }
 
 ModInstallResult InstallMod(const std::filesystem::path& path, const u64 program_id, const bool copy) {
-    const auto program_id_string = fmt::format("{:016X}", program_id);
+    const auto program_id_string = fmt::format("{:016X}", FileSys::GetBaseTitleID(program_id));
     const auto mod_name = path.filename();
     const auto mod_dir =
         DataManager::GetDataDir(DataManager::DataDir::Mods) / program_id_string / mod_name;

src/qt_common/util/game.cpp

@@ -5,6 +5,7 @@
 
 #include "common/fs/fs.h"
 #include "common/fs/path_util.h"
+#include "core/file_sys/common_funcs.h"
 #include "core/file_sys/savedata_factory.h"
 #include "core/hle/service/am/am_types.h"
 #include "frontend_common/content_manager.h"
@@ -305,6 +306,7 @@ void RemoveAllTransferableShaderCaches(u64 program_id) {
 }
 
 void RemoveCustomConfiguration(u64 program_id, const std::string& game_path) {
+    program_id = FileSys::GetBaseTitleID(program_id);
     const auto file_path = std::filesystem::path(Common::FS::ToU8String(game_path));
     const auto config_file_name =
         program_id == 0 ? Common::FS::PathToUTF8String(file_path.filename()).append(".ini")

src/yuzu/configuration/configure_per_game.cpp

@@ -24,6 +24,7 @@
 #include "common/settings_input.h"
 #include "configuration/shared_widget.h"
 #include "core/core.h"
+#include "core/file_sys/common_funcs.h"
 #include "core/file_sys/control_metadata.h"
 #include "core/file_sys/patch_manager.h"
 #include "core/file_sys/xts_archive.h"
@@ -50,7 +51,7 @@
 ConfigurePerGame::ConfigurePerGame(QWidget* parent, u64 title_id_, const std::string& file_name,
                                    std::vector<VkDeviceInfo::Record>& vk_device_records,
                                    Core::System& system_)
-    : QDialog(parent), ui(std::make_unique<Ui::ConfigurePerGame>()), title_id{title_id_},
+    : QDialog(parent), ui(std::make_unique<Ui::ConfigurePerGame>()), title_id{FileSys::GetBaseTitleID(title_id_)},
       system{system_},
       builder{std::make_unique<ConfigurationShared::Builder>(this, !system_.IsPoweredOn())},
       tab_group{std::make_shared<std::vector<ConfigurationShared::Tab*>>()} {

src/yuzu/configuration/configure_per_game_addons.cpp

@@ -24,6 +24,7 @@
 #include "common/fs/path_util.h"
 #include "configuration/addon/mod_select_dialog.h"
 #include "core/core.h"
+#include "core/file_sys/common_funcs.h"
 #include "core/file_sys/patch_manager.h"
 #include "core/loader/loader.h"
 #include "frontend_common/mod_manager.h"
@@ -137,7 +138,7 @@ void ConfigurePerGameAddons::LoadFromFile(FileSys::VirtualFile file_) {
 }
 
 void ConfigurePerGameAddons::SetTitleId(u64 id) {
-    this->title_id = id;
+    this->title_id = FileSys::GetBaseTitleID(id);
 }
 
 void ConfigurePerGameAddons::InstallMods(const QStringList& mods) {

src/yuzu/main_window.cpp

@@ -1922,7 +1922,7 @@ void MainWindow::BootGame(const QString& filename, Service::AM::FrontendAppletPa
             std::filesystem::path{Common::U16StringFromBuffer(filename.utf16(), filename.size())};
         const auto config_file_name = title_id == 0
                                           ? Common::FS::PathToUTF8String(file_path.filename())
-                                          : fmt::format("{:016X}", title_id);
+                                          : fmt::format("{:016X}", FileSys::GetBaseTitleID(title_id));
         QtConfig per_game_config(config_file_name, Config::ConfigType::PerGameConfig);
         QtCommon::system->HIDCore().ReloadInputDevices();
         QtCommon::system->ApplySettings();
@@ -2544,9 +2544,11 @@ void MainWindow::OnGameListDumpRomFS(u64 program_id, const std::string& game_pat
     }
 
     const FileSys::NCA update_nca{packed_update_raw, nullptr};
+    const auto selected_update_id = FileSys::GetUpdateTitleID(title_id);
+    const auto application_update_id = FileSys::GetUpdateTitleID(FileSys::GetBaseTitleID(title_id));
     if (type != FileSys::ContentRecordType::Program ||
         update_nca.GetStatus() != Loader::ResultStatus::ErrorMissingBKTRBaseRomFS ||
-        update_nca.GetTitleId() != FileSys::GetUpdateTitleID(title_id)) {
+        (update_nca.GetTitleId() != selected_update_id && update_nca.GetTitleId() != application_update_id)) {
         packed_update_raw = {};
     }
 
@@ -4421,6 +4423,7 @@ void MainWindow::SetFPSSuffix() {
 
 bool MainWindow::SelectRomFSDumpTarget(const FileSys::ContentProvider& installed, u64 program_id,
                                        u64* selected_title_id, u8* selected_content_record_type) {
+    program_id = FileSys::GetBaseTitleID(program_id);
     using ContentInfo = std::tuple<u64, FileSys::TitleType, FileSys::ContentRecordType>;
     boost::container::flat_set<ContentInfo> available_title_ids;