feat: migrate Flatpak integrations with native updates

8 files changed, 381 insertions, 41 deletions

diff --git a/README.md b/README.md
index a1c233c..12a8ecc 100644
--- a/README.md
+++ b/README.md
@@ -79,6 +79,7 @@ For per-game feedback and community support, please join the [decky-lsfg-vk Disc
 The plugin:
 - Downloads checksum-pinned x86_64 or Armada/aarch64 lsfg-vk v2 assets from the owner-fork release to `~/.local/lib/`
 - Bundles checksum-pinned lsfg-vk v2 Flatpak extensions for runtimes 23.08, 24.08, and 25.08, and installs the selected local bundle
+- Updates already-installed user Flatpak runtimes and migrates the plugin's legacy app overrides when the native layer is updated
 - Configures the v2 Vulkan layer in `~/.local/share/vulkan/implicit_layer.d/`
 - Migrates the existing `~/.config/lsfg-vk/conf.toml` from v1 to v2 automatically on layer update, retaining a one-time `.v1.bak` backup
 - Automatically detects your Lossless Scaling DLL installation
diff --git a/py_modules/lsfg_vk/flatpak_service.py b/py_modules/lsfg_vk/flatpak_service.py
index 5832cf4..fe965aa 100644
--- a/py_modules/lsfg_vk/flatpak_service.py
+++ b/py_modules/lsfg_vk/flatpak_service.py
@@ -18,6 +18,9 @@ from .constants import (
 from .types import BaseResponse
 
 
+SUPPORTED_FLATPAK_VERSIONS = ("23.08", "24.08", "25.08")
+
+
 class FlatpakExtensionStatus(BaseResponse):
     """Response for Flatpak extension status"""
     def __init__(self, success: bool = False, message: str = "", error: str = "", 
@@ -88,6 +91,25 @@ class FlatpakService(BaseService):
         plugin_dir = Path(__file__).resolve().parent.parent.parent
         return plugin_dir / BIN_DIR / filename
 
+    def _get_installed_extension_versions(self) -> list[str]:
+        """Return installed lsfg-vk runtime branches from the user Flatpak installation."""
+        result = self._run_flatpak_command(
+            ["list", "--user", "--runtime"],
+            capture_output=True,
+            text=True,
+            check=True,
+        )
+        installed_runtimes = result.stdout
+        base_extension_name = "org.freedesktop.Platform.VulkanLayer.lsfgvk"
+        return [
+            version
+            for version in SUPPORTED_FLATPAK_VERSIONS
+            if any(
+                base_extension_name in line and version in line
+                for line in installed_runtimes.splitlines()
+            )
+        ]
+
     def _remove_legacy_app_overrides(self, app_id: str) -> list[str]:
         """Remove only the v1 overrides previously created by this plugin."""
         legacy_dll_path = self.user_home / ".local/share/Steam/steamapps/common/Lossless Scaling/Lossless.dll"
@@ -175,26 +197,10 @@ class FlatpakService(BaseService):
                                           error_msg,
                                           installed_23_08=False, installed_24_08=False, installed_25_08=False)
 
-            result = self._run_flatpak_command(
-                ["list", "--runtime"],
-                capture_output=True, text=True, check=True
-            )
-
-            installed_runtimes = result.stdout
-
-            base_extension_name = "org.freedesktop.Platform.VulkanLayer.lsfgvk"
-            installed_23_08 = False
-            installed_24_08 = False
-            installed_25_08 = False
-
-            for line in installed_runtimes.split('\n'):
-                if base_extension_name in line:
-                    if "23.08" in line:
-                        installed_23_08 = True
-                    elif "24.08" in line:
-                        installed_24_08 = True
-                    elif "25.08" in line:
-                        installed_25_08 = True
+            installed_versions = self._get_installed_extension_versions()
+            installed_23_08 = "23.08" in installed_versions
+            installed_24_08 = "24.08" in installed_versions
+            installed_25_08 = "25.08" in installed_versions
 
             status_msg = []
             if installed_23_08:
@@ -220,9 +226,9 @@ class FlatpakService(BaseService):
                                       installed_23_08=False, installed_24_08=False, installed_25_08=False)
 
     def install_extension(self, version: str) -> BaseResponse:
-        """Install a specific version of the lsfg-vk Flatpak extension"""
+        """Install or update a specific version of the lsfg-vk Flatpak extension."""
         try:
-            if version not in ["23.08", "24.08", "25.08"]:
+            if version not in SUPPORTED_FLATPAK_VERSIONS:
                 return self._error_response(BaseResponse, "Invalid version. Must be '23.08', '24.08', or '25.08'")
 
             if not self.check_flatpak_available():
@@ -235,7 +241,14 @@ class FlatpakService(BaseService):
                 return self._error_response(BaseResponse, error_msg)
 
             result = self._run_flatpak_command(
-                ["install", "--user", "--noninteractive", str(bundle_path)],
+                [
+                    "install",
+                    "--user",
+                    "--or-update",
+                    "--assumeyes",
+                    "--noninteractive",
+                    str(bundle_path),
+                ],
                 capture_output=True, text=True
             )
 
@@ -255,10 +268,161 @@ class FlatpakService(BaseService):
             self.log.error(error_msg)
             return self._error_response(BaseResponse, error_msg)
 
+    def _get_flatpak_app_ids(self) -> list[str]:
+        """Return application IDs in the user Flatpak installation."""
+        result = self._run_flatpak_command(
+            ["list", "--app"],
+            capture_output=True,
+            text=True,
+            check=True,
+        )
+        app_ids = []
+        for line in result.stdout.splitlines():
+            parts = line.split("\t")
+            if len(parts) >= 2 and parts[1].strip():
+                app_ids.append(parts[1].strip())
+        return app_ids
+
+    def _get_app_override_output(self, app_id: str) -> Optional[str]:
+        """Return an app's user override output, or None if it cannot be read."""
+        result = self._run_flatpak_command(
+            ["override", "--user", "--show", app_id],
+            capture_output=True,
+            text=True,
+        )
+        if result.returncode != 0:
+            return None
+        return result.stdout
+
+    def _has_legacy_app_override(self, output: str) -> bool:
+        """Detect only overrides written by the v1 plugin."""
+        config_path, _ = self._get_lsfg_paths()
+        legacy_dll_path = self.user_home / ".local/share/Steam/steamapps/common/Lossless Scaling/Lossless.dll"
+        legacy_config = f"LSFG_CONFIG={config_path}/conf.toml"
+        return (
+            legacy_config in output
+            or str(legacy_dll_path) in output
+            or str(self.lsfg_launch_script_path) in output
+        )
+
+    def _migrate_legacy_app_overrides(self) -> Dict[str, Any]:
+        """Upgrade v1 app overrides without changing unrelated Flatpak apps."""
+        migrated_apps = []
+        failed_apps = []
+        try:
+            for app_id in self._get_flatpak_app_ids():
+                output = self._get_app_override_output(app_id)
+                if output is None or not self._has_legacy_app_override(output):
+                    continue
+
+                result = self.set_app_override(app_id)
+                if result.get("success"):
+                    migrated_apps.append(app_id)
+                else:
+                    failed_apps.append({"app_id": app_id, "error": result.get("error", "unknown error")})
+        except (subprocess.CalledProcessError, OSError) as error:
+            stderr = getattr(error, "stderr", None)
+            return self._error_response(
+                BaseResponse,
+                f"Could not inspect Flatpak applications: {stderr or error}",
+                migrated_apps=migrated_apps,
+                failed_apps=failed_apps,
+            )
+
+        if failed_apps:
+            return self._error_response(
+                BaseResponse,
+                f"Failed to migrate overrides for {len(failed_apps)} Flatpak application(s)",
+                migrated_apps=migrated_apps,
+                failed_apps=failed_apps,
+            )
+        return self._success_response(
+            BaseResponse,
+            f"Migrated {len(migrated_apps)} legacy Flatpak app override(s)",
+            migrated_apps=migrated_apps,
+            failed_apps=failed_apps,
+        )
+
+    def update_installed_extensions(self) -> Dict[str, Any]:
+        """Update existing user Flatpak extensions and migrate their v1 app overrides."""
+        empty_result = {
+            "updated_versions": [],
+            "failed_versions": [],
+            "migrated_apps": [],
+            "failed_apps": [],
+        }
+        try:
+            if not self.check_flatpak_available():
+                return self._success_response(
+                    BaseResponse,
+                    "Flatpak is unavailable; skipped runtime and app-override migration",
+                    skipped=True,
+                    **empty_result,
+                )
+
+            installed_versions = self._get_installed_extension_versions()
+            if not installed_versions:
+                return self._success_response(
+                    BaseResponse,
+                    "No installed lsfg-vk Flatpak runtimes require migration",
+                    skipped=True,
+                    **empty_result,
+                )
+
+            updated_versions = []
+            failed_versions = []
+            for version in installed_versions:
+                result = self.install_extension(version)
+                if result.get("success"):
+                    updated_versions.append(version)
+                else:
+                    failed_versions.append({"version": version, "error": result.get("error", "unknown error")})
+
+            if failed_versions:
+                return self._error_response(
+                    BaseResponse,
+                    "Flatpak runtime migration failed; legacy app overrides were left unchanged",
+                    skipped=False,
+                    updated_versions=updated_versions,
+                    failed_versions=failed_versions,
+                    migrated_apps=[],
+                    failed_apps=[],
+                )
+
+            override_result = self._migrate_legacy_app_overrides()
+            response = {
+                "updated_versions": updated_versions,
+                "failed_versions": [],
+                "migrated_apps": override_result.get("migrated_apps", []),
+                "failed_apps": override_result.get("failed_apps", []),
+            }
+            if not override_result.get("success"):
+                return self._error_response(
+                    BaseResponse,
+                    override_result.get("error", "Flatpak app override migration failed"),
+                    skipped=False,
+                    **response,
+                )
+            return self._success_response(
+                BaseResponse,
+                f"Updated {len(updated_versions)} Flatpak runtime(s); "
+                f"migrated {len(response['migrated_apps'])} app override(s)",
+                skipped=False,
+                **response,
+            )
+        except (subprocess.CalledProcessError, OSError) as error:
+            stderr = getattr(error, "stderr", None)
+            return self._error_response(
+                BaseResponse,
+                f"Could not migrate installed Flatpak runtimes: {stderr or error}",
+                skipped=False,
+                **empty_result,
+            )
+
     def uninstall_extension(self, version: str) -> BaseResponse:
         """Uninstall a specific version of the lsfg-vk Flatpak extension"""
         try:
-            if version not in ["23.08", "24.08", "25.08"]:
+            if version not in SUPPORTED_FLATPAK_VERSIONS:
                 return self._error_response(BaseResponse, "Invalid version. Must be '23.08', '24.08', or '25.08'")
 
             if not self.check_flatpak_available():
@@ -301,7 +465,7 @@ class FlatpakService(BaseService):
                                           apps=[], total_apps=0)
 
             result = self._run_flatpak_command(
-                ["list", "--app"],
+                ["list", "--user", "--app"],
                 capture_output=True, text=True, check=True
             )
 
@@ -337,15 +501,9 @@ class FlatpakService(BaseService):
     def _check_app_override_status(self, app_id: str) -> Dict[str, bool]:
         """Check if an app has lsfg-vk overrides set"""
         try:
-            result = self._run_flatpak_command(
-                ["override", "--user", "--show", app_id],
-                capture_output=True, text=True
-            )
-
-            if result.returncode != 0:
+            output = self._get_app_override_output(app_id)
+            if output is None:
                 return {"filesystem": False, "env": False}
-
-            output = result.stdout
             config_path, dll_directory = self._get_lsfg_paths()
 
             filesystem_section = ""
diff --git a/py_modules/lsfg_vk/plugin.py b/py_modules/lsfg_vk/plugin.py
index c2f22e3..1b99501 100644
--- a/py_modules/lsfg_vk/plugin.py
+++ b/py_modules/lsfg_vk/plugin.py
@@ -37,12 +37,23 @@ class Plugin:
         self.flatpak_service = FlatpakService()
 
     async def install_lsfg_vk(self) -> Dict[str, Any]:
-        """Install lsfg-vk by extracting the zip file to ~/.local
+        """Install/update the native layer and migrate installed Flatpak integrations.
         
         Returns:
             InstallationResponse dict with success status and message/error
         """
-        return self.installation_service.install()
+        installation_result = self.installation_service.install()
+        if not installation_result.get("success"):
+            return installation_result
+
+        flatpak_result = self.flatpak_service.update_installed_extensions()
+        installation_result["flatpak_update"] = flatpak_result
+        if not flatpak_result.get("success") and not flatpak_result.get("skipped"):
+            installation_result["message"] = (
+                f"{installation_result.get('message', 'lsfg-vk updated successfully')}; "
+                f"Flatpak migration warning: {flatpak_result.get('error', 'unknown error')}"
+            )
+        return installation_result
 
     async def check_lsfg_vk_installed(self) -> Dict[str, Any]:
         """Check if lsfg-vk is already installed
@@ -359,7 +370,7 @@ class Plugin:
         return self.flatpak_service.get_extension_status()
 
     async def install_flatpak_extension(self, version: str) -> Dict[str, Any]:
-        """Install lsfg-vk Flatpak runtime extension
+        """Install or update an lsfg-vk Flatpak runtime extension
         
         Args:
             version: Runtime version to install ("23.08", "24.08", or "25.08")
diff --git a/py_modules/lsfg_vk/types.py b/py_modules/lsfg_vk/types.py
index 6f3cd05..3210d25 100644
--- a/py_modules/lsfg_vk/types.py
+++ b/py_modules/lsfg_vk/types.py
@@ -25,6 +25,7 @@ class InstallationResponse(BaseResponse):
     """Response for installation operations"""
     message: str
     error: Optional[str]
+    flatpak_update: Optional[Dict[str, Any]]
 
 
 class UninstallationResponse(BaseResponse):
diff --git a/src/api/lsfgApi.ts b/src/api/lsfgApi.ts
index 8378a7f..f112d39 100644
--- a/src/api/lsfgApi.ts
+++ b/src/api/lsfgApi.ts
@@ -7,6 +7,18 @@ export interface InstallationResult {
   error?: string;
   message?: string;
   removed_files?: string[];
+  flatpak_update?: FlatpakMigrationResult;
+}
+
+export interface FlatpakMigrationResult {
+  success: boolean;
+  message: string;
+  error?: string;
+  skipped?: boolean;
+  updated_versions: string[];
+  failed_versions: Array<{ version: string; error: string }>;
+  migrated_apps: string[];
+  failed_apps: Array<{ app_id: string; error: string }>;
 }
 
 export interface InstallationStatus {
diff --git a/src/hooks/useInstallationActions.ts b/src/hooks/useInstallationActions.ts
index f184145..8a43257 100644
--- a/src/hooks/useInstallationActions.ts
+++ b/src/hooks/useInstallationActions.ts
@@ -23,8 +23,8 @@ export function useInstallationActions() {
       const result = await installLsfgVk();
       if (result.success) {
         setIsInstalled(true);
-        setInstallationStatus("lsfg-vk installed");
-        showInstallSuccessToast();
+        setInstallationStatus(result.message || "lsfg-vk installed");
+        showInstallSuccessToast(result.message);
 
         // Reload lsfg config after installation
         if (reloadConfig) {
diff --git a/src/utils/toastUtils.ts b/src/utils/toastUtils.ts
index dce0a59..198ec0e 100644
--- a/src/utils/toastUtils.ts
+++ b/src/utils/toastUtils.ts
@@ -75,8 +75,8 @@ export function showErrorToastWithMessage(title: string, error: unknown): void {
 /**
  * Show installation success toast
  */
-export function showInstallSuccessToast(): void {
-  showSuccessToast(ToastMessages.INSTALL_SUCCESS.title, ToastMessages.INSTALL_SUCCESS.body);
+export function showInstallSuccessToast(body?: string): void {
+  showSuccessToast(ToastMessages.INSTALL_SUCCESS.title, body || ToastMessages.INSTALL_SUCCESS.body);
 }
 
 /**
diff --git a/tests/test_lsfg_v2_migration.py b/tests/test_lsfg_v2_migration.py
index bb5a0b1..ee1fcba 100644
--- a/tests/test_lsfg_v2_migration.py
+++ b/tests/test_lsfg_v2_migration.py
@@ -1,3 +1,4 @@
+import asyncio
 import logging
 import sys
 import tempfile
@@ -226,11 +227,167 @@ class FlatpakMigrationTests(unittest.TestCase):
 
             self.assertTrue(result["success"])
             service._run_flatpak_command.assert_called_once_with(
-                ["install", "--user", "--noninteractive", str(bundle_path)],
+                [
+                    "install",
+                    "--user",
+                    "--or-update",
+                    "--assumeyes",
+                    "--noninteractive",
+                    str(bundle_path),
+                ],
                 capture_output=True,
                 text=True,
             )
 
+    def test_update_installed_extensions_only_updates_user_runtimes_and_migrates_apps(self):
+        from lsfg_vk.flatpak_service import FlatpakService
+
+        service = FlatpakService.__new__(FlatpakService)
+        service.log = mock.Mock()
+        service.check_flatpak_available = mock.Mock(return_value=True)
+        service._get_installed_extension_versions = mock.Mock(return_value=["23.08", "25.08"])
+        service.install_extension = mock.Mock(
+            side_effect=[{"success": True}, {"success": True}]
+        )
+        service._migrate_legacy_app_overrides = mock.Mock(
+            return_value={
+                "success": True,
+                "migrated_apps": ["org.example.Game"],
+                "failed_apps": [],
+            }
+        )
+
+        result = service.update_installed_extensions()
+
+        self.assertTrue(result["success"])
+        self.assertEqual(result["updated_versions"], ["23.08", "25.08"])
+        self.assertEqual(result["migrated_apps"], ["org.example.Game"])
+        self.assertEqual(
+            service.install_extension.call_args_list,
+            [mock.call("23.08"), mock.call("25.08")],
+        )
+        service._migrate_legacy_app_overrides.assert_called_once_with()
+
+    def test_installed_runtime_scan_is_scoped_to_user_installation(self):
+        from lsfg_vk.flatpak_service import FlatpakService
+
+        service = FlatpakService.__new__(FlatpakService)
+        service._run_flatpak_command = mock.Mock(
+            return_value=types.SimpleNamespace(
+                returncode=0,
+                stdout=(
+                    "lsfg-vk\torg.freedesktop.Platform.VulkanLayer.lsfgvk\t"
+                    "2.0\t23.08\tx86_64\n"
+                ),
+                stderr="",
+            )
+        )
+
+        self.assertEqual(service._get_installed_extension_versions(), ["23.08"])
+        service._run_flatpak_command.assert_called_once_with(
+            ["list", "--user", "--runtime"],
+            capture_output=True,
+            text=True,
+            check=True,
+        )
+
+    def test_failed_runtime_update_leaves_legacy_overrides_untouched(self):
+        from lsfg_vk.flatpak_service import FlatpakService
+
+        service = FlatpakService.__new__(FlatpakService)
+        service.log = mock.Mock()
+        service.check_flatpak_available = mock.Mock(return_value=True)
+        service._get_installed_extension_versions = mock.Mock(return_value=["24.08"])
+        service.install_extension = mock.Mock(
+            return_value={"success": False, "error": "bundle unavailable"}
+        )
+        service._migrate_legacy_app_overrides = mock.Mock()
+
+        result = service.update_installed_extensions()
+
+        self.assertFalse(result["success"])
+        self.assertEqual(result["failed_versions"][0]["version"], "24.08")
+        service._migrate_legacy_app_overrides.assert_not_called()
+
+    def test_native_install_runs_flatpak_migration_after_success(self):
+        from lsfg_vk.plugin import Plugin
+
+        plugin = Plugin.__new__(Plugin)
+        plugin.installation_service = mock.Mock()
+        plugin.flatpak_service = mock.Mock()
+        plugin.installation_service.install.return_value = {
+            "success": True,
+            "message": "lsfg-vk v2 installed successfully",
+            "error": None,
+        }
+        plugin.flatpak_service.update_installed_extensions.return_value = {
+            "success": True,
+            "message": "Updated one Flatpak runtime",
+            "skipped": False,
+            "updated_versions": ["23.08"],
+            "failed_versions": [],
+            "migrated_apps": [],
+            "failed_apps": [],
+        }
+
+        result = asyncio.run(plugin.install_lsfg_vk())
+
+        self.assertTrue(result["success"])
+        self.assertIn("flatpak_update", result)
+        plugin.flatpak_service.update_installed_extensions.assert_called_once_with()
+
+    def test_legacy_override_detection_does_not_match_v2_environment(self):
+        from lsfg_vk.flatpak_service import FlatpakService
+
+        with tempfile.TemporaryDirectory() as directory:
+            home = Path(directory)
+            service = FlatpakService.__new__(FlatpakService)
+            service.user_home = home
+            service.config_dir = home / ".config/lsfg-vk"
+            service.config_file_path = service.config_dir / "conf.toml"
+            service.lsfg_launch_script_path = home / "lsfg"
+            service.log = mock.Mock()
+
+            self.assertTrue(
+                service._has_legacy_app_override(
+                    f"LSFG_CONFIG={service.config_file_path}\n"
+                )
+            )
+            self.assertFalse(
+                service._has_legacy_app_override(
+                    f"LSFGVK_CONFIG={service.config_file_path}\n"
+                )
+            )
+
+    def test_legacy_override_migration_only_touches_plugin_owned_apps(self):
+        from lsfg_vk.flatpak_service import FlatpakService
+
+        with tempfile.TemporaryDirectory() as directory:
+            home = Path(directory)
+            service = FlatpakService.__new__(FlatpakService)
+            service.user_home = home
+            service.config_dir = home / ".config/lsfg-vk"
+            service.config_file_path = service.config_dir / "conf.toml"
+            service.lsfg_launch_script_path = home / "lsfg"
+            service.log = mock.Mock()
+            service._get_flatpak_app_ids = mock.Mock(
+                return_value=["org.example.Legacy", "org.example.V2", "org.example.Other"]
+            )
+            service._get_app_override_output = mock.Mock(
+                side_effect=[
+                    f"LSFG_CONFIG={service.config_file_path}\n",
+                    f"LSFGVK_CONFIG={service.config_file_path}\n",
+                    "",
+                ]
+            )
+            service.set_app_override = mock.Mock(return_value={"success": True})
+
+            result = service._migrate_legacy_app_overrides()
+
+            self.assertTrue(result["success"])
+            self.assertEqual(result["migrated_apps"], ["org.example.Legacy"])
+            service.set_app_override.assert_called_once_with("org.example.Legacy")
+
     def test_v2_override_setup_and_removal_clean_legacy_overrides(self):
         from lsfg_vk.flatpak_service import FlatpakService