fix: resolve flatpak privileges, dnf cache loops, and ui queue state (#2, #3)

.gitignore

@@ -38,4 +38,5 @@ __pycache__/
 # Local Package Builds
 /build
 
-docs/marketing
+docs/marketing
+.antigravitycli

CHANGELOG.md

@@ -0,0 +1,22 @@
+# Changelog
+
+All notable changes to CleanMyLinux will be documented in this file.
+
+## [v1.0.0-beta.2] - 2026-05-24
+
+### Fixed
+- **Ghost Updates:** Resolved an issue where native DNF packages (like Brave Browser) would continuously reappear in the update list after successfully updating, caused by stale cache queries ([#3](https://github.com/Better-Linux/CleanMyLinux/issues/3)).
+- **Flatpak Privilege Blindspot:** Fixed an issue where the updater could not detect or update user-installed flatpaks. Flatpak updates now seamlessly integrate with the system polkit for native permission handling ([#3](https://github.com/Better-Linux/CleanMyLinux/issues/3)).
+- **System App Protection:** Fixed a bug where third-party apps were incorrectly flagged as protected system applications, which prevented users from uninstalling them ([#2](https://github.com/Better-Linux/CleanMyLinux/issues/2)).
+- **KDE Dock Icon:** Fixed missing app icon in the KDE panel. ([#1](https://github.com/Better-Linux/CleanMyLinux/issues/1)) by @Joy-Majumder in [#4](https://github.com/Better-Linux/CleanMyLinux/pull/4).
+- **Queue Manager UX:** Fixed a bug where a single failed application update would wipe the entire operations queue and force a false "Success" screen. Failed operations now correctly stay in the queue with visible error badges.
+- **Queue Operation Clashing:** Fixed an issue where restarting an operation in the queue manager would overwrite previous operations. Every queued action now generates a mathematically unique ID.
+
+## [v1.0.0-beta.1] - 2026-05-22
+
+### Added
+- **Initial Beta Release:** First public preview of CleanMyLinux.
+- **Unified App Manager:** Core architecture to scan, manage, update, and uninstall Native (RPM/APT/Pacman), Flatpak, and Snap packages.
+- **System Optimizer:** Initial modules for cleaning system caches, logs, and unused dependencies.
+- **Operations Queue:** Real-time background progress tracking for batch uninstalls and updates.
+- **Polkit Integration:** Secure privilege escalation layer for system-level operations.

package.json

@@ -1,7 +1,7 @@
 {
   "name": "cleanmylinux",
   "private": true,
-  "version": "1.0.0-beta.1",
+  "version": "1.0.0-beta.2",
   "type": "module",
   "scripts": {
     "dev": "vite",

src-tauri/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "cleanmylinux"
-version = "1.0.0-beta.1"
+version = "1.0.0-beta.2"
 description = "A premium, high performance system maintenance and optimization tool for Linux desktops."
 authors = ["Better Linux"]
 edition = "2021"

src-tauri/src/system_info/commands/run_app_updates.rs

@@ -37,7 +37,7 @@ pub async fn run_app_updates(app: tauri::AppHandle, updates: Vec<AppUpdate>) ->
 
     // STEP 1: Process Native Packages in a single unified TTY-style batch console invocation
     if !native_updates.is_empty() {
-        let op_id = "batch-update-native".to_string();
+        let op_id = format!("batch-update-native-{}", std::time::SystemTime::now().duration_since(std::time::UNIX_EPOCH).unwrap().as_millis());
         let first_app = &native_updates[0];
         let base_title = "Updating System Packages".to_string();
         let target_apps_clone = native_updates.clone();
@@ -58,6 +58,7 @@ pub async fn run_app_updates(app: tauri::AppHandle, updates: Vec<AppUpdate>) ->
             } else if let Ok(st2) = Command::new("dnf").arg("--version").output() {
                 if st2.status.success() {
                     base_args.push("upgrade".to_string());
+                    base_args.push("--refresh".to_string());
                     base_args.push("-y".to_string());
                     base_args.extend(pkg_ids);
                     "dnf"
@@ -76,6 +77,7 @@ pub async fn run_app_updates(app: tauri::AppHandle, updates: Vec<AppUpdate>) ->
         } else if let Ok(st2) = Command::new("dnf").arg("--version").output() {
             if st2.status.success() {
                 base_args.push("upgrade".to_string());
+                base_args.push("--refresh".to_string());
                 base_args.push("-y".to_string());
                 base_args.extend(pkg_ids);
                 "dnf"
@@ -134,7 +136,7 @@ pub async fn run_app_updates(app: tauri::AppHandle, updates: Vec<AppUpdate>) ->
         let app_clone = app.clone();
         let app_emitter = app.clone();
         join_handles.push(tauri::async_runtime::spawn(async move {
-            let op_id = "batch-update-flatpak".to_string();
+            let op_id = format!("batch-update-flatpak-{}", std::time::SystemTime::now().duration_since(std::time::UNIX_EPOCH).unwrap().as_millis());
             let base_title = "Updating Flatpak Apps".to_string();
             let first_icon = flatpak_updates[0].icon.clone();
             let target_apps_clone = flatpak_updates.clone();
@@ -145,7 +147,7 @@ pub async fn run_app_updates(app: tauri::AppHandle, updates: Vec<AppUpdate>) ->
             }
 
             let stream_res = tauri::async_runtime::spawn_blocking(move || {
-                let mut base_args = vec!["update".to_string(), "-y".to_string(), "--noninteractive".to_string()];
+                let mut base_args = vec!["update".to_string(), "-y".to_string()];
                 base_args.extend(pkg_ids);
                 let arg_refs: Vec<&str> = base_args.iter().map(|s| s.as_str()).collect();
 
@@ -157,7 +159,7 @@ pub async fn run_app_updates(app: tauri::AppHandle, updates: Vec<AppUpdate>) ->
                     "update",
                     "flatpak",
                     &arg_refs,
-                    true,
+                    false,
                     first_icon,
                     Some(target_apps_clone),
                 )
@@ -189,7 +191,7 @@ pub async fn run_app_updates(app: tauri::AppHandle, updates: Vec<AppUpdate>) ->
         let app_clone = app.clone();
         let app_emitter = app.clone();
         join_handles.push(tauri::async_runtime::spawn(async move {
-            let op_id = "batch-update-snap".to_string();
+            let op_id = format!("batch-update-snap-{}", std::time::SystemTime::now().duration_since(std::time::UNIX_EPOCH).unwrap().as_millis());
             let base_title = "Updating Snap Apps".to_string();
             let first_icon = snap_updates[0].icon.clone();
             let target_apps_clone = snap_updates.clone();

src-tauri/src/system_info/commands/uninstall_app.rs

@@ -35,7 +35,7 @@ pub async fn uninstall_app(
 
     // STEP 1: Process Native Packages via single unified console removal
     if !native_apps.is_empty() {
-        let op_id = "batch-uninstall-native".to_string();
+        let op_id = format!("batch-uninstall-native-{}", std::time::SystemTime::now().duration_since(std::time::UNIX_EPOCH).unwrap().as_millis());
         let first_app = &native_apps[0];
         let base_title = if native_apps.len() == 1 {
             first_app.name.clone()
@@ -155,7 +155,7 @@ pub async fn uninstall_app(
     if !flatpak_apps.is_empty() {
         let app_clone = app_handle.clone();
         join_handles.push(tauri::async_runtime::spawn(async move {
-            let op_id = "batch-uninstall-flatpak".to_string();
+            let op_id = format!("batch-uninstall-flatpak-{}", std::time::SystemTime::now().duration_since(std::time::UNIX_EPOCH).unwrap().as_millis());
             let first_app = &flatpak_apps[0];
             let base_title = if flatpak_apps.len() == 1 {
                 first_app.name.clone()
@@ -256,7 +256,7 @@ pub async fn uninstall_app(
     if !snap_apps.is_empty() {
         let app_clone = app_handle.clone();
         join_handles.push(tauri::async_runtime::spawn(async move {
-            let op_id = "batch-uninstall-snap".to_string();
+            let op_id = format!("batch-uninstall-snap-{}", std::time::SystemTime::now().duration_since(std::time::UNIX_EPOCH).unwrap().as_millis());
             let first_app = &snap_apps[0];
             let base_title = if snap_apps.len() == 1 {
                 first_app.name.clone()

src-tauri/src/system_info/updates.rs

@@ -296,7 +296,7 @@ pub fn check_flatpak_updates(target_apps: &[String]) -> Vec<AppUpdate> {
         .filter_map(|line| {
             let parts: Vec<&str> = line.split('\t').collect();
 
-            if parts.len() < 3 {
+            if parts.len() < 2 {
                 return None;
             }
 
@@ -309,9 +309,11 @@ pub fn check_flatpak_updates(target_apps: &[String]) -> Vec<AppUpdate> {
             }
 
             let name = parts[0].trim().to_string();
-            let new_version = parts[2].trim().to_string();
-
             let current_version = get_flatpak_app_version(&app_id);
+            let mut new_version = parts.get(2).unwrap_or(&"").trim().to_string();
+            if new_version.is_empty() {
+                new_version = current_version.clone();
+            }
 
             Some(AppUpdate {
                 name,
@@ -431,7 +433,7 @@ pub fn check_native_updates(target_apps: &[String]) -> HashMap<String, String> {
     }
 
     // Try Fedora/RHEL (dnf check-update)
-    if let Ok(output) = Command::new("dnf").args(["check-update"]).output() {
+    if let Ok(output) = Command::new("dnf").args(["check-update", "--refresh"]).output() {
         let stdout = String::from_utf8_lossy(&output.stdout);
         available.extend(check_dnf_updates(&stdout, target_apps));
     }

src/views/app_manager/store.ts

@@ -166,8 +166,26 @@ export const useAppManagerStore = create<AppManagerStore>((set, get) => ({
     try {
       const targetUpdates = updates.filter((u) => selectedPackageIds.includes(u.package_id));
       await invoke("run_app_updates", { updates: targetUpdates });
+
+      set((state) => {
+        const hasErrors = targetUpdates.some(t => {
+          const st = state.appStatuses.find(a => a.name === t.name);
+          return st?.status === "error";
+        });
+
+        return {
+          // If there were errors, stay on the progress view so they can read the error badges
+          modalPhase: hasErrors ? "progress" : "done",
+          // Only remove apps that actually completed successfully
+          updates: state.updates.filter((u) => {
+            const st = state.appStatuses.find(a => a.name === u.name);
+            return st?.status !== "done";
+          }),
+          selectedPackageIds: [],
+        };
+      });
     } catch {
-      // Preserve status
+      set({ modalPhase: "done" });
     } finally {
       unlisten();
       set((state) => {