Flatpak autostart breaks with Tauri autostart plugin (Exec should use flatpak app id)

[Hakanbaban53]

Describe the bug

When using the Tauri autostart functionality in Flatpak-distributed apps, the generated autostart entry is incorrect and causes the app to fail on login.

Tauri currently assumes a native desktop binary, but Flatpak apps must be launched via flatpak run <APP_ID>. As a result, the autostart entry generated by Tauri does not work for Flatpak builds.

This issue affects any Tauri app distributed via Flathub that enables autostart.

---

Actual Behavior

Tauri generates an autostart entry similar to:

Exec=/app/bin/my-app --tray

This command cannot be executed outside the Flatpak sandbox, so the app does not start on login.

---

Why This Happens

Flatpak apps are containerized and must be launched via Flatpak itself.
Unlike native binaries, the app binary inside /app/bin is not directly executable by the host session manager at login.

---

Workaround

I implemented a manual Flatpak-specific autostart handler to bypass Tauri’s autostart module when the flatpak feature is enabled.

Example workaround code:

#[cfg(feature = "flatpak")]
pub fn manage_flatpak_autostart(enable: bool) -> Result<(), String> {
    use std::fs;
    use std::path::PathBuf;

    let home = std::env::var("HOME")
        .map_err(|_| "Could not find HOME environment variable")?;
    let autostart_dir = PathBuf::from(home).join(".config/autostart");
    let desktop_file_path =
        autostart_dir.join("io.github.zarestia_dev.rclone-manager.desktop");

    if enable {
        fs::create_dir_all(&autostart_dir)
            .map_err(|e| format!("Failed to create autostart directory: {e}"))?;

        let content = r#"[Desktop Entry]
Type=Application
Name=RClone Manager
Comment=RClone Manager flatpak autostart entry (Not handled by tauri)
Exec=/usr/bin/flatpak run io.github.zarestia_dev.rclone-manager --tray
X-Flatpak=io.github.zarestia_dev.rclone-manager
Terminal=false
"#;

        fs::write(&desktop_file_path, content)
            .map_err(|e| format!("Failed to write autostart file: {e}"))?;
    } else if desktop_file_path.exists() {
        fs::remove_file(&desktop_file_path)
            .map_err(|e| format!("Failed to remove autostart file: {e}"))?;
    }

    Ok(())
}

While this works, it feels like something the Tauri autostart plugin (or docs) should handle or at least document.

---

Documentation Gap

There is currently no mention in the Tauri docs that:

• Autostart behaves differently for Flatpak
• The default autostart plugin is not compatible with Flatpak packaging

---

Additional Suggested Solution: Flatpak App ID Override

Allow developers to provide a static Flatpak App ID at build time, which Tauri can use when generating autostart entries for Flatpak bundles.

For example, Tauri could read an environment variable such as:

TAURI_FLATPAK_ID

When this variable is set, the autostart plugin would generate:

Exec=/usr/bin/flatpak run <TAURI_FLATPAK_ID>

instead of pointing to a native binary path.

This approach works well with Flathub’s build system, where environment variables are commonly defined in the manifest:

- name: rclone-manager
  buildsystem: simple
  build-options:
    append-path: /usr/lib/sdk/node20/bin:/usr/lib/sdk/rust-stable/bin
    env:
      CARGO_HOME: /run/build/rclone-manager/cargo
      NPM_CONFIG_LOGLEVEL: info
      npm_config_cache: /run/build/rclone-manager/flatpak-node/npm-cache
      npm_config_nodedir: /usr/lib/sdk/node20
      npm_config_offline: 'true'
      TAURI_FLATPAK_ID: "io.github.zarestia_dev.rclone-manager"
  sources:
    - type: git
      url: https://github.com/Zarestia-Dev/rclone-manager.git
      tag: v0.1.8
    - npm-sources.json
    - cargo-sources.json

Reproduction

Reproduction Steps (Flatpak + Autostart)

Steps

1. Install the Flatpak application from Flathub:

   flatpak install io.github.zarestia_dev.rclone-manager

Not gonna work after v0.1.9

2. Launch the application.

3. Inside the app open preferences, enable Autostart using the built-in Tauri autostart feature.

4. Inspect the generated autostart entry:

   cat ~/.config/autostart/*.desktop

5. Observe the generated .desktop file for the app (for example):

   Exec=/app/bin/rclone-manager --tray

6. Reboot the system or log out and log back in.

---

Expected Result

The application should start automatically on login using Flatpak:

Exec=/usr/bin/flatpak run io.github.zarestia_dev.rclone-manager --tray

---

Actual Result

The autostart entry points to a non-existent native binary path:

Exec=/app/bin/rclone-manager --tray

As a result:

• The app does not start on login
• Autostart silently fails
• Users must manually fix or recreate the autostart entry

Expected behavior

For Flatpak builds, the autostart entry should be compatible with Flatpak, e.g.:

Exec=/usr/bin/flatpak run io.github.example.app --tray

Full tauri info output

[✔] Environment
    - OS: Arch Linux Rolling Release x86_64 (X64) (gnome on wayland)
    ✔ webkit2gtk-4.1: 2.50.3
    ✔ rsvg2: 2.61.3
    ✔ rustc: 1.91.1 (ed61e7d7e 2025-11-07)
    ✔ cargo: 1.91.1 (ea2d97820 2025-10-10)
    ✔ rustup: 1.28.2 (2025-07-07)
    ✔ Rust toolchain: stable-x86_64-unknown-linux-gnu (default)
    - node: 25.2.1
    - npm: 11.6.4

[-] Packages
    - tauri 🦀: 2.9.4, (outdated, latest: 2.9.5)
    - tauri-build 🦀: 2.5.3
    - wry 🦀: 0.53.5
    - tao 🦀: 0.34.5
    - @tauri-apps/api  ⱼₛ: 2.9.1
    - @tauri-apps/cli  ⱼₛ: 2.9.5 (outdated, latest: 2.9.6)


[-] Plugins
    - tauri-plugin-notification 🦀: 2.3.3
    - @tauri-apps/plugin-notification  ⱼₛ: 2.3.3
    - tauri-plugin-store 🦀: 2.4.1
    - @tauri-apps/plugin-store  ⱼₛ: 2.4.1
    - tauri-plugin-os 🦀: 2.3.2
    - @tauri-apps/plugin-os  ⱼₛ: 2.3.2
    - tauri-plugin-updater 🦀: 2.9.0
    - @tauri-apps/plugin-updater  ⱼₛ: 2.9.0
    - tauri-plugin-fs 🦀: 2.4.4
    - @tauri-apps/plugin-fs  ⱼₛ: not installed!
    - tauri-plugin-shell 🦀: 2.3.3
    - @tauri-apps/plugin-shell  ⱼₛ: 2.3.3
    - tauri-plugin-global-shortcut 🦀: 2.3.1
    - @tauri-apps/plugin-global-shortcut  ⱼₛ: not installed!
    - tauri-plugin-dialog 🦀: 2.4.2
    - @tauri-apps/plugin-dialog  ⱼₛ: 2.4.2
    - tauri-plugin-autostart 🦀: 2.5.1
    - @tauri-apps/plugin-autostart  ⱼₛ: 2.5.1
    - tauri-plugin-http 🦀: 2.5.4
    - @tauri-apps/plugin-http  ⱼₛ: 2.5.4
    - tauri-plugin-single-instance 🦀: 2.3.6
    - @tauri-apps/plugin-single-instance  ⱼₛ: not installed!
    - tauri-plugin-opener 🦀: 2.5.2
    - @tauri-apps/plugin-opener  ⱼₛ: 2.5.2

[-] App
    - build-type: bundle
    - CSP: unset
    - frontendDist: ../dist/rclone-manager/browser
    - devUrl: http://localhost:1420/
    - framework: Angular
    - bundler: Webpack

Stack trace

Additional context

No response