[BUG] Problems with Flatpak sandboxing causing incomplete ML4W installation

[Crispy8047]

Describe the bug

Hello, and thank you for your work on ML4W and the Dotfiles Installer.

I would like to report several issues related specifically to the Flatpak version of the installer. Even on a clean system, many components of the ML4W setup fail to install or function correctly due to Flatpak sandbox restrictions.

Steps to reproduce

The installer cannot access essential system paths such as /usr, /etc, and /usr/share, which prevents it from installing themes, icons, fonts, and system-wide configuration files.

User configuration directories such as ~/.config/hypr, ~/.config/waybar, ~/.config/kitty, and others are not fully writable from inside the sandbox.

Systemd services required by ML4W cannot be created or enabled.

Some scripts and helper tools fail because they expect direct access to the host filesystem.

Waybar modules and Hyprland configuration files are only partially applied or not applied at all.

Flatpak sandboxing prevents the installer from accessing required host paths. Even with Flatseal, granting permissions manually is not always sufficient, and some operations still fail.

Expected behavior

The installer should be able to:

Write to user configuration directories without restrictions

Install system-wide assets (themes, icons, fonts)

Manage systemd user services

Apply all Hyprland and Waybar configurations correctly

Screenshots

No response

Distribution

Other (please specify below)

If Other, specify

CachyOS

Additional context

It may be helpful to:

Provide a non-Flatpak installer option (AppImage, native binary, or script)

Document required Flatpak permissions explicitly

Add a warning inside the installer when sandbox restrictions block critical operations

Thank you for your time and for maintaining this project. I hope this report helps improve the installation experience.

Code of Conduct

• I agree to follow this project's Code of Conduct

[mylinuxforwork]

Thanks for testing and your feedback. You can extend the file access with flatseal. But what’s your use case? When do you need write access to system level?

[Crispy8047]

"The main issue is that after using your official dotsinstall, it's impossible to configure even the most basic parameters (like keyboard layouts, window behavior, or gaps) without manually installing and configuring Flatseal.
The settings apps run in a sandbox that doesn't 'see' the actual Hyprland configuration or lacks the permissions to apply changes to the host. This creates a broken 'out-of-the-box' experience for Arch/CachyOS users, as the GUI buttons simply do nothing until the user manually punches holes in the Flatpak sandbox. If the goal of ML4W is a seamless setup, the installer should either handle these permissions or provide a native (non-flatpak) version of the tools."

[mylinuxforwork]

On Arch, everything is working fine and the flatpak can see the home directory. You can see it in the manifest.
https://github.com/mylinuxforwork/dotfiles-settings/blob/master/com.ml4w.settings.json

Is there maybe a special flatpak setting enabled in CachyOS?

Thanks for testing and your feedback.

[mylinuxforwork]

@Crispy8047 Just tested the latest rolling release on a fresh CachyOS with Plasma. Worked without any issue.
The only thing that I needed to do is to enter bash in the terminal first to switch from fish to bash. Then I could start the installation command.

[Crispy8047]

Thanks for the update, @mylinuxforwork.
I’ve also tested the latest rolling release, and the return to the git clone method has indeed resolved the installation issues I previously encountered on CachyOS. Everything now installs and links correctly without the sandbox restrictions of the previous Flatpak installer.
Regarding the shell, yes, switching to bash for the initial setup script is a necessary step since CachyOS uses fish or zsh by default.
Since the installation process is now stable, I’m closing this issue. Thanks for your work on this project!