Immutability - Package management - apt - reactivation and sources lists files - How to?

TrueNAS General
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Following redirection by your support staff to the forum :

I am interested in installing additional packages and setting up a custom source list (mirror) within the bare OS system, at my own risk.

My question:

How can I achieve this without having to modify and recompile the system from source ?

Issue Details:

  • The root filesystem is effectively immutable as it is read-only, with the apt package manager disabled.
  • Previous forum posts suggested that overriding permissions with chmod +x (e.g., chmod +x /usr/bin/apt) was possible.
  • Currently, in version 25.04.2.3 (branch TrueNAS-Fangtooth), attempting to change permissions results in:
    chmod: changing permissions of '/usr/bin/apt': Read-only file system
  • As a result, the current software design actively prevents root users from modifying the base system and its binaries, including installing custom kernel, custom tools, without rebuilding the entire product.

Observations:
It seems no longer possible to alter permissions on the apt or /bin directories via chmod +x, even as root.

System Details:

  • Product: TrueNAS SCALE Community Edition (likely applicable to Enterprise as well)
  • Branch: TrueNAS-Fangtooth 25.04.0
  • Version: 25.04.2.3

Additional Context:

  • I have root access to the machine.
  • Since the base system of TrueNAS SCALE is Debian-based, GPLv3 released and contains FSF software, I would expect apt to be available for root-level package management, event at my own risks.
  • The console copyright notice states:
    “TrueNAS (c) 2009-2025, iXsystems, Inc. dba TrueNAS. All rights reserved. TrueNAS code is released under the LGPLv3 and GPLv3 licenses with some source files copyrighted by (c) iXsystems, Inc. All other
    components are released under their own respective licenses.”
  • While the use of the shell is not explicitly prohibited, the console states:
    “The supported mechanisms for making configuration changes are the TrueNAS WebUI, CLI, and API exclusively. ALL OTHERS ARE NOT SUPPORTED AND MAY RESULT IN UNDEFINED BEHAVIOR AND SYSTEM FAILURE.”
  • It is not a technical limitation as root access for package management is available in similar open-source Debian-based appliances such as Proxmox.
  • I would also like to remind of the software freedoms under GPLv3, which include the rights to study, modify, and improve the software.
  • The system’s immutability prevents customization, making the system resemble a closed firmware despite being open source based and including FSF sofware (grub2 and parted).
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Thanks dan.