bug: programs.bash (genericLinux): reorders PATH/XDG_DATA_DIRS and introduces duplicates; this breaks some Flatpak behavior

[Labaman]

Are you following the right branch?

• My Nixpkgs and Home Manager versions are in sync

Is there an existing issue for this?

• I have searched the existing issues

Issue description

• Enabling programs.bash on non-NixOS (genericLinux) causes incorrect reordering and duplication of PATH and XDG_DATA_DIRS.
• The module moves Nix paths ahead of system/Flatpak paths, which breaks certain Flatpak handlers/desktop entries.
• Even when the user explicitly defines these variables (via let … in and home.sessionVariables/home.sessionPath), the reordering and duplicates still appear after enabling programs.bash.

envs.before_bash_enable.txt
envs.with_bash_enable.txt

Minimal repro
home.nix:

{ config, pkgs, lib, ... }:
{
  home.username = "deck";
  home.homeDirectory = "/home/deck";
  home.stateVersion = "25.05";

  targets.genericLinux.enable = true;
  xdg.enable = true;

  programs.bash.enable = true;   

  programs.home-manager.enable = true;
}

Steps:

1. home-manager switch --flake .#deck -b hm-bak
2. exec bash -l
3. Inspect:

echo $XDG_DATA_DIRS
echo $PATH

Actual

• XDG_DATA_DIRS: Nix paths end up before system/Flatpak, and duplicates appear.
• PATH: multiple instances of ~/.nix-profile/bin and duplicated system paths — despite explicit user ordering.
• Result: some Flatpaks fail to resolve system handlers/desktop entries correctly.

Expected
Enabling programs.bash should not reorder PATH/XDG_DATA_DIRS (expected order: Flatpak → system → Nix) and should not introduce duplicates, especially when the user has explicitly set these variables.

Maintainer CC

@rycee

System information

- system: `"x86_64-linux"`
 - host os: `Linux 6.11.11-valve24-2-neptune-611-gfd0dd251480d, SteamOS, noversion, 20250903.1`
 - multi-user?: `no`
 - sandbox: `yes`
 - version: `nix-env (Determinate Nix 3.11.3) 2.31.2`
 - nixpkgs: `not found`