nix does not clean the remaining files

[KCynk]

Describe the bug

nix does not clean the remaining files

Steps To Reproduce

Steps to reproduce the behavior:

1. vim /etc/nixos/configuration.conf
2. Content of the config file

{ config, pkgs, ... }:

{
  services.freshrss = {
    enable = true;
    defaultUser = "kcynk";
    passwordFile = "/run/secrets/freshrss";
    dataDir = "/var/lib/freshrss";
    baseUrl = "https://freshrss.localhost";
    database = {
      type = "sqlite";
    };
  };

3. sudo nixos-rebuild switch
4. Reboot
5. Delete content related to freshrss service
6. sudo nixos-rebuild switch
7. Reboot
8. Files are still there

[kcynk@nixos:/var/lib/freshrss] sudo find / -name 'freshrss'
[sudo] password for kcynk: 
/var/lib/freshrss
/nix/store/sw8kbzmalpiq4kmlrp5s1zg9cjkr43rp-nixos/nixos/pkgs/servers/web-apps/freshrss**

[kcynk@nixos:/var/lib/freshrss] cd /var/lib/freshrss/
[kcynk@nixos:/var/lib/freshrss] ll
total 36
-rw-rw---- 1 992 990    0 11-10 18:49 applied_migrations.txt
drwxrwx--- 2 992 990 4096 11-10 20:59 cache
-rw-rw---- 1 992 990 1688 11-10 19:11 config.php
-rw-rw---- 1 992 990 1688 11-10 19:04 config.php.bak.php
drwxrwx--- 2 992 990 4096 11-10 18:49 extensions-data
drwxrwx--- 2 992 990 4096 11-10 20:59 favicons
drwxrwx--- 2 992 990 4096 11-10 18:49 fever
-rw-rw---- 1 992 990    0 11-10 21:55 index.html
-rw-r--r-- 1 992 990    0 11-10 19:39 last_update.txt
drwxrwx--- 4 992 990 4096 11-10 18:49 PubSubHubbub
drwxrwx--- 2 992 990 4096 11-10 18:49 tokens
drwxrwx--- 4 992 990 4096 11-10 18:49 users

9. Executing following commands:

• nix-collect-garbage -d
• nix-collect-garbage
• nix-store --gc

10. Files still there

[kcynk@nixos:/var/lib/freshrss] sudo nix-store --query --roots /nix/store/sw8kbzmalpiq4kmlrp5s1zg9cjkr43rp-nixos/nixos/pkgs/servers/web-apps/freshrss/
/nix/var/nix/profiles/per-user/root/channels-3-link -> /nix/store/18ic13fhdq5mgdnhym22pz2a20pci571-user-environment
/proc/13969/environ -> /nix/store/sw8kbzmalpiq4kmlrp5s1zg9cjkr43rp-nixos
/proc/13971/environ -> /nix/store/sw8kbzmalpiq4kmlrp5s1zg9cjkr43rp-nixos

Expected behavior

Old files should be deleted after rebuild or after one of mentioned command

Metadata

[kcynk@nixos:/var/lib/freshrss] nix-shell -p nix-info --run "nix-info -m"
these 6 paths will be fetched (0.75 MiB download, 10.18 MiB unpacked):
  /nix/store/h5pshzq92r2xcv6w1p10cmkar4nyv0xp-file-5.45
  /nix/store/azkk9647ivcaa29fpb8viwj879q7yjw4-gnu-config-2023-07-31
  /nix/store/9dh2csn531by6b1vr9jv85v4k17xwkid-gnumake-4.4.1
  /nix/store/znqwpxy9jlxcgi2ms2hga0ch87bbbr9g-patchelf-0.15.0
  /nix/store/bbxdw4rgwwl3gnajri82yidr1nlsfskf-stdenv-linux
  /nix/store/6g3mnziija245czxdqvs4k4sc6lad0sw-update-autotools-gnu-config-scripts-hook
copying path '/nix/store/azkk9647ivcaa29fpb8viwj879q7yjw4-gnu-config-2023-07-31' from 'https://cache.nixos.org'...
copying path '/nix/store/h5pshzq92r2xcv6w1p10cmkar4nyv0xp-file-5.45' from 'https://cache.nixos.org'...
copying path '/nix/store/znqwpxy9jlxcgi2ms2hga0ch87bbbr9g-patchelf-0.15.0' from 'https://cache.nixos.org'...
copying path '/nix/store/9dh2csn531by6b1vr9jv85v4k17xwkid-gnumake-4.4.1' from 'https://cache.nixos.org'...
copying path '/nix/store/6g3mnziija245czxdqvs4k4sc6lad0sw-update-autotools-gnu-config-scripts-hook' from 'https://cache.nixos.org'...
copying path '/nix/store/bbxdw4rgwwl3gnajri82yidr1nlsfskf-stdenv-linux' from 'https://cache.nixos.org'...
 - system: `"x86_64-linux"`
 - host os: `Linux 6.1.61, NixOS, 23.11 (Tapir), 23.11pre544052.85f1ba3e5167`
 - multi-user?: `yes`
 - sandbox: `yes`
 - version: `nix-env (Nix) 2.17.1`
 - channels(root): `"nixos"`
 - nixpkgs: `/nix/var/nix/profiles/per-user/root/channels/nixos`

Related issue:
NixOS/nix#6141

[KCynk]

[kcynk@nixos:~] nix-store --query --referrers /nix/store/sw8kbzmalpiq4kmlrp5s1zg9cjkr43rp-nixos/nixos/pkgs/servers/web-apps/freshrss
/nix/store/5bbvjnhpkzgmb2piay1002ajnlgd1yva-env-manifest.nix
/nix/store/18ic13fhdq5mgdnhym22pz2a20pci571-user-environment

sudo nix-store --query --referrers /nix/store/sw8kbzmalpiq4kmlrp5s1zg9cjkr43rp-nixos/nixos/pkgs/servers/web-apps/freshrss | xargs nix-store --delete
[sudo] password for kcynk: 
finding garbage collector roots...
0 store paths deleted, 0.00 MiB freed
error: Cannot delete path '/nix/store/18ic13fhdq5mgdnhym22pz2a20pci571-user-environment' since it is still alive. To find out why, use: nix-store --query --roots

[KCynk]

grep nix /etc/nixos/configuration.conf
nix.settings.experimental-features = [ "nix-command" ];
sudo nixos-rebuild switch

[kcynk@nixos:~] sudo nix store delete --ignore-liveness /nix/store/sw8kbzmalpiq4kmlrp5s1zg9cjkr43rp-nixos/nixos/pkgs/servers/web-apps/freshrss
0 store paths deleted, 0.00 MiB freed
error: Cannot delete path '/nix/store/sw8kbzmalpiq4kmlrp5s1zg9cjkr43rp-nixos' since it is still alive. To find out why, use: nix-store --query --roots

[kcynk@nixos:~] sudo nix-store --query --roots /nix/store/sw8kbzmalpiq4kmlrp5s1zg9cjkr43rp-nixos/nixos/pkgs/servers/web-apps/freshrss
removing stale link from '/nix/var/nix/gcroots/auto/9g1mgvqfhlgw56vjanjsc96pznafm0c3' to '/tmp/nixos-rebuild.BZ6w8a/nix'
removing stale link from '/nix/var/nix/gcroots/auto/v1ychyhf92phfq3q30h1aqscw191hyi1' to '/tmp/nix-build-18502-0/result'
removing stale link from '/nix/var/nix/gcroots/auto/rm0qjaxlggkzdwnsmsdfk521qw0ld493' to '/tmp/nix-build-18475-0/result'
removing stale link from '/nix/var/nix/gcroots/auto/zr57fvv42ysai0xgnd1p5jhny9i9c10d' to '/tmp/nixos-rebuild.BZ6w8a/nix.drv'
/proc/20282/environ -> /nix/store/sw8kbzmalpiq4kmlrp5s1zg9cjkr43rp-nixos
/proc/20284/environ -> /nix/store/sw8kbzmalpiq4kmlrp5s1zg9cjkr43rp-nixos
/nix/var/nix/profiles/per-user/root/channels-3-link -> /nix/store/18ic13fhdq5mgdnhym22pz2a20pci571-user-environment

[kcynk@nixos:~] find /nix/store -name freshrss
/nix/store/sw8kbzmalpiq4kmlrp5s1zg9cjkr43rp-nixos/nixos/pkgs/servers/web-apps/freshrss

[kcynk@nixos:~/Downloads] printenv -0 > env
[kcynk@nixos:~/Downloads] grep -i freshrss env 
[kcynk@nixos:~/Downloads] 

[root@nixos:~] printenv -0 > env
[root@nixos:~] grep -i fresh env 
[root@nixos:~]