9.0: Critical: GitLab Omnibus changes owner for OTHER software in /var/opt/

Summary

After installing GitLab 9.0.2 over latest 8.17 release, the Jfrog Artifactory software on my system, which is also installed in /var/opt/, has changes usergroups to gitlab-prometheus.

root@zelos:/var/opt# ll
total 16K
drwxr-xr-x  4 root root 4.0K Jan 29 18:34 ./
drwxr-xr-x 13 root root 4.0K Mar 29  2016 ../
drwxr-xr-x 19 root root 4.0K Mar 31 13:38 gitlab/
drwxr-xr-x  4 root root 4.0K Jan 29 18:34 jfrog/
root@zelos:/var/opt# cd jfrog/
root@zelos:/var/opt/jfrog# ll
total 16K
drwxr-xr-x 4 root        root              4.0K Jan 29 18:34 ./
drwxr-xr-x 4 root        root              4.0K Jan 29 18:34 ../
drwxr-xr-x 7 artifactory gitlab-prometheus 4.0K Mar 23 19:05 artifactory/
drwxr-xr-x 2 artifactory gitlab-prometheus 4.0K Mar 23 19:01 run/

Steps to reproduce

1. Install Jfrog Artifactory from DPKG package on an existing Gitlab Omnibus installation.
2. Upgrade Gitlab Omnibus from 8.17 to 9.0
3. check directory /var/opt/jfrog for changed usergroup

What is the current bug behavior?

Artifactory is having trouble to run with the wrong usergroup.

What is the expected correct behavior?

Gitlab should NOT touch any other files in /var/opt/

Relevant logs and/or screenshots

(Paste any relevant logs - please use code blocks (```) to format console output, logs, and code as it's very hard to read otherwise.)

Output of checks

(If you are reporting a bug on GitLab.com, write: This bug happens on GitLab.com)

Results of GitLab environment info

(For installations with omnibus-gitlab package run and paste the output of: sudo gitlab-rake gitlab:env:info)

System information
System:         Ubuntu 16.04
Current User:   git
Using RVM:      no
Ruby Version:   2.3.3p222
Gem Version:    2.6.6
Bundler Version:1.13.7
Rake Version:   10.5.0
Redis Version:  3.2.5
Git Version:    2.10.2
Sidekiq Version:4.2.7

GitLab information
Version:        9.0.2
Revision:       3e59fd2
Directory:      /opt/gitlab/embedded/service/gitlab-rails
DB Adapter:     postgresql
URL:            https://sub.host.tld
HTTP Clone URL: https://sub.host.tld/some-group/some-project.git
SSH Clone URL:  git@sub.host.tld:some-group/some-project.git
Using LDAP:     no
Using Omniauth: yes
Omniauth Providers: github

GitLab Shell
Version:        5.0.0
Repository storage paths:
- default:      /var/opt/gitlab/git-data/repositories
Hooks:          /opt/gitlab/embedded/service/gitlab-shell/hooks/
Git:            /opt/gitlab/embedded/bin/git

Results of GitLab application Check

(For installations with omnibus-gitlab package run and paste the output of: sudo gitlab-rake gitlab:check SANITIZE=true)

Checking GitLab Shell ...

GitLab Shell version >= 5.0.0 ? ... OK (5.0.0)
Repo base directory exists?
default... yes
Repo storage directories are symlinks?
default... no
Repo paths owned by git:git?
default... yes
Repo paths access is drwxrws---?
default... yes
hooks directories in repos are links: ...
2/3 ... ok
2/4 ... ok
3/6 ... ok
17/7 ... ok
17/8 ... ok
2/9 ... ok
17/10 ... ok
2/11 ... ok
3/12 ... ok
2/13 ... ok
2/14 ... ok
2/15 ... ok
2/16 ... ok
2/17 ... ok
2/18 ... ok
3/19 ... ok
2/20 ... ok
2/21 ... ok
3/22 ... ok
2/25 ... ok
8/26 ... ok
19/27 ... ok
19/28 ... ok
19/29 ... ok
31/30 ... ok
17/31 ... ok
31/32 ... ok
10/33 ... ok
31/34 ... ok
3/35 ... ok
3/36 ... ok
1/37 ... ok
32/38 ... ok
32/39 ... ok
1/40 ... ok
32/41 ... ok
17/42 ... ok
17/43 ... ok
3/44 ... ok
36/46 ... ok
17/48 ... ok
2/51 ... ok
26/52 ... repository is empty
27/57 ... ok
27/58 ... ok
27/60 ... ok
27/61 ... ok
28/63 ... ok
28/64 ... ok
28/66 ... ok
28/69 ... ok
29/70 ... ok
28/72 ... ok
3/73 ... ok
3/74 ... ok
2/75 ... ok
28/76 ... ok
29/77 ... ok
10/78 ... ok
17/79 ... ok
10/80 ... ok
3/81 ... ok
3/82 ... ok
10/83 ... ok
36/84 ... ok
30/85 ... ok
26/86 ... ok
34/90 ... ok
3/91 ... ok
9/92 ... ok
10/95 ... repository is empty
36/96 ... ok
32/97 ... ok
10/98 ... ok
19/99 ... ok
36/100 ... ok
3/101 ... ok
3/102 ... ok
17/103 ... ok
3/105 ... ok
36/106 ... ok
17/110 ... ok
3/111 ... ok
17/112 ... ok
3/114 ... ok
16/115 ... ok
29/116 ... ok
3/117 ... ok
9/118 ... ok
26/119 ... ok
16/120 ... ok
25/121 ... ok
13/122 ... ok
24/123 ... ok
8/124 ... repository is empty
25/126 ... ok
25/127 ... ok
26/128 ... ok
10/129 ... ok
2/130 ... ok
17/131 ... ok
17/132 ... ok
Running /opt/gitlab/embedded/service/gitlab-shell/bin/check
Check GitLab API access: OK
Access to /var/opt/gitlab/.ssh/authorized_keys: OK
Send ping to redis server: OK
gitlab-shell self-check successful

Checking GitLab Shell ... Finished

Checking Sidekiq ...

Running? ... yes
Number of Sidekiq processes ... 1

Checking Sidekiq ... Finished

Checking Reply by email ...

Reply by email is disabled in config/gitlab.yml

Checking Reply by email ... Finished

Checking LDAP ...

LDAP is disabled in config/gitlab.yml

Checking LDAP ... Finished

Checking GitLab ...

Git configured with autocrlf=input? ... yes
Database config exists? ... yes
All migrations up? ... yes
Database contains orphaned GroupMembers? ... no
GitLab config exists? ... yes
GitLab config outdated? ... no
Log directory writable? ... yes
Tmp directory writable? ... yes
Uploads directory setup correctly? ... yes
Init script exists? ... skipped (omnibus-gitlab has no init script)
Init script up-to-date? ... skipped (omnibus-gitlab has no init script)
projects have namespace: ...
2/3 ... yes
2/4 ... yes
3/6 ... yes
17/7 ... yes
17/8 ... yes
2/9 ... yes
17/10 ... yes
2/11 ... yes
3/12 ... yes
2/13 ... yes
2/14 ... yes
2/15 ... yes
2/16 ... yes
2/17 ... yes
2/18 ... yes
3/19 ... yes
2/20 ... yes
2/21 ... yes
3/22 ... yes
2/25 ... yes
8/26 ... yes
19/27 ... yes
19/28 ... yes
19/29 ... yes
31/30 ... yes
17/31 ... yes
31/32 ... yes
10/33 ... yes
31/34 ... yes
3/35 ... yes
3/36 ... yes
1/37 ... yes
32/38 ... yes
32/39 ... yes
1/40 ... yes
32/41 ... yes
17/42 ... yes
17/43 ... yes
3/44 ... yes
36/46 ... yes
17/48 ... yes
2/51 ... yes
26/52 ... yes
27/57 ... yes
27/58 ... yes
27/60 ... yes
27/61 ... yes
28/63 ... yes
28/64 ... yes
28/66 ... yes
28/69 ... yes
29/70 ... yes
28/72 ... yes
3/73 ... yes
3/74 ... yes
2/75 ... yes
28/76 ... yes
29/77 ... yes
10/78 ... yes
17/79 ... yes
10/80 ... yes
3/81 ... yes
3/82 ... yes
10/83 ... yes
36/84 ... yes
30/85 ... yes
26/86 ... yes
34/90 ... yes
3/91 ... yes
9/92 ... yes
10/95 ... yes
36/96 ... yes
32/97 ... yes
10/98 ... yes
19/99 ... yes
36/100 ... yes
3/101 ... yes
3/102 ... yes
17/103 ... yes
3/105 ... yes
36/106 ... yes
17/110 ... yes
3/111 ... yes
17/112 ... yes
3/114 ... yes
16/115 ... yes
29/116 ... yes
3/117 ... yes
9/118 ... yes
26/119 ... yes
16/120 ... yes
25/121 ... yes
13/122 ... yes
24/123 ... yes
8/124 ... yes
25/126 ... yes
25/127 ... yes
26/128 ... yes
10/129 ... yes
2/130 ... yes
17/131 ... yes
17/132 ... yes
Redis version >= 2.8.0? ... yes
Ruby version >= 2.1.0 ? ... yes (2.3.3)
Your git bin path is "/opt/gitlab/embedded/bin/git"
Git version >= 2.7.3 ? ... yes (2.10.2)
Active users: 21

Checking GitLab ... Finished

(we will only investigate if the tests are passing)

Possible fixes

(If you can, link to the line of code that might be responsible for the problem)