ERROR on gitlab-ctl reconfigure after update to gitlab 12.3.2

Summary

The instance is running after update to 12.2.3, however I'm getting errors when I run gitlab-ctl reconfigure.

Steps to reproduce

Issue encountered after updating gitlab-ee from 11.xx to 12.2.3 in a single step.

Example Project

(If possible, please create an example project here on GitLab.com that exhibits the problematic behavior, and link to it here in the bug report)

(If you are using an older version of GitLab, this will also determine whether the bug is fixed in a more recent version)

What is the current bug behavior?

(What actually happens)

What is the expected correct behavior?

(What you should see instead)

Relevant logs and/or screenshots

Starting Chef Client, version 14.13.11
resolving cookbooks for run list: ["gitlab-ee"]
Synchronizing Cookbooks:
  - gitlab-ee (0.0.1)
  - package (0.1.0)
  - gitlab (0.0.1)
  - consul (0.1.0)
  - runit (4.3.0)
  - repmgr (0.1.0)
  - redis (0.1.0)
  - registry (0.1.0)
  - nginx (0.1.0)
  - postgresql (0.1.0)
  - mattermost (0.1.0)
  - monitoring (0.1.0)
  - gitaly (0.1.0)
  - crond (0.1.0)
  - letsencrypt (0.1.0)
  - acme (4.0.0)
Installing Cookbook Gems:
Compiling Cookbooks...

================================================================================
  ERROR: Encountered unsupported config key 'docs' in /etc/gitlab/gitlab.rb.
================================================================================

================================================================================
Recipe Compile Error in /opt/gitlab/embedded/cookbooks/cache/cookbooks/gitlab-ee/recipes/default.rb
================================================================================

NoMethodError
-------------
undefined method `gitlab' for nil:NilClass

Cookbook Trace:
---------------
  /opt/gitlab/embedded/cookbooks/cache/cookbooks/package/libraries/helpers/settings_helper.rb:101:in `block in from_file'
  /opt/gitlab/embedded/cookbooks/cache/cookbooks/package/libraries/config_mash.rb:29:in `auto_vivify'
  /opt/gitlab/embedded/cookbooks/cache/cookbooks/package/libraries/helpers/settings_helper.rb:101:in `from_file'
  /opt/gitlab/embedded/cookbooks/cache/cookbooks/gitlab/recipes/config.rb:22:in `from_file'
  /opt/gitlab/embedded/cookbooks/cache/cookbooks/gitlab/recipes/default.rb:26:in `from_file'
  /opt/gitlab/embedded/cookbooks/cache/cookbooks/gitlab-ee/recipes/default.rb:20:in `from_file'

Relevant File Content:
----------------------
/opt/gitlab/embedded/cookbooks/cache/cookbooks/package/libraries/helpers/settings_helper.rb:

 94:    def ee_attribute(name, **config)
 95:      config = { ee: true }.merge(config)
 96:      attribute(name, **config)
 97:    end
 98:
 99:    def from_file(_file_path)
100:      # Allow auto mash creation during from_file call
101>>     Gitlab::ConfigMash.auto_vivify { super }
102:    end
103:
104:    def method_missing(method_name, *arguments) # rubocop:disable Style/MissingRespondToMissing
105:      # Give better message for NilClass errors
106:      # If there are no arguments passed, this is a 'GET' call, and if
107:      # there is no matching key in the configuration, then it has not been set (not even to nil)
108:      # and we will output a nicer error above the exception
109:      if arguments.length.zero? && !configuration.key?(method_name)
110:        breaktxt = '=' * 80

System Info:
------------
chef_version=14.13.11
platform=centos
platform_version=7.6.1810
ruby=ruby 2.6.3p62 (2019-04-16 revision 67580) [x86_64-linux]
program_name=/opt/gitlab/embedded/bin/chef-client
executable=/opt/gitlab/embedded/bin/chef-client


Running handlers:
There was an error running gitlab-ctl reconfigure:

undefined method `gitlab' for nil:NilClass

Running handlers complete
Chef Client failed. 0 resources updated in 06 seconds

Output of checks

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

Results of GitLab environment info

System information
System:
Proxy:          no
Current User:   git
Using RVM:      no
Ruby Version:   2.6.3p62
Gem Version:    2.7.9
Bundler Version:1.17.3
Rake Version:   12.3.2
Redis Version:  3.2.12
Git Version:    2.22.0
Sidekiq Version:5.2.7
Go Version:     unknown

GitLab information
Version:        12.2.3-ee
Revision:       3a1dd80d30c
Directory:      /opt/gitlab/embedded/service/gitlab-rails
DB Adapter:     PostgreSQL
DB Version:     10.9
URL:            https://git.mydomain.com
HTTP Clone URL: https://git.mydomain.com/some-group/some-project.git
SSH Clone URL:  git@git.mydomain.com:some-group/some-project.git
Elasticsearch:  no
Geo:            no
Using LDAP:     no
Using Omniauth: yes
Omniauth Providers:

GitLab Shell
Version:        9.3.0
Repository storage paths:
- default:      /var/opt/gitlab/git-data/repositories
GitLab Shell path:              /opt/gitlab/embedded/service/gitlab-shell
Git:            /opt/gitlab/embedded/bin/git

Results of GitLab application Check

Checking GitLab subtasks ...

Checking GitLab Shell ...

GitLab Shell: ... GitLab Shell version >= 9.3.0 ? ... OK (9.3.0)
Running /opt/gitlab/embedded/service/gitlab-shell/bin/check
Check GitLab API access: OK
Redis available via internal API: OK

Access to /var/opt/gitlab/.ssh/authorized_keys: OK
gitlab-shell self-check successful

Checking GitLab Shell ... Finished

Checking Gitaly ...

Gitaly: ... default ... OK

Checking Gitaly ... Finished

Checking Sidekiq ...

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

Checking Sidekiq ... Finished

Checking Incoming Email ...

Incoming Email: ... Reply by email is disabled in config/gitlab.yml

Checking Incoming Email ... Finished

Checking LDAP ...

LDAP: ... LDAP is disabled in config/gitlab.yml

Checking LDAP ... Finished

Checking GitLab App ...

Git configured correctly? ... yes
Database config exists? ... yes
All migrations up? ... yes
Database contains orphaned GroupMembers? ... no
GitLab config exists? ... yes
GitLab config up to date? ... yes
Log directory writable? ... yes
Tmp directory writable? ... yes
Uploads directory exists? ... yes
Uploads directory has correct permissions? ... yes
Uploads directory tmp has correct permissions? ... 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: ...
8/7 ... yes
8/9 ... yes
16/10 ... yes
8/11 ... yes
23/12 ... yes
23/14 ... yes
21/15 ... yes
24/16 ... yes
24/17 ... yes
18/19 ... yes
18/20 ... yes
Redis version >= 2.8.0? ... yes
Ruby version >= 2.5.3 ? ... yes (2.6.3)
Git version >= 2.22.0 ? ... yes (2.22.0)
Git user has default SSH configuration? ... yes
Active users: ... 8
Elasticsearch version 5.6 - 6.x? ... skipped (elasticsearch is disabled)

Checking GitLab App ... Finished

Checking GitLab subtasks ... Finished

Possible fixes

Edited Sep 03, 2019 by Fabrizio