Fix spec failures in spec/lib/gitlab/git/gitlab_projects_spec.rb

Closes #41264

See merge request gitlab-org/gitlab-ce!16015

Fix onion-skin re-entering state

Closes #38533

See merge request gitlab-org/gitlab-ce!15815

Remove related links in MR widget when empty state

Closes #36764

See merge request gitlab-org/gitlab-ce!15888

Show inline edit button for issues

Closes #37474

See merge request gitlab-org/gitlab-ce!15812

Fix tags in the Activity tab not being clickable

Closes #33028

See merge request gitlab-org/gitlab-ce!15996

Do not generate links for private NPM modules in blob view

Closes #36020

See merge request gitlab-org/gitlab-ce!16002

Improve performance of Pipelines#index.json

See merge request gitlab-org/gitlab-ce!14846

Fix shortcut links on help page

Closes #41097

See merge request gitlab-org/gitlab-ce!16001

Update axios.md

See merge request gitlab-org/gitlab-ce!16008

Preserve gem path so that we use the same gems

See merge request gitlab-org/gitlab-ce!15986

* master:
  Tidy up the documentation of Gitlab HA/Gitlab Application
  Make sure two except won't overwrite each other

Tidy up the documentation of Gitlab HA/Gitlab Application

See merge request gitlab-org/gitlab-ce!16011

Make sure two except won't overwrite each other

See merge request gitlab-org/gitlab-ce!16010

This is a pretty boring solution, but I can't
think of a good idea right now and this might be
good enough for now...

Without this patch, I would end up with:

```
An error occurred in a `before(:suite)` hook.
Failure/Error: raise "could not connect to gitaly at #{socket.inspect} after #{sleep_time} seconds"

RuntimeError:
  could not connect to gitaly at "tmp/tests/gitaly/gitaly.socket" after 10 seconds
```

Digging into it, it's because `scripts/gitaly-test-spawn` could not
spawn the process, because it cannot find the installed gems.

I personally installed all my gems under $HOME, namely with:

* `gem install rake --user-install` or:
* `bundle install --path ~/.gem`

The gems would be installed to `~/.gem/ruby/2.4.0/gems`, where
the version is Ruby ABI version.

Now we're changing $HOME, making RubyGems think that the gems
would be installed to `tmp/tests/ruby/2.4.0/gems` which is
apparently not the case.

In order to workaround this, we could preserve $GEM_PATH
populated by RubyGems, ignoring the default path based on $HOME.

Uses `list_commits_by_oid` on the CommitService, to request the needed
commits for pipelines. These commits are needed to display the user that
created the commit and the commit title.

This includes fixes for tests failing that depended on the commit
being `nil`. However, now these are batch loaded, this doesn't happen
anymore and the commits are an instance of BatchLoader.

Fix cluster enviroment missing

See merge request gitlab-org/gitlab-ce!15973

Resolve "Codequality and qa:internal is leaking to Shared Runners"

Closes #41139

See merge request gitlab-org/gitlab-ce!15957

Fix missing WHERE clause in 20171106135924_issues_milestone_id_foreign_key migration

Closes gitlab-com/infrastructure#3416

See merge request gitlab-org/gitlab-ce!15997

If milestone_id is NULL, we shouldn't need to update it to be NULL again. This
was causing us to touch almost all rows in the issues table for no good
reason.

Closes https://gitlab.com/gitlab-com/infrastructure/issues/3416

fix the commit diff discussion sending the wrong url

See merge request gitlab-org/gitlab-ce!15988

Use queue_namespace rather than enqueue_in

See merge request gitlab-org/gitlab-ce!15989

Export and use Notes ES module

See merge request gitlab-org/gitlab-ce!15953