Refactor how we fetch ref for merge requests

Closes #36089 and #36296

See merge request !13416

Enforce boolean defaults on Application Settings

Closes #2750

See merge request !13144

Migrate `Git::Repository.ls_files` to Gitaly

Closes gitaly#404

See merge request !13302

Update rails tempalte to not contain gitlab-test

See merge request !13537

So that we could limit the access to Repository#fetch_ref
See: https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/13416#note_37487433

[ci skip]

Use Prev/Next pagination for exploring projects

Closes #27390

See merge request !13456

Revert "Merge branch 'zj-fix-charlock_holmes' into 'master'"

See merge request !13533

Fix: Thread safe GPGME tmp directory

Closes #35986

See merge request !13481

This reverts merge request !13523

Add dynamic navigation tunnel to fly-out menus

Closes #35949

See merge request !13315

This changes the pagination of the "Explore" pages so they use a simpler
pagination system that only shows "Prev" and "Next" buttons. This
removes the need for getting the total number of rows to display, a
process that can easily take up to 2 seconds when browsing through a
large list of projects.

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/27390

* upstream/master: (47 commits)
  Update CHANGELOG.md for 9.4.5
  Update charlock_holmes
  add a changelog entry
  switch to multi-line before block
  restructure the #new_key notification spec
  don't send devise notifications to the ghost user
  reset_delivered_emails before testing #new_key
  skip the :read_project check for new_project_member
  move the member spec to be with the other ones
  add a spec for new_group_member
  add a spec for never emailing the ghost user
  rubocop fix
  a membership with no user is always notifiable
  check notifiability for more emails
  add Member#notifiable?(type, opts)
  make NotificationRecipient a little more customizable
  Add notes about database performance for MySQL
  fix confidential border issue as well as confidential styles leaking on new MR
  Migrate force push check to Gitaly
  Add option to disable project export on instance
  ...

[ci skip]

Update charlock_holmes

See merge request !13523

setting of the gpg home directory is not thread safe, as the directoy
gets stored on the class.

if multiple threads change the directory at the same time, one of the
threads will be working in the wrong directory.

Resolve "Project overview page doesn't load commit metadata for repo view"

Closes #36133

See merge request !13362

Wait for requests to finish before running the ace JS

Closes #36191

See merge request !13405

The compiler needs to be pinned to c++11, which is done by
https://github.com/brianmario/charlock_holmes/commit/51d8a2f0eb1e9d3e476482727d4122b3d11b2bc6

Without this patch it won't install charlock_holmes on newer compilers.

Increase z-index of pipeline dropdown

Closes #36325

See merge request !13507

Don't rename system when migrating from 9.x -> 9.4

Closes #35525 and #36148

See merge request !13228

Bugfix.silence on disabled notifications

Closes #23714

See merge request !13325

Add notes about database performance for MySQL

See merge request !13516

since the mere act of creating the key sends an email :|

since we're just adding them as a member, the permission may still
return false.

and add one