CE upstream

Closes omnibus-gitlab#2988 et gitlab-com/infrastructure#3260

See merge request gitlab-org/gitlab-ee!3570

Add feature flag to use gitaly-ssh mirroring when cloning internal repos

Closes gitaly#739

See merge request gitlab-org/gitlab-ee!3479

Add a section on Connection flows

Closes gitlab-org/build/team-tasks#28

See merge request gitlab-org/gitlab-ee!3562

Geo - Does not sync repos on unhealthy shards in non-backfill conditions

Closes #3690

See merge request gitlab-org/gitlab-ee!3540

As part of the architecture, say what ports are used by what services
when.  This should add value in debugging data flows, and opening
firewalls.

Fix wiki retry count typo

Closes #4177

See merge request gitlab-org/gitlab-ee!3569

[EE] Hashed Storage Attachments migration path

See merge request gitlab-org/gitlab-ee!3544

[EE] Strip leading & trailing whitespaces in CI/CD secret variable keys, and environment scope

Closes gitlab-ce#40561

See merge request gitlab-org/gitlab-ee!3563

Resolved for:
- lib/api/namespaces.rb
- spec/policies/namespace_policy_spec.rb
- spec/requests/api/namespaces_spec.rb

Upgrade codeclimate image to latest

Closes #40255

See merge request gitlab-org/gitlab-ce!15461

Add new API endpoint - list jobs of a specified runner

Closes #39699

See merge request gitlab-org/gitlab-ce!15432

Add new API endpoint - get a namespace by ID

See merge request gitlab-org/gitlab-ee!3450