Update gitlab-shell version and doc to 2.6.12



See merge request !280

Disable githoooks for git annex commits

Fixes https://gitlab.com/gitlab-org/gitlab-ee/issues/40

<s>This fix checks if the commit `SHA` is also in one of the synced `git-annex` branches, which means that it should safely skip git hooks. </s> This may not work with multiple commits to the synced branch

These `git-annex` commits also consistently have a message starting with git-annex blah... Using this, as probability of false positives is very low.

See merge request !272

Add confidential issues

Closes gitlab-org/gitlab-ce#3678

Tasks:

- [X] Add `confidential` flag to `issues` table
- [X] Allow user to mark/unmark an issue as confidential
- [X] Restrict access to confidential issues for non-members/author/assignee
  - [X] Issues list
  - [X] Issue details
  - [X] API
  - [X] Search results when Elasticsearch is disabled
  - [X] Search results when Elasticsearch is enabled, and search by term
  - [x] Search results when Elasticsearch is enabled, and search by iid
- [X] Remove references for confidential issues
  - [X] Issue/MR Description
  - [X] Notes
  - [X] Autocomplete
- [x] Milestone overview
  - [x] Hide confidential issues for non-members/author/assignee
  - [x] Does not count confidential issues for non-members/author/assignee
- [X] Add a lock icon to confidential issues
  - [X] Issues list
  - [X] Issue details
  - [X] Search results
- [x] Activity Feed
  - [x] Hide confidential issues for non-members/author/assignee

Screenshots:

* New issue (1):

![new-issue-1](/uploads/b07f8e72cb2183492c142fdeba7ad8a1/new-issue-1.png)

* New issue (2):

![new-issue-2](/uploads/ac3d6ed96d1e5ab95b076bc09c829b3e/new-issue-2.png)

* Issues:

![issues](/uploads/2c891fbe536962a1501723b4cb4681a3/issues.png)

* Issue:

![issue](/uploads/5b11db32ea618c590fc378f21589dd0c/issue.png)

* Search:

![search](/uploads/88591dfc794d7bce097c72d286c87610/search.png)

* Milestone:

![milestone](/uploads/c26b48a1786514b3a3d66026053e9277/milestone.png)

See merge request !227

ES: Index recreation



See merge request !264

Handle duplicate appearances table creation issue with upgrade from CE to EE

Closes #391

See merge request !278

Hide builds from Project's settings when the feature is disabled (EE)

Related to https://gitlab.com/gitlab-org/gitlab-ce/issues/13944

See merge request !268

Geo: ReadOnly middleware improvements

We should handle API requests (JSON) in a different way we handle normal requests.

Current implementation always redirect to root and display error messages using `flash[:alert]`.
This MR adds `{ message: "..." }` type of response when request is under `application/json` content_type.

This is a small patch/enhancement for Geo (#76)

See merge request !274