CE upstream

@iamphill All these conflicts are frontend related, could you resolve/reassign them?
```
Unmerged paths:
  (use "git add <file>..." to mark resolution)

	both added:      app/assets/javascripts/application.js
	both added:      app/assets/javascripts/confirm_danger_modal.js
	both added:      app/assets/javascripts/dispatcher.js
	both added:      app/assets/javascripts/groups_select.js
	both added:      app/assets/javascripts/lib/utils/common_utils.js
	both added:      app/assets/javascripts/merge_request_widget.js
	both added:      app/assets/javascripts/notes.js
	both added:      app/assets/javascripts/project_new.js
	both added:      app/assets/javascripts/users_select.js
	both modified:   app/views/projects/branches/index.html.haml
```

See merge request !595

Signed-off-by: Rémy Coutable <remy@rymai.me>

Fix broken user_allowed check in Git Annex push

https://gitlab.com/gitlab-org/gitlab-ee/commit/3e4934cea6e2909fe978e5e38a659e4e6f818430 seems to have moved`user_allowed` into the `UserAccess` class, but since no specs tested `git_annex_access_check` a push from Git Annex would fail with an undefined method.

Closes #816

See merge request !597

Closes #816

Fix pagination on search result page when ES search is enabled

Fixes https://gitlab.com/gitlab-org/gitlab-ee/issues/811

See merge request !592

Dicouple an ES index update from RepositoryUpdateMirrorWorker

Fixes https://gitlab.com/gitlab-org/gitlab-ee/issues/812

See merge request !593

Added '*.js.es6 gitlab-language=javascript' to .gitattributes

## What does this MR do?

According to the branch name this adds the `sytanx` highlighting for `.js.es6` files, but this actually adds the `syntax` highlighting. 😆 

## Are there points in the code the reviewer needs to double check?

Is this the right place? 🏃 

## Why was this MR needed?

We need pretty ES6 diffs.

## What are the relevant issue numbers?

Flyin' solo 🛫 

## Screenshots (if relevant)

## Does this MR meet the acceptance criteria?

- [ ] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- [ ] [Documentation created/updated](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/doc/development/doc_styleguide.md)
- [ ] API support added
- Tests
  - [ ] Added for this feature/bug
  - [ ] All builds are passing
- [ ] Conform by the [style guides](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CONTRIBUTING.md#style-guides)
- [ ] Branch has no merge conflicts with `master` (if you do - rebase it please)
- [ ] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

See merge request !5486

Fix CI status icon link underline

## What does this MR do?

Changes the CSS so that CI status icon does not underline when it is hovered over.

## Are there points in the code the reviewer needs to double check?

Just need to make sure there aren't any side effects (`.ci-status-link` being used without an icon).
To my knowledge, every instance of `.ci-status-link` is tied to a `.ci-status-icon-{statusName}`.

## Why was this MR needed?

Resolves existing bug

## What are the relevant issue numbers?

#20103 

## Does this MR meet the acceptance criteria?

- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- Tests
  - [x] All builds are passing
- [x] Conform by the [style guides](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CONTRIBUTING.md#style-guides)
- [x] Branch has no merge conflicts with `master` (if you do - rebase it please)
- [x] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

See merge request !5408

Fixed dropdown search field height in ie11

## What does this MR do?

Fixes the height of the search input in dropdown menus.

## What are the relevant issue numbers?

Closes #19684 

## Screenshots (if relevant)

![Screen_Shot_2016-07-11_at_11.49.52](/uploads/fc25bc3d2c3bbd195f30d1953dc12662/Screen_Shot_2016-07-11_at_11.49.52.png)

See merge request !5179

Reduced diff email CSS

## What does this MR do?

Reduces the amount of inline CSS on the diff emails.

## What are the relevant issue numbers?

#15178 

See merge request !5203

Add green outline to New Branch button

## What does this MR do?

Add green outline to New Branch button on issue page.

## Are there points in the code the reviewer needs to double check?

Nope.

## Why was this MR needed?

The button was not very visible.

## What are the relevant issue numbers?

fixes #18928 

## Screenshots

### Before

![before](/uploads/3bc890e249ef4c3852605a6350c05b9a/before.png)

### After

![after](/uploads/bc627902ffa7c7b4ab20ee7a269fa44f/after.png)

See merge request !5447

Add es6 gem

## What does this MR do?
Add ES6 to ES5 compiling via Babel and the sprockets es6 gem.

## Are there points in the code the reviewer needs to double check?

## Why was this MR needed?
So we can write ES6

## What are the relevant issue numbers?
https://gitlab.com/gitlab-org/gitlab-ce/issues/20098

## Screenshots (if relevant)
![Screen_Shot_2016-07-25_at_10.56.02_AM](/uploads/04ceeedb8235fd3a7601bc4bece313a8/Screen_Shot_2016-07-25_at_10.56.02_AM.png)

![Screen_Shot_2016-07-25_at_10.55.54_AM](/uploads/163c46a3d878924ab1717fccca468003/Screen_Shot_2016-07-25_at_10.55.54_AM.png)

## Does this MR meet the acceptance criteria?

- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- [x] [Documentation created/updated](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/doc/development/doc_styleguide.md)
- [ ] API support added
- Tests
  - [ ] Added for this feature/bug
  - [x] All builds are passing
- [ ] Conform by the [style guides](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CONTRIBUTING.md#style-guides)
- [ ] Branch has no merge conflicts with `master` (if you do - rebase it please)
- [ ] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

See merge request !5473

Signed-off-by: Rémy Coutable <remy@rymai.me>

Signed-off-by: Rémy Coutable <remy@rymai.me>

Fix backup restore

## What does this MR do?

This MR fixes the backup restore task.

## Are there points in the code the reviewer needs to double check?

Whether the mode 0277 makes sense. (Group SUID + group/user read/write permissions)

## Why was this MR needed?

86359ec8 broke this, and it was not caught by any specs. Users would see:

```
Restoring repositories ...
rake aborted!
NameError: undefined local variable or method `repos_path' for #<Backup::Repository:0x00000007cea1d8>
/opt/gitlab/embedded/service/gitlab-rails/lib/backup/repository.rb:59:in `restore'
/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/backup.rake:79:in `block (4 levels) in <top (required)>'
/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/backup.rake:54:in `block (3 levels) in <top (required)>'
Tasks: TOP => gitlab:backup:repo:restore
(See full trace by running task with --trace)
```

## What are the relevant issue numbers?

#20188

## Does this MR meet the acceptance criteria?

- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- Tests
  - [ ] Added for this feature/bug
  - [x] All builds are passing
- [x] Conform by the [style guides](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CONTRIBUTING.md#style-guides)
- [x] Branch has no merge conflicts with `master` (if you do - rebase it please)
- [x] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

See merge request !5459

Instrument Nokogiri parsing methods

## What does this MR do?

This MR instruments the various parsing methods of Nokogiri.

## Are there points in the code the reviewer needs to double check?

No.

## Why was this MR needed?

This allows us to see how much time is spent in Nokogiri.

## Does this MR meet the acceptance criteria?

- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- Tests
  - [x] ~~Added for this feature/bug~~
  - [ ] All builds are passing
- [x] Conform by the [style guides](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CONTRIBUTING.md#style-guides)
- [ ] Branch has no merge conflicts with `master` (if you do - rebase it please)
- [x] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

See merge request !5470

This allows us to see how much time is being spent in just parsing
HTML/XML documents.

Set permissions of backup dir to g+s

Closes #20188

Use project ID in repository cache to prevent stale data from persisting across projects

See merge request !5460

Add iid to MR API response

## What does this MR do?

Adds `iid` parameter to the MR API docs. 

## Why was this MR needed?

It is missing.

## What are the relevant issue numbers?

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/19578

## Does this MR meet the acceptance criteria?

- [x] [Documentation created/updated](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/doc/development/doc_styleguide.md)


See merge request !5468

We have a number of bugs caused by cache keys not being flushed
properly during deletion of a project. Add the project ID to ensure
this never happens.

Closes #20027

Users can filter branches by name on project branches page

This MR aims to solve #18674 by adding the possibility to filter project branches by name

![Screen_Shot_2016-07-07_at_17.21.25](/uploads/b674765d2b1cb8a121c2101715a4568b/Screen_Shot_2016-07-07_at_17.21.25.png)

See merge request !5144

Remove magic comments from Ruby files

## What does this MR do?

Remove magic comments (`# encoding: UTF-8`) from Ruby files.

## Why was this MR needed?

Since Ruby 2, UTF-8 is the default encoding and those comments are no longer necessary.

## What are the relevant issue numbers?

https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/5163#note_13134307

cc @rymai 

See merge request !5456

Make fork counter always clickable

## What does this MR do?

Make the fork counter on project pages clickable for people who forked the project.

## Why was this MR needed?

The fork counter was not clickable.

## What are the relevant issue numbers?

fixes #20205


See merge request !5463

See !5454.
Signed-off-by: Rémy Coutable <remy@rymai.me>