Update gitlab-shell to v3.4.0

Part of Redis Sentinel support: gitlab-org/gitlab-shell#29

See merge request !5920

Fix Error 500 resulting when loading network graph

`discussion_id` may not be present when the SELECT call for notes does not include this attribute. Don't attempt to set the discussion ID unless the model contains the attribute:

```ruby
irb(main):019:0> notes[0]
  Note Load (10.3ms)  SELECT notes.commit_id, count(notes.id) as note_count FROM "notes" WHERE "notes"."project_id" = $1 AND (noteable_type = 'Commit') GROUP BY notes.commit_id  [["project_id", 13083]]
ActiveModel::MissingAttributeError: missing attribute: discussion_id
```

Closes #21119, #21128

See merge request !5922

Backport  changes from gitlab-org/gitlab-ee!581



See merge request !5884

Disable “issue by email” feature until it uses a different token

Separate token being worked on in https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/5914, but too late for 8.11.

See merge request !5915

Todos sorting dropdown

Implements #18135 

![todos_sorting](/uploads/bff76827c421628134dfb8b864e47c74/todos_sorting.png)  


- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- Tests
  - [x] 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 !5691

Call `set_discussion_id` again in DiffNote `before_validation` because the order is important



See merge request !5913

Refactor description templates documentation

## What are the relevant issue numbers?

Refactors docs introduced by https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/4981

See merge request !5839

Koding Integration

## What does this MR do?

Will provide Koding integration with GitLab services. Forked from !4914.

## Are there points in the code the reviewer needs to double check?
I've introduced new layouts which might not be necessary, first time contributor. 

## Why was this MR needed?
We're planning to ship Koding with GitLab.

## What are the relevant issue numbers?
#12759 #14698 

## Screenshots (if relevant)

### Screencasts

http://recordit.co/BDMbhwgxPD
http://recordit.co/By0qiz1ClC

### Enable Koding in Application Settings

![image](/uploads/73a69421105c03aa2b0b47e2617d3fbc/image.png)

### Koding Dashboard
![image](/uploads/6c7dda34792280c0e4791e36af4eba11/image.png)

### Set up Koding Stack
1 - ![image](/uploads/d5c2b93f8e61b5cbffdb06f0267d485f/image.png)
2 - ![image](/uploads/44d9a9b574b8ac0c5eb553fb9653d5da/image.png)

### Run on Koding on Project Page

![image](/uploads/7d2b46221009074ffff75d66d5a1a555/image.png)

### Run in IDE on Merge Requests
![image](/uploads/65eed90c34c34b5fe7ad29ef9c717640/image.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)
- [x] Tests
  - [x] 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 !5909

Ace ventura

## What does this MR do?

Makes Ace only load when it's actually necessary. The only two places it seems to be used is for Snippets and the File (Blob) Editor.

Before minification or compression, this takes the application.js down from 2.2MB to 1.6MB, and also removes two inline scripts :D

Compressed/Minified: master: 317KB/1.1MB, ace-ventura: 220KB/771KB

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

That this doesn't just completely break anything.

## Why was this MR needed?

Ace is a big library, this allows us to only load it when necessary.

## What are the relevant issue numbers?

#14372

## Does this MR meet the acceptance criteria?

- [ ] [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 !4914

Added tooltip to label value in collapsed sidebar

## What does this MR do?

Adds a list of the issuables labels to a tooltip in the collapsed
sidebar. Limited to 5 otherwise the list could get crazy long.

Closes #19398

See merge request !5232

Implement pipeline hooks, extracted from !5525

Closes #20115

See merge request !5620

Wrap single lines of code; horizontally scroll multi-line code blocks

## What does this MR do?
Original problem: code blocks were wrapping in issue body

* Multi-line code blocks (```) should scroll horizontally
* Single lines of code (`) should wrap

## Why was this MR needed?
Inconsistent scrolling vs wrapping behavior

## What are the relevant issue numbers?
Closes #19619 

## Screenshots (if relevant)
![Screen_Shot_2016-08-04_at_2.32.30_PM](/uploads/a4abcc81b57ffaa8dc8ce2b70a24bc21/Screen_Shot_2016-08-04_at_2.32.30_PM.png)


See merge request !5675

Show wall-clock time when showing pipeline

Show wall-clock time when showing pipeline instead of cumulative builds time.

Closes #17007

See merge request !5734

Pipelines ui updates

* Fixes hover color width on build list
* Fixes alignment of status icon on commits page
* Add play icon SVG

Small UI bugs with recent MRs

![Screen_Shot_2016-08-17_at_5.54.32_PM](/uploads/a5f1a38eac332865b17d8d74eeaa5142/Screen_Shot_2016-08-17_at_5.54.32_PM.png)
![Screen_Shot_2016-08-17_at_5.56.43_PM](/uploads/90608eee3e83dbe14244ff2be5a8867e/Screen_Shot_2016-08-17_at_5.56.43_PM.png)
![Screen_Shot_2016-08-18_at_9.18.37_AM](/uploads/9c1265fc3efa7b6084e2368d3fe458cd/Screen_Shot_2016-08-18_at_9.18.37_AM.png)

See merge request !5856

Render coverage badge using latest successful pipeline

## What does this MR do?

This MR make test coverage badge to report value for the latest successful pipeline, instead of the latest one, regardless the status.

Latest pipeline is often running, which makes coverage report inaccurate. Latest pipeline can be also the failed one, which may mean that not all stages got processed, therefore coverage report can be inaccurate as well.

This also improves coverage badge performance because it is not necessary to touch repository to get recent SHA on the branch.

## Why was this MR needed?

See #21013

## What are the relevant issue numbers?

Closes #21013

## 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)
- Tests
  - [x] 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 !5862

Fix layout of edit tags page

#### What does this MR do?
Fixes layout of edit tags page

#### Why was this MR needed?
Layout was broken

#### Screenshots (if relevant)
Before:    
![Screen_Shot_2016-08-18_at_1.33.00_PM](/uploads/9e9e52bdc0743971d6e0996e2c2030a0/Screen_Shot_2016-08-18_at_1.33.00_PM.png)
After:    
![Screen_Shot_2016-08-18_at_1.32.08_PM](/uploads/0a4a93508f0c98cb0788a2c70ee33f4e/Screen_Shot_2016-08-18_at_1.32.08_PM.png)


See merge request !5874

Add space under MR title

## What does this MR do?
Adds space underneath MR title because right now it's impossible to tell where the title ends and the first header of the MR body begins. 
Before:   
![Screen_Shot_2016-08-18_at_1.43.05_PM](/uploads/4e07892036b1d90217fdecbed31a9494/Screen_Shot_2016-08-18_at_1.43.05_PM.png)

After:    
![Screen_Shot_2016-08-18_at_1.42.22_PM](/uploads/1341d4d7c5bd0db21233f6ebb961bafc/Screen_Shot_2016-08-18_at_1.42.22_PM.png)


Note: We need to change our template to have the md headers `####` instead of `##`. Once that's been done it will look like this:
![Screen_Shot_2016-08-18_at_1.46.46_PM](/uploads/e30d432551debc15ec210e76dfcd3451/Screen_Shot_2016-08-18_at_1.46.46_PM.png)

See merge request !5875

Expiration date on memberships

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/17495

See merge request !5876

Do not escape URI when extracting path

## What does this MR do?

- remove escaping of URI parameters after they have already been unescaped in `ExtractsPath`
- remove spec that is relying on that behavior

## Why was this MR needed?

- spaces in directory names were escaped leading to 404 errors on repository files page

## What are the relevant issue numbers?

fixes gitlab-com/support-forum#952, #21106

See merge request !5878

Make all future skipped builds as processable when retrying a build

## What does this MR do?

Makes a builds that are marked as skipped when a pipeline is processed to be reprocessed by changing their's state to created.

## Why was this MR needed?

Currently retry is broken. When you retry a build of pipeline it will succeed and be marked as succeeded, when the next stages should be triggered.

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/21066

See merge request !5879

Add boards controller to issue nav item

#### What does this MR do?
Adds active state to top level nav

Before: 
![Screen_Shot_2016-08-18_at_7.56.56_PM](/uploads/c5db0e9e077f0970b6b7b7d8d7a08147/Screen_Shot_2016-08-18_at_7.56.56_PM.png)

After:   
![Screen_Shot_2016-08-18_at_7.56.10_PM](/uploads/6b46e6f093c02fb44e25cf6952638a5b/Screen_Shot_2016-08-18_at_7.56.10_PM.png)


See merge request !5883

Add a spec testing a second side effect of `Repository#merge`.

## What are the relevant issue numbers?

- Closes #21081
- Related to gitlab-org/gitlab-ee!671
- Related to gitlab-org/gitlab-ee#900

See merge request !5886

Issue boards tooltip hide

- Hides & disables tooltips when dragging issues or lists
- Fixes bug where cursor wouldn't change when dragging.

See merge request !5889

Fixed keyboard shortcuts not working on issue boards

## What does this MR do?

Fixes keyboard shortcuts not working on issue boards page.

## What are the relevant issue numbers?

Closes #21071 

See merge request !5890

Fix notification_service argument error of declined invitation emails

## What does this MR do?

Remove unused arguments that raised the argument error after a refactor, more details in the commit message.

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

## Why was this MR needed?

## What are the relevant issue numbers?

Closes #21039

## Screenshots (if relevant)

## Does this MR meet the acceptance criteria?

- [x] [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
  - [x] 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 !5893

Merge branch '21010-emailsonpushworker-incorrectly-claims-deleted-a-commit-after-a-push' into 'master'

Resolve "EmailsOnPushWorker incorrectly claims deleted a commit after a push"

## What does this MR do?

Fix the comparison order in the emails on push worker, so regular pushes don't show a message about force pushing.

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

Don't think so, it was just a typo: `after_sha` should map to the `source_branch` argument, because it's the head of the comparison.

## Why was this MR needed?

To fix a regression!

## What are the relevant issue numbers?

Closes #21010.

## 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)~~
- [x] ~~API support 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)
- [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 !5894

Improvements to issue boards on mobile

- Removes the drag handles
- Adds a delay before dragging can start otherwise you can't scroll the page

See merge request !5897

Added text color to issues labels in issue board lists

## What does this MR do?

Adds the text color for labels in the response. The frontend was
already setup to handle this, just needed the data from the backend.

See merge request !5898

Fix line commenting for the initial commit

## What does this MR do?

Support line positions on the initial commit, where we can't compare because there's no parent commit.

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

I chose to use the blank SHA to represent the initial commit, but it could as easily be the same SHA. I just thought this was clearer.

## Why was this MR needed?

People couldn't add line comments to the initial commit!

## What are the relevant issue numbers?

Closes #20895.

## Screenshots (if relevant)

![Comment_on_initial_commit](/uploads/1164448462ff55d133f3ff51c98044df/Comment_on_initial_commit.gif)

## Does this MR meet the acceptance criteria?

- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added (N/A, regression)
- [x] [Documentation created/updated](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/doc/development/doc_styleguide.md) (N/A)
- [x] API support added (N/A)
- Tests
  - [x] 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 !5900

Increased vertical alignment of labels for issues in lists

## What does this MR do?

Increases the vertical alignment between labels on issues in issue boards lists.

## Screenshots (if relevant)

![Screen_Shot_2016-08-19_at_16.05.31](/uploads/4edc0fa520d1a0bf692d42d5f99ce4d7/Screen_Shot_2016-08-19_at_16.05.31.png)

See merge request !5902

Fix bug where notes weren’t shown in discussion when the code had changed after creation

See merge request !5908

Load issue templates from repository

part of #18656 


## 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)
- [x] API support added
- Tests
  - [x] 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 !4981

Diff line comments resolve

## What does this MR do?

Diff line comments can be resolved.

Part of #10325 

To do:

- [x] Backend (@DouweM)
  - [x] Fix https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/5022#note_13319326. Will be made easier by https://gitlab.com/gitlab-org/gitlab-ce/issues/17237#note_13370331
  - [x] System note when all discussions are resolved
  - [x] Notification when all discussions are resolved
  - [x] Write unit tests
  - [x] Look at resolve time https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/5022#note_13912743 - Fixed by 4a13aa9f
- [x] Frontend (@iamphill)
  - [x] Fix bugs
  - [x] Write more feature tests 
- [x] Frontend (@connorshea)
  - [x] Address frontend feedback
  - [x] Feature specs for Jump feature
  - [x] Documentation
  - [x] Add Vue.js in a standard way

See merge request !5022

Fix same tiny grammar mistake as in ee

This is a tiny grammar fix that was already merged into EE

https://gitlab.com/gitlab-org/gitlab-ee/merge_requests/667#note_14043471

See merge request !5865

Support slash commands in issues / MR description & comments

See merge request !5021

Merge branch '3225-ace-editor-causing-404-errors-every-time-you-try-to-edit-a-file-in-the-webui' into 'master'

Fix Ace syntax highlighting with compiled assets

## What does this MR do?

Update ACE to 4.1.0 to allow modes (syntax highlighting files for particular languages) to be lazily loaded.

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

Don't think so.

## Why was this MR needed?

Syntax highlighting in the file editor only worked in development and test modes, not in production!

## What are the relevant issue numbers?

Closes #3225.

## Screenshots (if relevant)

First, the test setup - add these lines to `development.rb`:
```ruby
  config.assets.debug = false
  config.assets.compile = false
  config.assets.digest = true
```

Then, before starting the server, run `bundle exec rake assets:clobber assets:precompile`.

Before:

![image](/uploads/486198e273019f8969d2e90560d82928/image.png)

There is an error in the console because `/assets/ace/mode-ruby.js` was not found (it's only available when assets are compiled on demand).

After:

![image](/uploads/6aa0d69b7efdfd6fe6aa22b9a49e9716/image.png)

This loads `/assets/ace/mode-ruby-3915f95a6cc47306b1305e4dcb7aca25b2ef9c49b18ec6011707135b6575d8f3.js`, which works because the precompile step included it and told ACE where to find it.

## Does this MR meet the acceptance criteria?

- [x] [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~~
  - [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 !5501

2FA checks for Git over HTTP

## What does this MR do?

This MR allows the use of `PersonalAccessTokens` to access Git over HTTP and makes that the only allowed method if the user has 2FA enabled. If a user with 2FA enabled tries to access Git over HTTP using his username and password the request will be denied and the user will be presented with the following message:

```
remote: HTTP Basic: Access denied
remote: You have 2FA enabled, please use a personal access token for Git over HTTP.
remote: You can generate one at http://localhost:3000/profile/personal_access_tokens
fatal: Authentication failed for 'http://localhost:3000/documentcloud/underscore.git/'
```

## What are the relevant issue numbers?

Fixes #13568 

See merge request !5764