Set `in_progress_merge_commit_sha` for fast-forward merges.

- Closes #900

1. This flag is used in conjunction with the "Developers can Merge"
   branch permission, to allow a user to merge MRs without push access
   to a branch.

2. Without this flag set, the user doesn't have access to the protected
   branch, and the merge fails.

3. This flag was previously set for the `Repository#merge` method, but
   not the `Repository#ff_merge` method.

See merge request !671

Resolve templates docs



See merge request !672

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

Allow LDAP `sync_ssh_keys` setting to be set to `true`

In that case `sync_ssh_keys` will default to the `sshPublicKey` value

Fixes #8

See merge request !670

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

2FA checks for API workflows

## What does this MR do?

It adds a check to the API `/session` endpoint that will deny authentication requests to users that have 2FA enabled. In the error message it will instruct them to use a Personal Access Token instead.

It adds a check to the `/oauth/token` endpoint, when `grant_type: 'password'` is used, so that no OAuth2 access token can be generated if the user has 2FA enabled. This endpoint should not be used by OAuth applications, anyway. OAuth apps should follow the flow of redirecting the user to GitLab, where 2FA access restrictions apply and logging them in there. Once successfully authenticated, the OAuth token is passed to the client.

## Why was this MR needed?

No 2FA check on API endpoints.

## What are the relevant issue numbers?

Fixes #2979

See merge request !5820

Update Hamlit to 2.6.1

Fixes gitlab-org/gitlab-ce#21025 and gitlab-org/gitlab-ce#21017

See merge request !5873

Handle legacy sort order values

Convert the legacy sort order values id_asc / id_desc into the ones we use now, created_at / created_desc, to stop the dropdown being blank.

Closes #21028.

See merge request !5880

Update doorkeeper to 4.2.0

Changelog: https://git.io/v6PnV

See merge request !5881

Deployment and Play endpoints

See merge request !5825

Allow naming (and deleting) U2F devices.

## What does this MR do?

- Allow giving each U2F device a name (at the time of registration).
- Allow deleting individual U2F devices.
- Display a list of registered U2F devices.

## What are the relevant issue numbers?

- Closes #17334 
- Closes #17335 

See merge request !5833

Add endpoints for pipelines

- [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)
- [ ] 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 !5837

Fix email line-height in Outlook

On Outlook.com:

![image](/uploads/4bfa8daacce39a640428dff6eec0c098/image.png)

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/19060.

See merge request !5843

edit_blob_link can receive the blob to avoid access to the repository

## What does this MR do?

Avoid access to the repository to get the blob when can be passed on context

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

## Why was this MR needed?

#20454 to try to speed up the diff pages

## What are the relevant issue numbers?

Relates #20454 probably we want and UI solution not just a backend solution

## 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
  - [ ] 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 !5850

Add merge conflict resolution to CHANGELOG

😊 

See merge request !5863

Hide "Create new list button" on Issues and MRs pages

![1](/uploads/d8b08cb62cfc9e9d29e3e64b2ed0a8af/1.png)

/cc @jschatz1 

See merge request !5852

Attempted improvement to stop boards spec failing



See merge request !5869

I've accidentally forgot to resolve it

Allow syncing a group against all providers at once

Allows `Sync::Group` to sync members for a single group across all providers at once. Closes #399

No

The current implementation of LDAP group sync manages members based on a single LDAP provider. This is optimal because we can open a single connection to a given LDAP server (provider) and run all queries needed to sync all GitLab groups with links to that provider. If we want to sync a single group at a time we need to flip that model - for a single group, run the sync for all providers.

This presents a few challenges since we have a state machine on the group. In the former/current model we need to set the state inside the loop. However, if we do that in the latter model we will likely run into a race condition. At least, it will execute unnecessary queries against the database. Other than adding the functionality needed to sync a single group, the MR moves the state machine handling to the respective class method.

See merge request !636

Fix broken feature spec.

This older spec was failing: features/project/issues/issues.feature

Looks like before we were doing an exact match for queries, that's why
it was passing with this existing issue: https://gitlab.com/gitlab-org/gitlab-ce/blob/59fa031e6f7d5a1b658c370f581c4caaf4493150/features/project/issues/issues.feature#L128

Failed build: https://gitlab.com/gitlab-org/gitlab-ce/builds/3178231

See merge request !5857

[ES] Limit amount of retries for sidekiq jobs

ES index data is not that critical and in most of the cases sidekiq jobs fails due to bugs.
What do you think @jnijhof and @pcarranza 

See merge request !666

[ES] Fix for unborn head

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/21038

See merge request !669

Simplify SQL queries of marking a todo as done

See merge request !5832

Update gitlab_git gem to 10.4.7

See merge request !5851

Update changelog

## What does this MR do?
Updates Changelog: https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/5485#note_14008742

See merge request !5854

Don't show comment button in gutter of diffs on MR discussion tab

When browsing to an MR, switching to the Changes tab, and switching back to the Discussions tab, the gutter of the diffs on that page would show the comment button on-hover, while it shouldn't, since comments on new lines can only be created from the Changes tab.

![Screen_Shot_2016-07-25_at_22.01.11](/uploads/6b044e1a3ecb34ddaa0af432833473aa/Screen_Shot_2016-07-25_at_22.01.11.png)

`8-10-stable` counterpart at https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/5493

See merge request !5492

Issue boards

- Issue: #17907
- Issue backend: #20335
- Backend MR: !5548
- Frontend MR: !5554
- Documentation !5713

- [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)
- [ ] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

See merge request !5548

Collapse build tabs that don't fit

## What does this MR do?
* Orders tests from `failed` > `pending` > `running` > `canceled` > `skipped` > `success`
* Put stages in one dropdown
* Once stage is selected, second dropdown shows all builds/jobs for that stage

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

## Why was this MR needed?
So many tests!   
<img src="/uploads/d581b2670588121c6d64823f61906a1a/Screen_Shot_2016-08-01_at_9.52.50_AM.png" width="600px">

## What are the relevant issue numbers?
Closes #18516    
Part of #19982

## Screenshots (if relevant)
![Screen_Shot_2016-08-17_at_1.14.20_PM](/uploads/fa183361ed13137257caf20a6afc4ef1/Screen_Shot_2016-08-17_at_1.14.20_PM.png)
![Screen_Shot_2016-08-17_at_1.14.39_PM](/uploads/f568cac463abf5c625cf31912ddbd00a/Screen_Shot_2016-08-17_at_1.14.39_PM.png)

See merge request !5595

Add pipeline graph

## What does this MR do?
Adds pipeline visualization

## What are the relevant issue numbers?
Closes #18141    
Part of #19982 

## Screenshots (if relevant)
![Screen_Shot_2016-08-16_at_7.59.52_PM](/uploads/c9dd695d2ddbd2a85e98a5b4e500d52c/Screen_Shot_2016-08-16_at_7.59.52_PM.png)
![Screen_Shot_2016-08-16_at_7.55.49_PM](/uploads/5ab548cc5fc8a42371d3b54108798c02/Screen_Shot_2016-08-16_at_7.55.49_PM.png)

See merge request !5742

Remove sleep calls introduced in !5740

See merge request !5815