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

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

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

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

Make new tabs persistent when changing view.

## What does this MR do?

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

## Why was this MR needed?

## What are the relevant issue numbers?

## 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)

cc @stanhu @DouweM @rdavila 

See merge request !5859

Send notification emails when users are newly mentioned in issue or MR edits

## What does this MR do?

Introduces "new mention in issue" and "new mention in MR" email notifications.  Editing a Mentionable title or description and adding a mention to a user who was not previously mentioned will now send them a notification email, following usual permissions for doing so.

## Why was this MR needed?

Issues & MRs may be edited to include mentions to new people. We don't currently send out email notifications of these edits to anyone, although they do create TODOs. This brings email notifications into parity with TODOs.

## What are the relevant issue numbers?

Closes #2451

See merge request !5800

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

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

/cc @jschatz1 

See merge request !5852

Eliminate unneeded calls to Repository#blob_at when listing commits with no path

See merge request !5848

Added VueJS plugin

## What does this MR do?

Adds the VueJS & Vue resource plugin with environment detection. 

## What are the relevant issue numbers?

Closes #20738 

See merge request !5845

Fix downtime check formatting

## What does this MR do?

This MR adjusts the formatting of the migration downtime checker so messages are more readable.

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

Not specifically

## Why was this MR needed?

Formatting was somewhat hard to read and the online/offline indicators used the wrong colour.

## New Format

```
[online]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20140407135544_fix_namespaces.rb
[online]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160705054938_add_protected_branches_push_access.rb
[online]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160705054952_add_protected_branches_merge_access.rb
[offline]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160705055254_move_from_developers_can_merge_to_protected_branches_merge_access.rb:

We're creating a `merge_access_level` for each `protected_branch`. If a user creates a `protected_branch` while this
is running, we might be left with a `protected_branch` _without_ an associated `merge_access_level`. The `protected_branches`
table must not change while this is running, so downtime is required.

https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/5081#note_13247410

[offline]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160705055308_move_from_developers_can_push_to_protected_branches_push_access.rb:

We're creating a `push_access_level` for each `protected_branch`. If a user creates a `protected_branch` while this
is running, we might be left with a `protected_branch` _without_ an associated `push_access_level`. The `protected_branches`
table must not change while this is running, so downtime is required.

https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/5081#note_13247410

[online]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160705055809_remove_developers_can_push_from_protected_branches.rb
[online]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160705055813_remove_developers_can_merge_from_protected_branches.rb
[online]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160716115711_add_queued_at_to_ci_builds.rb
[online]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160725083350_add_external_url_to_enviroments.rb
[online]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160727163552_create_user_agent_details.rb
[online]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160728081025_add_pipeline_events_to_web_hooks.rb
[online]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160728103734_add_pipeline_events_to_services.rb
[offline]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160729173930_remove_project_id_from_spam_logs.rb:

Removing a column that contains data that is not used anywhere.

[online]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160801163709_add_submitted_as_ham_to_spam_logs.rb
[online]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160802010328_remove_builds_enable_index_on_projects.rb
[online]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160805041956_add_deleted_at_to_namespaces.rb
[online]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160810102349_remove_ci_runner_trigram_indexes.rb
[online]: /home/yorickpeterse/Projects/gitlab/gitlab-ce/db/migrate/20160810142633_remove_redundant_indexes.rb
```

## Does this MR meet the acceptance criteria?

- 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 !5840

Tracking of custom events

## What does this MR do?

This MR adds the ability to track custom events such as the number of Git pushes.

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

The usual stuff.

## Why was this MR needed?

We want to track more business level data such as the number of Git pushes, how many repositories are imported (and from where), etc.

## What are the relevant issue numbers?

gitlab-org/gitlab-ce#13720

## 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)

cc @pcarranza 

See merge request !5830

Move to project dropdown with infinite scroll for better performance

See merge request !5828

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

## What does this MR do?

Backports changes that were made in gitlab-org/gitlab-ee!581, to avoid potential merge conflicts in the future.

## What are the relevant issue numbers?

- Related to gitlab-org/gitlab-ee!581

## Does this MR meet the acceptance criteria?

## Tasks

- [ ]  !5824 Backport changes from EE!581 to CE
    - [x]  Implementation
        - [x]  ::ProtectedBranches::CreateService.new
        - [x]  Can't remove `load_protected_branches_gon_variables`
        - [x]  `has_many` with count enforced
        - [x]  Extract from access levels
        - [x]  project.protected_branches.create(params)
        - [x]  Improve "access_levels.first"
        - [x]  Fix tests
    - [x]  Fix build
    - [x]  Assign to Douwe
    - [ ]  Wait for review/merge

See merge request !5824