Allow JIRA references for project snippets

closes #24303

See merge request !7541

Allow to block JIRA events for commits and merge requests

implements #5541 

See merge request !7469

Add JIRA remotelinks and prevent duplicated closing messages

implements #13232  
closes #20479   

See merge request !7413

makes compare previous version link easily clickable

## What does this MR do?
This MR does a minor fix about `Compare previous link` which is not easily clickable when long commit list are expanded

## Are there points in the code the reviewer needs to double check?
NR
## Why was this MR needed?
For better UX and make browse easy

## Screenshots (if relevant)

**Before:**
![BrRs](/uploads/11e60ef150a9035ae94d6ed69c3038b5/BrRs.gif)

**After**
![2016-11-19_02.02.42](/uploads/961bac1ddcdc4338ac72bc690c52b7f1/2016-11-19_02.02.42.gif)

## Does this MR meet the acceptance criteria?

- [ ] [Changelog entry](https://docs.gitlab.com/ce/development/changelog.html) 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
- [ ] Conform by the [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [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 it does - rebase it please)
- [ ] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

## What are the relevant issue numbers?


Closes #24658

See merge request !7587

Smarter cache invalidation

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/23550

See merge request !7360

Do not create TODO when build is allowed to fail

## What does this MR do?

Do not create a TODO when build that failed is allowed to fail.

## Does this MR meet the acceptance criteria?

- [x] [Changelog entry](https://docs.gitlab.com/ce/development/changelog.html) 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
  - [ ] All builds are passing

## What are the relevant issue numbers?

Closes #22280

See merge request !7618

Add constraints to group id in routing

To prevent 404 when visit page like https://gitlab.com/groups/group.with.dot/activity

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/24622

See merge request !7614

Added permissions per stage to cycle analytics endpoint

See merge request !7613

Backport some changes done from Time Tracking feature in EE.

See merge request !7604

Fixes regression causing an error message to appear when user first enters the Merge Request form.

Closes #24627

See merge request !7599

Merge branch '24616-mr-shows-the-build-for-this-merge-request-failed-although-builds-still-running' into 'master'

Resolve "MR shows "The build for this merge request failed" although builds still running"

Closes #24616

See merge request !7579

Merge branch '24552-js-environment-timeago-is-not-rendered-and-text-shows-object-object-in-mr-widget' into 'master'

Fix timeago rendering for environment timeago

## What does this MR do?

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

## Why was this MR needed?

## Screenshots (if relevant)

## Does this MR meet the acceptance criteria?

- [ ] [Changelog entry](https://docs.gitlab.com/ce/development/changelog.html) 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 [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [ ] 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 it does - rebase it please)
- [ ] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

## What are the relevant issue numbers?


Closes #24552

See merge request !7539

Add API endpoint for creating a pipeline

Fixes #23468

See merge request !7209

Resolve "Display "folders" for environments"

## What does this MR do?
Adds the ability to show the grouped environments inside "folders".
Adds several reusable vue components in order to accomplish the recursive tree data structure presented.

For the individual components, Jasmine tests were added.
For the ones that depend of an API response, rspec tests are used.


## Screenshots (if relevant)
![Screen_Shot_2016-11-16_at_02.00.13](/uploads/1278012c8639b999b53f080728d283e1/Screen_Shot_2016-11-16_at_02.00.13.png)
![Screen_Shot_2016-11-16_at_02.00.25](/uploads/a3d65416ddb553e1b8f0f4c8897a75dc/Screen_Shot_2016-11-16_at_02.00.25.png)
![Screen_Shot_2016-10-17_at_16.08.50](/uploads/af63efe1d2cbd5fc069408622ef4b607/Screen_Shot_2016-10-17_at_16.08.50.png)


![environments](/uploads/b5a1801766d82ab176fc60f96b6968cb/environments.gif)
## Does this MR meet the acceptance criteria?

- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG.md) 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 [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [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 it does - rebase it please)
- [x] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

## What are the relevant issue numbers?
Closes #22539

See merge request !7015

Remove duplicate sidekiq throttling parameters

Improves `db/schema` after merging https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/7015.

cc @grzesiek @filipa

See merge request !7603

Fix wrong link

Not a big one, just fix a wrong link to internal page.

See merge request !7597

Fix broken merge request widget spec

## What does this MR do?
Converts the invalid es6 syntax of the merge_request_widget_spec which is actually causing the spec not to run through teaspoon

## Are there points in the code the reviewer needs to double check?
None

## Why was this MR needed?
Get specs working again

## Screenshots (if relevant)
None

## Does this MR meet the acceptance criteria?

- [ ] [Changelog entry](https://docs.gitlab.com/ce/development/changelog.html) 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 [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [ ] 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 it does - rebase it please)
- [ ] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

## What are the relevant issue numbers?
Closes #24673

See merge request !7594

Resolve "Display "folders" for environments"

## What does this MR do?
Adds the ability to show the grouped environments inside "folders".
Adds several reusable vue components in order to accomplish the recursive tree data structure presented.

For the individual components, Jasmine tests were added.
For the ones that depend of an API response, rspec tests are used.


## Screenshots (if relevant)
![Screen_Shot_2016-11-16_at_02.00.13](/uploads/1278012c8639b999b53f080728d283e1/Screen_Shot_2016-11-16_at_02.00.13.png)
![Screen_Shot_2016-11-16_at_02.00.25](/uploads/a3d65416ddb553e1b8f0f4c8897a75dc/Screen_Shot_2016-11-16_at_02.00.25.png)
![Screen_Shot_2016-10-17_at_16.08.50](/uploads/af63efe1d2cbd5fc069408622ef4b607/Screen_Shot_2016-10-17_at_16.08.50.png)


![environments](/uploads/b5a1801766d82ab176fc60f96b6968cb/environments.gif)
## Does this MR meet the acceptance criteria?

- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG.md) 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 [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [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 it does - rebase it please)
- [x] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

## What are the relevant issue numbers?
Closes #22539

See merge request !7015

Slash command for mattermost

Closes  #22540

## Does this MR meet the acceptance criteria?

- [x] [Changelog entry](https://docs.gitlab.com/ce/development/changelog.html) added
- [ ] [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 [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [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 it does - rebase it please)


See merge request !7438

Fix broken commit metadata loading for large repository trees

## What does this MR do?

Fixes a regression introduced in !7208 in which a call to `ajaxGet()` would fail when loading metadata for large repository trees.

This call produced no errors in the console because it is contained in a sort of `eval` block in jQuery.  This is an ugly, easily broken method for loading data asynchronously whose problems were exemplified by this issue.  I'm opening a separate issue (#24660) to alter this implementation.

## Why was this MR needed?

The failing AJAX call was causing metadata to stop loading, and the `timeago` functionality to stop running due to script failure.

## Screenshots (if relevant)

![Screen_Shot_2016-11-18_at_2.03.13_PM_copy](/uploads/ab0c11d5c405c01d8e45818b3ca96f23/Screen_Shot_2016-11-18_at_2.03.13_PM_copy.png)

## Does this MR meet the acceptance criteria?

- [ ] All builds are passing
- [ ] Branch has no merge conflicts with `master` (if it does - rebase it please)

## What are the relevant issue numbers?

Closes #24652

See merge request !7588

Add logging for rack attack events

Patch for issue: https://gitlab.com/gitlab-org/gitlab-ce/issues/15612 and partial patch for https://gitlab.com/gitlab-com/support/issues/119.

Also related: https://gitlab.com/gitlab-org/gitlab-ce/issues/22527 

Adds logging for throttle and blacklist rack attack events to the production log.

@stanhu @MrChrisW

See merge request !7585

Make job script a required configuration entry

## What does this MR do?

This MR makes a job script a required configuration entry.

## Does this MR meet the acceptance criteria?

- [x] [Changelog entry](https://docs.gitlab.com/ce/development/changelog.html) added
- Tests
  - [x] Added for this feature/bug
  - [x] All builds are passing

## What are the relevant issue numbers?

Closes #24575

See merge request !7566

Fix typo in Build page JavaScript

## What does this MR do?

fixes #24614

See merge request !7563

Fix faulty deployment refs

In the 8.13 RC cycle, so before the release, there was a time in which
references in git where stored by id instead of iid. This could be fixed
by time, if the iid catches up with the id, it overwrites it. But in the
mean time we have wrong refs in the folder.

This commit fixes that. For all projects we have deployments we'll find
the ones where the ref has a higher number than the iid is now and calls
`#create_ref` on the corresponding deployment.

Fixes gitlab-com/infrastructure#683

cc @ayufan 

One worry: I tested this locally, couldn't find a way to do automate this.

See merge request !7352

Fix wrong link URL

See merge request !7554

Grammar fix in environments.md: s/base/basis

See merge request !7552

Resolve "Margins look weird in Project page with pinned sidebar in project stats bar"

## What does this MR do?
Fixes the margins of the project buttons in small screens and when the sidebar is pinned.

Both top and left margin were not aligned with the rest of the page.

## Screenshots (if relevant)
![Screen_Shot_2016-11-18_at_16.39.01](/uploads/9213cbbfba5fd4a57716c09d1807d2ea/Screen_Shot_2016-11-18_at_16.39.01.png)
![margins](/uploads/86bfad4fb48e67224e8bc8f9b8e38520/margins.gif)

## Does this MR meet the acceptance criteria?

- [x] [Changelog entry](https://docs.gitlab.com/ce/development/changelog.html) 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
- [x] Conform by the [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [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 it does - rebase it please)
- [x] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

## What are the relevant issue numbers?
Closes #24070

See merge request !7580

Fix focus state in preview tab

## What does this MR do?
Fixes the focus border in the preview tab by modifying the `line-height`, keeping the same height 🤸 

## Screenshots (if relevant)
![Screen_Shot_2016-11-18_at_18.35.36](/uploads/3ef96699194704f030cc8d2b5132226c/Screen_Shot_2016-11-18_at_18.35.36.png)

## Does this MR meet the acceptance criteria?

- [ ] [Changelog entry](https://docs.gitlab.com/ce/development/changelog.html) 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
- [x] Conform by the [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [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 it does - rebase it please)
- [x] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

## What are the relevant issue numbers?
Closes #24641

See merge request !7581

Improved Ruby code in autocomplete user search

## What does this MR do?

Improves the Ruby code for finding users in the assignee dropdown based on the Ruby review.

See merge request !7576

Fix migration missing ignored transaction method

Adds missing `disable_ddl_transaction!` to migration

See merge request !7569

Remove race condition while deleting groups

## What does this MR do?

The intended flow during a group deletion is:

```
  Soft-delete group (sync) -> Delete group projects (async) -> Hard-delete group (async)
```

The soft-delete was run in a transaction, which was committed only after
the async job (for hard-deletion) was kicked off. There was a race
condition here - the soft-delete transaction could complete _after_ the
hard delete completed, leaving a soft-deleted record in the database.

This MR removes this race condition. There is no need to run the
soft-delete in a transaction. The soft-delete completes before the async
job is kicked off.

This MR also adds a migration to delete all existing (soft-deleted) groups left in an inconsistent state
due to this bug.

- Closes #23223 
- EE merge request: gitlab-org/gitlab-ee!886

See merge request !7528

Fix missing URL from environments docs

See merge request !7542

500 error on project show when user is not logged in and project is still empty

## What does this MR do?

Aims to fix the 500 error when the project is empty and the user is not logged in and tries to access project#show

## Screenshots (if relevant)
When the project is empty and the user is not logged in we default to the empty project partial instead of readme.

![Screen_Shot_2016-11-11_at_22.54.21](/uploads/3d87e65195376c85d3e515e6d5a9a850/Screen_Shot_2016-11-11_at_22.54.21.png)

## Does this MR meet the acceptance criteria?

- [x] [Changelog entry](https://docs.gitlab.com/ce/development/changelog.html) 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 [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [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 it does - rebase it please)
- [x] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

## What are the relevant issue numbers?

Closes #23990

See merge request !7376

JiraService: simplify url generation

Fixes #24085

See merge request !7307

Mention Git strategy none

See merge request !7530

Allows configuration of idle_timeout for incoming email.

https://gitlab.com/gitlab-org/omnibus-gitlab/merge_requests/1087

See merge request !7423

Add documentation for Review Apps

## What does this MR do?

Add docs for review apps.

## What are the relevant issue numbers?

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/23484

See merge request !6982

Improvements to Redis HA docs

Following https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/6471

See merge request !7502

Refactor environments documentation

## What does this MR do?

Refactor environments docs.

## What are the relevant issue numbers?

https://gitlab.com/gitlab-org/gitlab-ce/issues/23484

See merge request !7107