CE upstream

See merge request !890

Remove Pages ToC from docs

Now that the docs portal supports ToC, remove them from the document itself

See merge request !891

[ci skip]

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

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 pipeline author for Slack and use pipeline id for pipeline link

[Context](https://gitlab.slack.com/archives/runner-builds/p1479238493000018)

Pipeline Slack message:

>  gitlab-org/gitlab-ci-multi-runner: Pipeline 8bed2a3b of fix/handle-failed-state-while-patching-trace branch by  failed in 1389 seconds 

Quotes:

> @godfat Take a look at these notifications, they seems to be missing author and should probably use Pipeline ID instead of SHA

See merge request !7506

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

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

Fix typo in Build page JavaScript

## What does this MR do?

fixes #24614

See merge request !7563

Integrate time tracking frontend and backend

Closes #985 

See merge request !870

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

Rely on Gitlab::Shell public API, not reading internal files it may use

EE brother of gitlab-org/gitlab-ce!7557 so that specs can pass on EE until the CE->EE merge (no need to pick it into stable since the CE MR will be picked already).

See merge request !887

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

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

Precalculate authorized projects in database

## What does this MR do?
It caches user's authorized projects in database instead of using multiple unions, which should simplify and speed-up things since this operation (getting authorized projects) is used a lot.

## Are there points in the code the reviewer needs to double check?
Did we miss a scenario where we need to refresh the list of projects?

## 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 [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?
#23150 

See merge request !6839

Adds MR ID to changelog entry

Removes changelog entry

Fixes after review

Closes #23150

Less intrusive system note

## What does this MR do?
This MR is for making system notes less intrusive by implementing proposed design
 
## Are there points in the code the reviewer needs to double check?
System notes are reusing in issues, commits and MR discussions. May need to double check to make sure that the design is not breaking anywhere

## Why was this MR needed?
This merge request solve issue #19797 

## Screenshots (if relevant)
**Before:**
![merge-request-before](/uploads/91953598087a613078d80333a43815a7/merge-request-before.png)
**After**
![2016-11-15_17.41.46](/uploads/c809ba53cc34ee83bb439ed741dc39f3/2016-11-15_17.41.46.gif)

## 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
  - [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?
#19797, #23129

See merge request !6755

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