Fix issues with wrong issues/merge request counts when filters are selected

Closes #15356 plus counter for issues and MR are now displayed for the these paths `https://gitlab.com/groups/group-name/issues`  `https://gitlab.com/groups/group-name/merge_requests`  `https://gitlab.com/dashboard/issues` and  `https://gitlab.com/dashboard/merge_requests`

See merge request !4960

Security and safety improvements for gitlab-workhorse integration

Companion to https://gitlab.com/gitlab-org/gitlab-workhorse/merge_requests/60

- Use a custom content type when sending data to gitlab-workhorse
- Verify (using JWT and a shared secret on disk) that internal API requests came from gitlab-workhorse

This will allow us to build features in gitlab-workhorse that require
more trust, and protect us against programming mistakes in the future.

This is designed so that no action is required for installations from
source. For omnibus-gitlab we need to add code that manages the shared
secret.

See merge request !5907
Conflicts:
	GITLAB_WORKHORSE_VERSION
	doc/install/installation.md
	doc/update/8.11-to-8.12.md
	lib/gitlab/workhorse.rb
	spec/lib/gitlab/workhorse_spec.rb
	spec/requests/ci/api/builds_spec.rb
	spec/requests/git_http_spec.rb

Allow the Rails cookie to be used for API authentication

Makes the Rails cookie into a valid authentication token for the Grape
API, and uses it instead of token authentication in frontend code that
uses the API.

Rendering the private token into client-side javascript is a security
risk; it may be stolen through XSS or other attacks. In general,
re-using API code in the frontend is more desirable than implementing
endless actions that return JSON. 

Closes #18302

See merge request !1995

Allow to set request_access_enabled for groups and projects using API

Closes #20978

See merge request !6359

Only create a protected branch upon a push to a new branch if a rule for that branch doesn't exist

A customer ran into an issue where a Sidekiq task retried over and over, leading to duplicate master branches in their protected branch list.
    
Closes #22177

See merge request !6399

Fixes labels multi-encode and selecting labels with single quotes

## What does this MR do?

Replaced single quotes with escaped single quotes when setting item `.is-active` and when removing its field.

Adds a test to test selecting 2 different labels _(one with a single quote)_ with a full page load inbetween, it checks the labels are selected as well as shown as `.is-active` in the list.

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



## Why was this MR needed?

The javascript handles the url encoding when it is sent to the server so we shouldn't let the javascript begin processing an already encoded string but we needed to stop single quotes from breaking a jquery selector.

## Screenshots (if relevant)

https://youtu.be/-H0_L2hV9tM

## 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 [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 you do - 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 #21961

Closes #21880

Closes #21248

Closes #20759

Closes #21935

See merge request !6313

Improve build trace scroll controls

## What does this MR do?

The trace step buttons now correctly scroll to the top or bottom of the build trace, rather than jumping inconsistently and never full reaching the top due to the fixed position of the header/navigation area.

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

## Why was this MR needed?

Build trace UX

## Screenshots (if relevant)

![2016-09-09_20.04.32](/uploads/efee5145fb505f8c9ae2a4cf24d842d3/2016-09-09_20.04.32.gif)

## 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 [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 you do - 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?

Contributes to #21832.

See merge request !6288

Fixed large comments messing with diff table widths

## What does this MR do?

Fixes the width of the diff table so that the content inside it can't increase or decrease the width of the table cells.

## Screenshots (if relevant)

![Screen_Shot_2016-09-12_at_14.44.44](/uploads/2ca483399d867153e6ae608360ffea5f/Screen_Shot_2016-09-12_at_14.44.44.png)

## What are the relevant issue numbers?

Closes #20694

See merge request !6309

Ensure invitees are not returned in Members API

## What are the relevant issue numbers?

Closes #22065

See merge request !6370

Use gitlab-workhorse 0.8.2

Fixes rejected API git archive extensions; improves Sentry errors.

https://gitlab.com/gitlab-org/gitlab-workhorse/blob/master/CHANGELOG

See merge request !6388

Fix broken spec due to last_activity_at updates being throttled

In https://gitlab.com/gitlab-org/gitlab-ce/builds/4218398, the build failed because the last_activity_at column was only being updated once per hour. We
can fix this spec by stubbing out the throttling and adjusting the spec to test the right event timestamp.

See merge request !6424

Strip comments before sending keys to gitlab-shell

## Why was this MR needed?

https://gitlab.com/gitlab-org/gitlab-ce/issues/22167 encoding issues in comment text.

## What are the relevant issue numbers?

https://gitlab.com/gitlab-org/gitlab-ce/issues/22167

See merge request !6381

Hide jump to next discussion button on commit notes

## What are the relevant issue numbers?

Closes #22354

See merge request !6428

Fix "Unsubscribe" link in notification emails that is triggered by anti-virus

## What does this MR do?

* The unsubscribe link in an email body only unsubscribes automatically when logged in, otherwise the user is asked for a confirmation.
* The unsubscribe link in an email header unsubscribes automatically whether logged in or not.

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

This addresses all the comments from https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/5241, I think!

## Why was this MR needed?

People were getting unsubscribed automatically by AV software.

## Screenshot

![Screen_Shot_2016-09-20_at_09.51.30](/uploads/083ee2865f1ad6c08e2ed97f1c4e7d0d/Screen_Shot_2016-09-20_at_09.51.30.png)

## Does this MR meet the acceptance criteria?

- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry 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 you do - 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?

Fixes #17198.

See merge request !6223

Lets the user choose a namespace and name on Github imports

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/14971

See merge request !5728

Use a ConnectionPool for Rails.cache on Sidekiq servers

See merge request !6429

Restrict last_activity_at updates to one per hour

This MR reduces the number of updates to `projects.last_activity_at` to once per hour.

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/22213

See merge request !6391

LFS support for ssh enabled

## What does this MR do?
This is follow-up after https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/6043 which is falsely shown as merged due to: https://gitlab.com/gitlab-org/gitlab-ce/issues/22334

## 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](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 [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 you do - 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?

See merge request !6413

Fix download artifacts button link

## What does this MR do?

Fix download artifacts button link.

## Does this MR meet the acceptance criteria?

- [ ] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- Tests
  - [x] Added for this feature/bug

## What are the relevant issue numbers?

Closes #22294

See merge request !6407

Render stages in valid order

Currently stages in stages dropdown on builds page are not in valid order. It is important to display stages in other those are defined in the pipeline.

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/21133

See merge request !6430

Frontend for Merge Request Diff

This merge request improves the UX for the merge request diff feature which was recently implemented here (https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/6127). Specifically, it styles various parts of the diff feature to match the designs, it disables comment-related buttons in states where comments are disabled, and it adds a 'Show latest version' button for convenience.

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

I could use feedback on this MR's fidelity to the design.  

## Why was this MR needed?

Neccessary styling improvements for basic UX of this feature, and enabled comment buttons are not functional and thus need to be disabled in certain states.

## Screenshots (if relevant)

![57dd0755f0b14342305909](/uploads/318a44a3bc8b7fc5c9c6ef92ba92e511/57dd0755f0b14342305909.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)
- [x] 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 you do - 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?

https://gitlab.com/gitlab-org/gitlab-ce/issues/21427
https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/6127

cc: @jschatz1 

See merge request !6343

Fix processing of events when build finished.

Update pipeline after processing builds. Otherwise we can get into scenario where pipeline will be marked as running.

This solves a quite significant regression in Pipeline processing.

Proper fix is to move all this to Sidekiq Worker and process pipeline there.
I'll do it after 8.12 release.

See merge request !6410

Fix note form hint showing slash commands supported for commits

## What are the relevant issue numbers?

Closes #22218

See merge request !6368

Add optional 'author' param when making commits

This fulfills https://gitlab.com/gitlab-org/gitlab-ce/issues/20789 by adding the ability to specify a user's ID to be used as the author of a commit.

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/20789

See merge request !5822

Make CI to use the permission of the user who is trigger the build

This is continuation of https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/5735, but with removed all LFS code that is added by: https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/6043.

This also incorporates most of LFS code added in !6043 to simplify further merge.

See merge request !6409

Fix import/export database errors

Fixes protected branches errors when importing a project including them

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/21295

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/21799

See merge request !6099

Add support for dynamic environments

Implements proposal described in https://gitlab.com/gitlab-org/gitlab-ce/issues/21971.

Specifically:
- it adds a `.gitlab-ci.yml` configuration,
- it allows environment name to have slashes,
- it allows environment names to use CI predefined variables,
- it allows to specify URL from `.gitlab-ci.yml`,
- it allows the URL to use CI predefined variables,
- it introduces `environment_type` to allow to easily group environments in the future

See merge request !6323