Rename `run` task helper method to prevent conflict with StateMachine

This prevents the following message from appearing whenever running a
Rake task:

    Instance method "run" is already defined in Object, use generic
    helper instead or set StateMachines::Machine.ignore_method_conflicts
    = true.

See merge request !5750

Add a method in Project to return a cached value of total count of projects

This is in preparation to address the DB load caused by the counting
in gitlab-com/infrastructure#303.

See merge request !5746

This prevents the following message from appearing whenever running a
Rake task:

    Instance method "run" is already defined in Object, use generic
    helper instead or set StateMachines::Machine.ignore_method_conflicts
    = true.

Check out GH pull requests locally where the source/target branch had been deleted

## What does this MR do?

Check out GitHub pull requests where source/target branches that had been deleted locally rather than temporarily restoring them on GitHub using their References API. This helps us to not get rate limited, and allow us to import cross-repository pull requests (those from forks).

## What are the relevant issue numbers?

Fixes #15528

Fixes #17766

Fixes #19310

Fixes #19439

Fixes #19998

Fixes #20153

Fixes #20552

Fixes https://gitlab.com/gitlab-com/support-forum/issues/801

#20385

## Screenshots (if relevant)

## 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 !5630

# Conflicts:
#	lib/gitlab/redis.rb

This is in preparation to address the DB load caused by the counting in
gitlab-com/infrastructure#303.

Do not look up commit again when it is passed to RelativeLinkFilter

## What does this MR do?

Use `context[:commit]` in RelativeLinkFilter instead of looking up commit using `context[:ref]`.

## Why was this MR needed?

Even though the commit object was already passed, unnecessary I/O is done to retrieve the commit object.

## What are the relevant issue numbers?

Fixes #20026

See merge request !5455

Align visibility icons on group page

## What does this MR do?
Aligns visibility icons on group page

## Why was this MR needed?
Because the icons looked like this:   
![Screen_Shot_2016-07-25_at_3.03.31_PM](/uploads/94205a609f803a36a7ba678332564c48/Screen_Shot_2016-07-25_at_3.03.31_PM.png)

Now it looks like this:   
![Screen_Shot_2016-07-25_at_3.06.29_PM](/uploads/efbf40105d91d05c8cf81761aa27c618/Screen_Shot_2016-07-25_at_3.06.29_PM.png)


See merge request !5482

Add JavaScript coverage analysis

## What does this MR do?

- configure teaspoon to calculate test coverage of JavaScript files
- publish result as GitLab pages

## Why was this MR needed?

- test coverage was not calculated for JavaScript files
- JavaScript wants to be under cover 🕶 

## What are the relevant issue numbers?

#19412 

See merge request !5052

Fix importing with an invalid MR source project

Source project shouldn't be -1 when both source and target are the same in the original export.

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/20611

See merge request !5679

TST: Use more accurate time windows so tests do not fail

This MR sets the Datetime attributes of the of the broadcast messages factory more precisely. 

This MR is necessary to ensure that all specs which use the broadcast message factory will pass when run anywhere at any time. Currently, the way the 'starts_at' and 'ends_at' attributes are set,if the specs are run at one second to midnight, the broadcast message will expire in one second. I have changed it so that we are guaranteed a period of one day until expiration. I believe this is the desired behaviour and it's also consistent with the rest of the factory. 

See merge request !5674

Rails prefers require_dependency so that it won't require twice:

## What does this MR do?

Fix warnings for loading constants twice

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

Now it's depending on `require_dependency`.

## Why was this MR needed?

Fixes #20724

Backtrace before this patch: $23876

See merge request !5727

Update Grape from 0.13.0 to 0.15.0

Changelog: https://github.com/ruby-grape/grape/blob/v0.15.0/CHANGELOG.md

Working on #18226.

See merge request !4601

Memoize CI config node validator to prevent leaks

## What does this MR do?

This MR memoizes CI configuration node validator, to prevent possible memory leak described in #20698.

## Why was this MR needed?

See #20698

## What are the relevant issue numbers?

Closes #20698

## 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
  - [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 !5733

Changelog: https://github.com/ruby-grape/grape/blob/v0.15.0/CHANGELOG.md

Works toward #18226.

Active tense test coverage

Fixes all tests to use active tense and follow [Four Phase Test]( https://robots.thoughtbot.com/four-phase-test#all-together)

See merge request !5233

Currently trees are sorted in the fashion:
- folders
- files
- submodules
with each section sorted alphabetically

This changes to this system:
- folders and submodules (sorted together)
- files

Remove offending empty line to make rubocop happy

see https://gitlab.com/gitlab-org/gitlab-ce/builds/2931496

See merge request !5732

See merge request !5712.

Closes #20724

Remove legacy Ci::StaticModel we do not use anymore

## What does this MR do?

This removes class that according to our code coverage report and
`grep` is a legacy and unused class.

See merge request !5710

Enable some Rubocop cops related to new lines

## What does this MR do?

This MR enabled two additional Rubocop cops:

Keeps track of empty lines around block bodies.  
`Style/EmptyLinesAroundBlockBody`

Keeps track of empty lines around method bodies.  
` Style/EmptyLinesAroundMethodBody`

See merge request !5637

Add newlines styleguide for Ruby code 

See merge request !5636

Update version_sorter and use new interface for faster tag sorting

See merge request !5723

Enable/Disable Deploy keys for a project

Closes #20123 

## 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

See merge request !5647

Stop 'git push' over HTTP early

Before this change we always let users push Git data over HTTP before
deciding whether to accept to push. This was different from pushing
over SSH where we terminate a 'git push' early if we already know the
user is not allowed to push.

This change let Git over HTTP follow the same behavior as Git over
SSH. We also distinguish between HTTP 404 and 403 responses when
denying Git requests, depending on whether the user is allowed to know
the project exists.


See merge request !5639