Re-use queries in reference parsers

This MR changes the reference parsing pipeline to cache queried objects and re-use them on subsequent runs. Data is cached in the `RequestStore` module so it's automatically flushed after a request.

Certain references are processed multiple times. For example, for every system note we check if it's a cross reference by getting the issues, MRs and commits it references. When redacting data we may end up querying these very same objects. By caching this we can quite drastically reduce timings and SQL query counts.

#15607

See merge request !5020

Fix typos in API documentation

See merge request !4949

Fix phpunit command in the docker example.

Closes https://gitlab.com/gitlab-org/gitlab-ci-multi-runner/issues/1478

See merge request !5147

Fix wrong gitlab-shell version in 8.9-8.10 update guide

See merge request !5153

Fix typo and explain the precedence of STDERR and STDOUT

## What does this MR do?

Addresses comments https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/5088#note_12884564

See merge request !5169

Make subnavigation a bit darker color



See merge request !5166

Signed-off-by: Dmitriy Zaporozhets <dmitriy.zaporozhets@gmail.com>

Update ui_guide.md with button capitalize rule

cc @jschatz1 @hazelyang @skyruler 

See merge request !5161

This caches various queries to ensure that multiple reference extraction
runs re-use any objects queried in previous runs.

Update New Snippet buttons.

## What does this MR do?

No longer shows New Snippet button to users who aren't able to create a new snippet in the given context.

Also removes the plus icon from the New Snippet buttons, as they're no longer used in other creation buttons.

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

Make sure the snippets pages don't break or show the buttons to users who shouldn't have access to them.

## Why was this MR needed?

Users that weren't logged in would click the New Snippet button and get a 404 error. You would also get 404 errors from the New Snippet button on project snippets for projects you weren't able to create snippets for.

## What are the relevant issue numbers?

Fixes #14595.

## Screenshots (if relevant)

Before:

![before1](/uploads/2c222cd981332d30772054cefadafa28/before1.png)

![before2](/uploads/2734f8a84ae293b08dd982f2ed7da028/before2.png)

After:

![after1](/uploads/c84aa9aec17056095271b0f24c6e9b5b/after1.png)

![after2](/uploads/70fe37ad7be5054bf20439ca0a1f5ccc/after2.png)

![after3](/uploads/afcd435c211482e9df25cb8971f1e65e/after3.png)

![after4](/uploads/9eab87440aae4991b508373ff36e3c7a/after4.png)

![after5](/uploads/f5ec167cb3e1115d3b3a43bd5231bc60/after5.png)

![after6](/uploads/c774cbb1f9babe3382ff69af7060b9c5/after6.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
  - [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 !4998

No longer shows New Snippet button to users who aren't able to create a new snippet in the given context.

Also removes the plus icon from the New Snippet buttons, as they're no longer used in other creation buttons.

Fixes #14595.

Split Cropper.js from the main JavaScript manifest.

## What does this MR do?

Splits Cropper.js from the main JavaScript file.

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

That the avatar uploader works. (It did in my testing)

## Why was this MR needed?

Smaller JS payload.

## What are the relevant issue numbers?

#14372 

## Does this MR meet the acceptance criteria?

- Tests
  - [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 !4978

Add min attribute to projects_limit field on user's form

This PR adds `min=0` attribute to `:projects_limit` field on user's form in the admin panel. It improves UX disallowing user to enter negative values in this field.

![](http://take.ms/70V8W)

See merge request !3622

Fix gemfile

1. replace `"` to `'` in Gemfile.

2. change `require: nil` to `require: false`.
`require: nil` and `require: false` get same result, but i think we shouldn't write it differently in other places.

3. set version for gems.
better gem's version control for prevent dependency errors.

See merge request !5078

Enable Style/IdenticalConditionalBranches Rubocop cop

## What does this MR do?

This MR enables Rubocop cop that checks for identical lines at the end of each branch of a conditional statement.

Examples:

```ruby
@bad
if condition
  do_x
  do_z
else
  do_y
  do_z
end

@good
if condition
  do_x
else
  do_y
end
do_z
```

## What are the relevant issue numbers?

#17478

See merge request !5011

Avoid calculation of closes_issues.

## What does this MR do?

Avoid unneeded calls to MR closes issues

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

I'm not sure if calling this method from a view is a good practice, but I cannot see another simple way of avoiding this problem. In case we want to avoid this in the controller we need to specify the action, format and status of the merge request, because in that case we know that the `_open` partial will render. We could add some lazy evaluation but it not a thing I see in use along the app but feedback is welcome

## What are the relevant issue numbers?

#14202 , #19490

## 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 !5140

Fix broken migration in MySQL

`keys` is a reserved name in MySQL, so if this migration actually attempted to remove any duplicate keys it would fail.

Closes #19344

See merge request !5005

See !4096.
Signed-off-by: Rémy Coutable <remy@rymai.me>

Fix documentation for Github integration authorization callback url.

There are two callbacks that could be used with Github integration:

  * /import/github/callback (used by project import)
  * /users/auth/github/callback (used by OmniAuth)

Github's documentation suggests that authorization callback url should be
set to the longest common path.

https://developer.github.com/v3/oauth/#redirect-urls

Configuring according to the previous documentation resulted in a
redirect_uri_mismatch error from Github when logging in via OmniAuth.

See merge request !4111

Fix CHANGELOG typo: by_pass -> bypass



See merge request !5048

Fix comment for project argument in commit_range.rb

## What does this MR do?
It fixes the documentation for commit_range project argument

## 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)

See merge request !4805

Fix: Infinity Bug in Commit Statistics

## What does this MR do?

It fixes a logic bug in the commits statistics: The code assumed that the amount of days involved in a commit range is equal to the difference between the first and last date. This is not true, though, as (from a human standpoint), a commit yesterday and a commit today involve two days, not one. Similarly, a fresh project with only commits made today already 'used' one day.

Since the number of involved days used to be zero for new projects, the result for commits per day quite often amounted to `Infinity`…

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

The test file. I hope it is up to the standards of GitLab.

## Why was this MR needed?

The bug occurres especially for new users with their first project while exploring GitLab.

## What are the relevant issue numbers?

This bug was reported as #1548.

## Screenshots (if relevant)

See merge request !4231

Fixed Typo in README.md

## What does this MR do?
Found a Typo in the README.md file.  before_script should be with ":"  Script didn't work for me without ":"

## Why was this MR needed?
Missing ":" can be irritating for new users.

See merge request !4419

Api shared projects

## What does this MR do?

Exposes the shared projects in the group endpoint

## What are the relevant issue numbers?

Builds upon !5148 and closes #18780

## 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 !5150

Memoize MR merged/closed events retrieval

## What does this MR do?

Memoize a database call that is execute 3 consecutive times 

## Why was this MR needed?

To speed up MR pages

## What are the relevant issue numbers?

#14202 , #19490

## Screenshots (if relevant)

The query is fast most of the times, but we can avoid the 3 call counts to the database

![Screen_Shot_2016-07-08_at_12.49.48](/uploads/ab0f6d843be30754a06e0f05bdf2102d/Screen_Shot_2016-07-08_at_12.49.48.png)

## 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~~
  - [ ] 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 !5151

Fix unarchive mistake in projects API documentation 

import_url migration performance improvements

 Nullifying empty import_urls upfront so the number of projects with import_url not NULL decreases to 1/5.

 Also, now processing batches in blocks of 1000, with a threaded process - a bit experimental.

See merge request !5149

 Nullifying empty import_urls upfront so the number of projects with import_url not NULL decreases to 1/5.

 Also, now processing batches in blocks of 1000, with a threaded process - a bit experimental.