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.

Added setting to set new users by default as external

## What does this MR do?
This implements the feature request #14508. It adds an option in the application settings to set new users by default as external.

## Are there points in the code the reviewer needs to double check?
Everything. Like I mentioned in the discussion of the issue my knowledge of Ruby basically doesn't exists. I tested it on my machine and it seems to work, but as I am very unexperienced in Ruby I highly recommend to  take a close look at the code.

## Why was this MR needed?
It was requested by @DouweM to work on the issue with the proposed changes by me.

## What are the relevant issue numbers?
This MR is for the issue #14508 that followed up after the implementation of #4009.

See merge request !4545

Link to the user's profile in the abuse reports

Link to the user's profile in the abuse reports and add a link to the
admin area view if the user viewing the profile is an admin

Fixes #9127

See merge request !5118

This reverts commit bf2a86b7.

Upgrade oauth2 from 1.0.0 to 1.2.0.

Changelog: https://github.com/intridea/oauth2/compare/v1.0.0...v1.2.0

Follow-up on !3434 since 1.2.0 doesn't limit the JWT version we can use.

Adds support for Rails 5. Working toward #14286.

See merge request !5041

Use scope rather than class method

## What does this MR do?

Use scope rather than class method

## Why was this MR needed?

I assume this would be useful and more clear.

See merge request !5133

Prefer ref rather than id because id is shadowing database id

## What does this MR do?

Just a local variable renaming.

## Why was this MR needed?

Prefer ref rather than id because id is shadowing database id.

See merge request !5134

Allow specifying protected branches using wildcards

Closes #18627 

# Tasks

- [ ]  #18627 !4665 Allow specifying protected branches using wildcards
    - [x]  Find existing usages of protected branches
        - Protecting branches
            - `ProtectedBranchesController` is used to mark a branch protected/unprotected
            - `API::Branches` can be used to mark a branch protected/unprotected
        - Enforcing branch protection
            - `Gitlab::GitAccess` has helpers (`can_push_to_branch?`, `check`) that are used to deny pushes if a branch is protected
            - Over SSH: `gitlab-shell` receives a push, and calls `/allowed` on the GitLab API, which calls `GitAccess.check`
            - Over HTTP: 
                - `gitlab-workhorse` receives the request, and forwards it to rails
                - Rails (in the `GitHttpController#git-recieve-pack`) runs basic checks (is the user logged in, not protected branch checks) and returns ok with `GL_ID` and `RepoPath`
                - `gitlab-workhorse` looks at the response, and calls the relevant `gitlab-shell` action from `git-http/handlePostRPC`
                - Rest of this flow is the same as the SSH flow above
    - [x]  Implementation
        - [x]  Backend
            - [x]  Change `project#protected_branch?` to look at wildcard protected branches
            - [x]  Change `project#developers_can_push_to_protected_branch?`
            - [x]  Change `project#open_branches`
            - [x]  Better error message when creating a disallowed branch from the Web UI
        - [x]  Frontend
            - [x]  Protected branches page should allow typing out a wildcard pattern
            - [x]  Add help text explaining the use of wildcards
            - [x]  Show matching branches for each protected branch
                - [x]  ~~On the index page~~
                - [x]  On a show page
                - [x]  Index?
            - [x]  Can't have the "last commit" column for wildcard protected branches
    - [x]  Fix / write tests
    - [x]  What happens if a hook is missing in dev?
    - [x]  Refactor
    - [x]  Test workflows
        - Create a branch matching a wildcard pattern
        - Push to a branch matching a wildcard pattern
        - Force push to a branch matching a wildcard pattern
        - Delete a branch matching a wildcard pattern
        - [x]  Test using Web UI
        - [x]  Test over SSH
        - [x]  Test over HTTP
        - [x]  Test as developer and master
    - [x]  Investigate performance
        - [x]  Test with a large number of protected branches / branches
        - [x]  Paginate list of protected branches
        - [x]  ~~Possibly rewrite `open_branches`~~
    - [x]  Add `iid`s to existing `ProtectedBranch`es
    - [x]  Add documentation
    - [x]  Add CHANGELOG entry
    - [x]  Add screenshots
    - [x]  Make sure [build](https://gitlab.com/gitlab-org/gitlab-ce/commit/2f753e3ed2ce681b4444944d521f4419e8ed37f7/builds) passes
    - [x]  Assign to endboss for review
    - [x]  Address @DouweM's comments
        - [x]  `protected_branch_params`
        - [x]  `exact_match` instead of `explicit_match`
        - [x]  When would self.name be blank?
        - [x]  Move `protected_branches.each` to a partial
        - [x]  Move `matching_branches.each` to a partial
        - [x]  If the branch is in @matching_branches, it's not been removed
        - [x]  move this regex to a method and memoize it
        - [x]  `commit_sha` directly for exact matches
        - [x]  Number of matches for wildcard matches, with a link
    - [x]  Wait for [build](https://gitlab.com/gitlab-org/gitlab-ce/commit/43f9ce0e88194b8f719bb1c1e656b7fc13278d56/builds) to pass
    - [x]  Respond to @DouweM's comments
        - [x]  Don't use iid
        - [x]  Controller should use `@project.protected_branches.new`
        - [x]  move the memoization to `def wildcard_regex`
        - [x]  render with `collection: @protected_branches`
    - [x]  Wait for [build](https://gitlab.com/gitlab-org/gitlab-ce/commit/f7beedf122fa0c7aa89e86181fe7499321fb10ca/builds) to pass
    - [x]  Wait for @DouweM's review
    - [x]  Wait for @jschatz1's review
    - [x]  Respond to @jschatz1's comments
        - [x]  Use the new dropdown style
        - [x]  description should be moved to the description section without the styling
        - [x]  Protect button should be disabled when no branch is selected
    - [x]  Update screenshots
    - [x]  Merge conflicts
    - [x]  Make sure [build](https://gitlab.com/gitlab-org/gitlab-ce/commit/20f3cfe8d5540eab64c2ba548043d600b28c61ba/builds) passes
    - [ ]  Revisit performance, possibly with staging/production data
        - [ ]  Get a dump of staging / run against staging live
            - [ ]  Get SSH access to staging
    - [ ]  Wait for review/merge






# Screenshots

## Creating wildcard protected branches

![1](/uploads/9446afccfdf6fa381e00c800dd2cc82e/1.png)
![2](/uploads/0b154503b297a818d3577488c575d845/2.png)
![3](/uploads/36217f79df9e41cc1550601f02627fe8/3.png)
![4](/uploads/041ca9bd529bcfa5373fca67e917cbcb/4.png)

### Using the `GLDropdown` component

![2016-06-30_14-16-15](/uploads/508afc2a5e2463c2954641409a560d88/2016-06-30_14-16-15.gif)

## Enforcing wildcard protected branches

### From the Web UI

![Screen_Shot_2016-06-20_at_1.21.18_PM](/uploads/8b5d4b1911e9152698a0488daf1880bc/Screen_Shot_2016-06-20_at_1.21.18_PM.png)

### Over SSH

![SSH](/uploads/7365989d7e4c406ef37b6ae5106442c9/SSH.gif)

### Over HTTPS

![HTTPS](/uploads/a7c0f56ae58efcffc75e6700fa2f4ac0/HTTPS.gif)

## Listing matching branches

![Screen_Shot_2016-06-20_at_1.33.44_PM](/uploads/d054113022f5d7ec64c0e57e501ac104/Screen_Shot_2016-06-20_at_1.33.44_PM.png)

See merge request !4665

This reverts commit 68155ee7, reversing
changes made to 7ebd011e.

Update time format of pipeline duration

Closes #18181

Part of #18920 

See merge request !5121

Added blank state to issues

## What does this MR do?

Adds new blank state to issues when no issues exist.

Part of #18519 

## Screenshots (if relevant)

![Screen_Shot_2016-06-24_at_16.37.12](/uploads/0c3f385615b29216ef1137bd6fac06af/Screen_Shot_2016-06-24_at_16.37.12.png)

See merge request !4908

New diff notes

Fixes #12732, #14731, #19375, #14783 

Builds on https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/4110

To do:
- [x] Get it mostly working
- [x] Validate position validity
- [x] Fix: Don’t link to `#`
- [x] Fix: Base ref can be `nil`, potentially, when the MR has an oprhan source branch => Yep, doesn’t work. We need to store a `start_id`
- [x] Optimize: Fewer duplicate `git diff` compares
- [x] Optimize: Pass paths to `PositionTracer#diff` for faster diffs
- [x] Refactor: Use `head_id` in `MergeRequest`/`MergeRequestDiff` instead of `source_sha`
- [x] Refactor: Convert existing array-based diff refs to the DiffRefs model
- [x] Tweak: Use `note_type` in `Autosave` key
- [x] Tweak: Remove `line_code: note.line_code` from `link_to_reply_discussion`
- [x] Update: `SentNotifications` and reply-by-email receiver
- [x] Update: MR diff notification email
- [x] Update: API (MR, Commit note creation and entity)
- [x] Update: GitHub importer
- [x] Address any other TODO comments
- [x] Fix: Suppress "edited 4 minutes ago"
- [x] Write tests
  - [x] `LineMapper`
  - [x] `PositionTracer`
  - [x] `Position`
  - [x] `DiffPositionUpdateService`
  - [x] `DiffNote`
  - [x] `MergeRequests::RefreshService` / `MergeRequest#update_diff_notes_positions`
- [x] Make sure commits with diff notes don't get cleaned up, since this would prevent the diff notes from being rendered (https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/5062)

Future improvements:
- Display unresolved comments on files outside the diff, if the comment was added when that file _was_ part of the diff
- Allow commenting on sections between hunks, when expanding the diff using `...`
  - (We'd need to generate line code based on Position if we have it, even if it falls outside bounds of diff)
- `diff_hunk` on diff note API entity
- Show diff hunk in notification email
- Resolved line notes would have a boolean, and be inactive through `notes.any? { !active? || resolved? }`
- Multi line notes would store a number of positions, and do the right thing (™) in grouping and then rendering if the first item is multiline? => true
- Image diff notes could store x,y,width,height instead of old_line,new_line for similar grouping. Does it need a reference to say if it's on old or new? These can't have line_codes, clearly. Rendering would be interesting.
- Show commit line comments in the MR diff
- Comment on specific selected words
- Comment on file header
- Unfold top of discussion diff note
- New diff notes API for commits and MRs

/cc @rspeicher

See merge request !4101

Exclude projects pending delete from notifications

Make `NotificationSetting.for_projects` exclude projects that are excluded by the default scope on `Project`. (At the moment, that's projects with `pending_delete: true`.)

See https://gitlab.com/gitlab-com/support-forum/issues/819

See merge request !5138

Improve UI consistency for admin area

Closes #3946

See merge request !4424

Remove icons from file edit tabs

We don't need this icons and it also inconsistent with current UI 

See merge request !5072

If the Sidekiq job fails for some reason, a project can be 'stuck'
pending deletion. The project can't be viewed, so it shouldn't be
available through the notification settings association as this will
throw an exception when we try to show the link.