Prevent stale data in LDAP group sync last owner check

Representing https://gitlab.com/gitlab-org/gitlab-ee/merge_requests/529

Fixes gitlab-org/gitlab-ce#17764

Turns out that switching to an AR association has resolved the issue. However, a merge problem from CE to EE caused the owners method to not be removed so it took precedence over the association. This removes that method and adds a test to ensure we don't have stale owner data in the future. 

See merge request !531

Avoid adding index if already exists

Closes #764

See merge request !539

This reverts commit bf2a86b7.

Improve UI consistency for admin area

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/3946

See merge request !537

CE-to-EE pre-RC2



See merge request !538

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

Fixed misplaced mirror button

The mirror repo button was misplaced on the tags page & made the content below look weird.

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/19191

![Screen_Shot_2016-07-07_at_11.35.35](/uploads/d7e87dfeb3491e53342e9e0a1a342f2f/Screen_Shot_2016-07-07_at_11.35.35.png)

See merge request !536

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

Add missing `storage` argument to some methods in `Gitlab::Shell`

The affected methods are EE only and were basically related to the sync
of local and remote mirrors.

Fixes: https://gitlab.com/gitlab-com/infrastructure/issues/155

Ref: https://gitlab.com/gitlab-com/support-forum/issues/816

See merge request !532

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

# Conflicts:
#	app/assets/stylesheets/pages/admin.scss
#	app/views/admin/users/index.html.haml

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.