When rendering the clone page, check user profile to decide default clone protocol. If the user has uploaded SSH-keys, use SSH; otherwise, use http(s). Close #3504.

Check GitLab Workhorse status in init.d script when reporting all components are up and running

Closes https://github.com/gitlabhq/gitlabhq/issues/9869

See merge request !1969

Fixed duplicated issue note email notifications.

Fixes #2560 



See issue for the details.

Without `uniq` modified tests were failing with:
```
     Failure/Error: notification.new_note(note)
       (Notify (class)).note_issue_email(21, 1)
           expected: 1 time with arguments: (21, 1)
           received: 2 times with arguments: (21, 1)
     # /home/bak1an/.rvm/gems/ruby-2.1.6@gitlab/gems/sidekiq-3.3.0/lib/sidekiq/extensions/action_mailer.rb:17:in `public_send'
     # /home/bak1an/.rvm/gems/ruby-2.1.6@gitlab/gems/sidekiq-3.3.0/lib/sidekiq/extensions/action_mailer.rb:17:in `perform'
     # /home/bak1an/.rvm/gems/ruby-2.1.6@gitlab/gems/sidekiq-3.3.0/lib/sidekiq/testing.rb:74:in `block in raw_push'
     # /home/bak1an/.rvm/gems/ruby-2.1.6@gitlab/gems/sidekiq-3.3.0/lib/sidekiq/testing.rb:69:in `each'
     # /home/bak1an/.rvm/gems/ruby-2.1.6@gitlab/gems/sidekiq-3.3.0/lib/sidekiq/testing.rb:69:in `raw_push'
     # /home/bak1an/.rvm/gems/ruby-2.1.6@gitlab/gems/sidekiq-3.3.0/lib/sidekiq/client.rb:68:in `push'
     # /home/bak1an/.rvm/gems/ruby-2.1.6@gitlab/gems/sidekiq-3.3.0/lib/sidekiq/worker.rb:85:in `client_push'
     # /home/bak1an/.rvm/gems/ruby-2.1.6@gitlab/gems/sidekiq-3.3.0/lib/sidekiq/extensions/generic_proxy.rb:19:in `method_missing'
     # ./app/services/notification_service.rb:144:in `block in new_note'
     # ./app/services/notification_service.rb:143:in `each'
     # ./app/services/notification_service.rb:143:in `new_note'
     # ./spec/services/notification_service_spec.rb:63:in `block (5 levels) in <top (required)>'
```

I have also added `once` to all `should_email` checks within `notification_service_spec.rb` since it's probably the correct behavior to notify users only once on the same event. Nothing else failed out of the box but we can keep these assertions for future.

See merge request !1925

Fixes #2560

Clarify Project Limit Reached

Recognize issue/MR/snippet/commit links as references.

Fixes #3744 and #3745

See merge request !1933

[ci skip]

Ensure "Remove Source Branch" button is not shown when branch is being deleted.

Given the merging of the Merge Request happens in the background, sometimes when the client JS code reloads the page the source branch is not still gone.

This fix appends a new query string parameter that is checked in the view before rendering the `Remove Source Branch` button.

Closes #3583

See merge request !1897

Fix application settings cache not expiring after changes

cache_key is an instance method that relies on updated_at. When changes
were made, the time-dependent key was being used instead of X.application_setting.last.

Closes #3609 


See merge request !1972

Make current user the first user in assignee dropdown in issues detail page

Closes #3679

See merge request !1913

Closes #3679

Closes https://github.com/gitlabhq/gitlabhq/issues/9869

cache_key is an instance method that relies on updated_at. When changes
were made, the time-dependent key was being used instead of X.application_setting.last.

Closes #3609

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

Add API endpoint to fetch merge request commits list

Fixes #3748 

See merge request !1984

Fix mailers queue

The `mailer` queue can be removed.

See merge request !1975

* add note to Events API
* add author section to Events API
* add noteable_id and noteable_type to Notes API
Signed-off-by: Dmitriy Zaporozhets <dmitriy.zaporozhets@gmail.com>

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

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

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

UI: Sidebar & header tweaks and fixes

Depends on !1953 

See the commits for more details, the messages mostly speak for themselves.

![Logo](https://gitlab.com/gitlab-org/gitlab-ce/uploads/ba088150165bb0a0aea1e894f3443f43/logo_tooltip.png)

![Sidebar](https://gitlab.com/gitlab-org/gitlab-ce/uploads/c1e8c09ac3bf489cdb9531eebea18c90/sidebar_tooltips.png)

Fixes #2928, #2071, https://dev.gitlab.org/gitlab/gitlabhq/issues/2575, and https://dev.gitlab.org/gitlab/gitlabhq/issues/2573

See merge request !1958

UI: Improve form consistency

Depends on !1953

See the commits for more details, the messages mostly speak for themselves.

# Highlights

## Tag form

Before:

![tag_before](/uploads/ee5ba6ef405749013f9e5717ebcf72f3/tag_before.png)

After:

![tag_after](/uploads/71bb543553190d91c03fd706cce35923/tag_after.png)


See merge request !1955

Fix background and padding of login and error pages

Was gray, is white again.

See merge request !1978

Correction of markdown in SSH docs

Correction of broken markdown in SSH docs

See merge request !1900

Don't show project fork event as imported

See merge request !1949

Add authorization to new branch/tag pages.

The create actions have authorization, the new actions didn't,
so no-one unauthorized could actually do anything, but it was wrong(TM).

See merge request !1979

Update .ruby-version to 2.1.7

Fixes #3835

See merge request !1980

fixes #3263 slashes are replaced with two underscores



See merge request !1981

Fixed invalid link on starred projects dashboard.

Fixes #3468

The MR fixes 'Project' links on a dashboard pages headers. See the issue for the details.

This MR does not include tests since the change is rather trivial and there are no (as far as I have seen) existing tests for checking links validity.

In case tests are required I would like to get some guidance on the implementation first. At least I would like to know what should be covered: changed links, all header links, all navigation?

See merge request !1926

UI: Use new style for wiki

Depends on !1953

See the commits for more details, the messages mostly speak for themselves.

# Highlights

## Wiki Page

Before:

![Screen_Shot_2015-12-02_at_17.48.45](/uploads/aa53f768b8760f2e15d765e06d5ff773/Screen_Shot_2015-12-02_at_17.48.45.png)

After:

![Screen_Shot_2015-12-02_at_17.48.16](/uploads/f8a376651aff9c8de82621578aaeb002/Screen_Shot_2015-12-02_at_17.48.16.png)

## Edit Wiki Page

Before:

![Screen_Shot_2015-12-02_at_17.48.59](/uploads/c9ffddaca3156046b99cba11bdb0ea4f/Screen_Shot_2015-12-02_at_17.48.59.png)

After:

![Screen_Shot_2015-12-02_at_17.48.26](/uploads/1aa62049f120c91436ed68fd7441c156/Screen_Shot_2015-12-02_at_17.48.26.png)

See merge request !1967

UI: New Project form tweaks

Depends on !1953 

See the commits for more details, the messages mostly speak for themselves.

Before:

![Screen_Shot_2015-12-02_at_17.43.23](/uploads/302e734f6796a85a9f4be9c2f494869d/Screen_Shot_2015-12-02_at_17.43.23.png)

After:

![Screen_Shot_2015-12-02_at_17.44.11](/uploads/411980e53a4f87cf0a04e5bcb7329f82/Screen_Shot_2015-12-02_at_17.44.11.png)


See merge request !1964

UI: Issuable filter tweaks

Depends on !1953

See the commits for more details, the messages mostly speak for themselves.

# Highlights

## Filter bar

Before:

![filter_before](/uploads/b061be7521c6d5babb77c7d12e77f65e/filter_before.png)

After:

![filter_after](/uploads/aadfbcd77caf1b49fde8ca6d781f1004/filter_after.png)

## Bulk edit bar

Before:

![bulk_before](/uploads/849c98224e1f335c65c0de5616bbcdae/bulk_before.png)

After:

![bulk_after](/uploads/185d29116663f9f663acab76d328096f/bulk_after.png)


See merge request !1963

Touch project when toggling stars to update cache

This is a fix for gitlab-org/gitlab-ce#3513.

When a star toggle event happens, we touch project to clear cache key.
This will trigger a new "updated_at" at the project model. If it's undesirable, please let me know and I will try to solve it in a different way.

See merge request !1970