Change default smpt port to 465 (default smtps port)

Add option to include the sender name in body of Notify email

_Originally opened at !2495 by @huacnlee._

- - -

Fixes #7824.

See merge request !2767

Add an option to supply root email through an environmental variable.

_Originally opened at !2499 by @3kami3._

---

Add an option to supply root email through an environmental variable.

See merge request !2751

Add a tooltip to the stuck warning build symbol

We want to give people an idea of what is wrong with their build, we do this by
adding a tooltip telling them where they can find more information about their
broken builds.

Fixes #10919

See merge request !2680

split gitlab-ci builds for ruby 2.1

Added breakdown of builds for Ruby 2.1 in .gitlab-ci.yml config file.

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/13252

See merge request !2746

Allow limited Markdown in Broadcast Messages

Closes #11853

See merge request !2695

Increase project import timeout from 4 minutes to 15 minutes

Many users were experiencing timeouts when we only allowed
4 minutes before a timeout. A 15 minute timeout is more
than reasonable and prevents us from having to add a
configuration for this.

Fixes gitlab-org/gitlab-ee#246

## Import screenshot

![Screen_Shot_2016-02-04_at_1.45.20_PM](/uploads/d9d71ec953afae31e6fbe54a8932b945/Screen_Shot_2016-02-04_at_1.45.20_PM.png)


See merge request !2717

do not rename .aToM but only .atom projects in migration

Sorry @DouweM forgot to add this.

See https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/2651/diffs#bc35672f73f4ee025132aee428f383acdf0f755e_0_51

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/3699

See merge request !2712

See merge request !2752

Improve CI builds API specs

This modifies a CI Runners Builds API, to improve performance, and add few missing examples.
Extracted from !2560 (cherry-picked + extended).

cc @ayufan 

See merge request !2698

Fix timeout issue for rake task gitlab:backup:create

This is a fix for a database timeout which can occur when the backup
create task is taking very long (1-2 hours).
It seems that ActiveRecord is loosing the connection after a hour
idleness and need to be reconnected before use.

See merge request !2757

Fix CurrentSettings autoload bug in development

_Originally opened at !2526 by @huacnlee._

- - -

In development env, when we changed any file hit Rails reload, it will failed with this message:

```
A copy of Gitlab::CurrentSettings has been removed from the module tree but is still active
```

See merge request !2753

Fix grammar in installation requirements.

Fixes #13274

See merge request !2759

Fixes #13274

Fixed init.d script not working on OS X

-s flag of su doesn't work correctly on OS X, logging in as the user
and not running the requested command. By moving the bash shell init
inside the su command we avoid the issue

Fixes Issue #3309 

See merge request !1728

suppress error in init-script while determining canonical path of gitlab_workhorse_dir

fixes #12693 
fixes #12954

See merge request !2697

-s flag of su doesn't work correctly on some systems, loging in the user
and not running the requested command. By moving the bash shell init
inside the su command we avoid the issue

This caches the output of the following methods:

* Repository#empty?
* Repository#has_visible_content?
* Repository#root_ref

The cache for Repository#has_visible_content? is flushed whenever a
commit is pushed to a new branch or an existing branch is removed.
The cache for Repository#root_ref is only flushed whenever a user
changes the default branch of a project. The cache for Repository#empty?
is never explicitly flushed as there's no need for it.

Error: A copy of Gitlab::CurrentSettings has been removed from the module tree but is still active

Remember user's inline/tabular diff view preference in a cookie

_Originally opened at !1677 by @kkm._

---

As per #3071, some users (we have a local EE installation) prefer 2-column view in diff. In this MR I add an implementation for this feature, using a cookie.

Fixes #3071.

See merge request !2723

Fixes #3903

Rearrange some sections in CONTRIBUTING.md

- Move 'Merge request description format' and
  'Contribution acceptance criteria' under 'Merge requests'
- Link to doc_styleguide where appropriate
- Provide markdown template for merge requests

See merge request !2748

[ci skip]

Add table of contents in CONTRIBUTING.md



See merge request !2745

We want to give people an idea of what is wrong with their build, we do this by
adding a tooltip telling them where they can find more information about their
broken builds.

Fixes #10919
Signed-off-by: Jeroen van Baarsen <jeroenvanbaarsen@gmail.com>

Clarify when JIRA service was backported to CE



See merge request !2744

[ci skip]

[ci skip]

Change logo image name in markdown documentation

Closes #13233

See merge request !2743

[ci skip]