Grapify the group API

## What are the relevant issue numbers?

Related to #22928

See merge request !7359

Grapify the merge request API

Grapfiy the merge request API. I removed the test for checking if the source branch can be changed since this is an unused parameter. IMHO the test does not make sense.

## What are the relevant issue numbers?

Related to #22928

See merge request !7358

Issue #4270: Recursive option for files through API

## What does this MR do?
- Adds recursive param to tree API request. With this param we can get all repository paths in a single request. 
- Related [old github pull request](https://github.com/gitlabhq/gitlabhq/pull/9311)

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

## Why was this MR needed?
Requested in #4270 
## Screenshots (if relevant)

## 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)

## What are the relevant issue numbers?
Requested in #4270

See merge request !6088

Add button to delete all merged branches

## What does this MR do?

It adds a button to the branches page that the user can use to delete all the branches that are already merged. This can be used to clean up all the branches that were forgotten to delete while merging MRs.

**Note**  
~~This MR is WIP until MR !6408 is merged.~~

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

The UX of the actual "Delete merged branches" button.

## Why was this MR needed?

Fixes #21076

## Screenshots
![Branches page without "Delete all merged" button](/uploads/3a2936a83c3547a0fce92a74af880a2d/Screen_Shot_2016-10-17_at_20.06.30.png)

Before:
![Screen_Shot_2016-10-17_at_20.07.11](/uploads/55efcebf4e0a45dbfc70ba4a11ca152c/Screen_Shot_2016-10-17_at_20.07.11.png)


After:

## 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 [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [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)

## What are the relevant issue numbers?

Closes #21076

See merge request !6449

Fix Error 500 when creating a merge request that contains an image that was deleted and added

_Originally opened at !4816 by @stanhu._

- - -

## What does this MR do?

This MR fixes an Error 500 when creating a merge request that contains an image that was deleted and added. Before, when displaying the before and after image, the code would always retrieve the image from the parent commit. However, in a diff, this could cause two different problems:
The "before" image may not actually be the image you want to compare against (regression of #14327)
It may appear as though a file was modified when it was really just added during the diff

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

There may be a more elegant to fix this bug.

## What are the relevant issue numbers?

Closes #3893, gitlab-org/gitlab-ee#678

See merge request !7457

Omniauth auto link LDAP user falls back to find by DN when user cannot be found by uid

Unfortunately, SAML IDs can be an LDAP UID, DN, or something else entirely. UID and DN are most common, though. This adds a fallback scenario so we first try to find a matching LDAP user by UID, then by DN. This will fix a problem for the customer in https://gitlab.zendesk.com/agent/tickets/43298

See merge request !7002

Move the `objects` method to `LfsHelper` so that it is also available to `LfsStorageController`

## What does this MR do?

Move the `objects` method to `LfsHelper` so that it is also available to `LfsStorageController`

It is needed for the `lfs_check_access!` callback when the repository size limit is enabled (EE only).

cc @stanhu @ahanselka 

## Why was this MR needed?

Errors shown here: gitlab-org/gitlab-ce#24392

Discovered thanks to gitlab-com/infrastructure#302

## What are the relevant issue numbers?

Fixes #24392 

Fixes gitlab-com/support-forum#1280

See merge request !7417

[ci skip]

clarify best way to install custom CA

See merge request !7434

Use `default_value_for` to handle null values in only_allow_merge_if_all_discussions_are_resolved

Small style improvement for !7427

See merge request !7460

[ci skip]

Issue #13823: random message when all Todos are Done

## What does this MR do?

Shows a random message every time the To Do list is empty: https://gitlab.com/gitlab-org/gitlab-ce/issues/13823

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

It's my first contribution to GitLab so I might need some help:

 - I'm loading a yaml file in the controller. I'm not sure where would be the best place to put it.
 - I'm also having the error below running the tests but it doesn't seem related to my changes. I think I might have some issue with my config. Could you double check if the tests pass for you?

/home/pep/.rvm/gems/ruby-2.3.1/gems/actionpack-4.2.7.1/lib/action_dispatch/middleware/debug_exceptions.rb:21:in `call': No route matches [GET] "/autocomplete/users/sjobs@apple.com.json" (ActionController::RoutingError)

## Why was this MR needed?

https://gitlab.com/gitlab-org/gitlab-ce/issues/13823

## Screenshots (if relevant)

## 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
  - [x] Added for this feature/bug
  - [ ] All builds are passing
- [x] Conform by the [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [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 it does - rebase it please)
- [x] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

## What are the relevant issue numbers?

https://gitlab.com/gitlab-org/gitlab-ce/issues/13823

See merge request !6818

21778 Correct css styles for pinned navigation

## What does this MR do?
Fixes css for header and comment notes when sidebar is pinned

## Screenshots (if relevant)
Before:
![Screen_Shot_2016-11-08_at_11.02.55_AM](/uploads/ae7bb1f477b2ffbd4d4e0364f2770816/Screen_Shot_2016-11-08_at_11.02.55_AM.png)
After:
![Screen_Shot_2016-11-08_at_11.02.34_AM](/uploads/cf0b9f9f175aa5c6c7e79640b76b1040/Screen_Shot_2016-11-08_at_11.02.34_AM.png)

Before:
![Screen_Shot_2016-11-08_at_11.03.21_AM](/uploads/f48ea742ee6dbb86874e47dd27eddadd/Screen_Shot_2016-11-08_at_11.03.21_AM.png)
After:
![Screen_Shot_2016-11-08_at_11.02.19_AM](/uploads/312b27ba07e04ceb96f8ed9d6f167bee/Screen_Shot_2016-11-08_at_11.02.19_AM.png)
## Does this MR meet the acceptance criteria?

- [ ] [Changelog entry](https://docs.gitlab.com/ce/development/changelog.html) 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 [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [ ] 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 it does - rebase it please)
- [ ] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

## What are the relevant issue numbers?
Closes #21778 

cc @mikegreiling

See merge request !7362

Give search-input correct padding-right value

## What does this MR do?
This fixes how `padding-right: 20px` was being applied to the style rule of `.search-input`, preventing text in that form from clipping through `.search-icon`

## Are there points in the code the reviewer needs to double check?
If there are any cases where `.search .search-input` is used in a search form where there is no right-side icon (I could not find such occurrence myself).

## Why was this MR needed?
Some text in long search queries were being hidden by the close icon being used in the search form. This makes it a bit more presentable. ;)

## Screenshots (if relevant)
__Before__
![before](/uploads/2757a6264a1d2053af7212f72df7c3f9/before.png)

__After__
![after](/uploads/322fbfa08594f0f33d10a3226c82326d/after.png)

See merge request !7407

Use declared_params helper in API

Related to https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/7406#note_18275781

See merge request !7455

Fixed issue boards when not logged in

## What does this MR do?

This managed to get through because their wasn't actually any tests for loading the lists when a user is not logged in. This fixes that by adding a test & also fixing the template not correctly compiling under VueJS v2.

See merge request !7452

Project download buttons always show

## What does this MR do?
Removes `hidden-xs hidden-sm` classes from `download-button` so it doesn’t hide itself individually from the rest of the `project-repo-buttons` block

## Why was this MR needed?
Fixes #23960. Not sure why this element had these classes in the first place, but at the very least we shouldn’t be hiding the Download button at the `hidden-sm` threshold since that’s still fairly large viewport and users with viewports of that size likely still want to download source code.

## Screenshots (if relevant)
Screenshots taken at ~830px width
__Before__
![before](/uploads/21955cf7a12f6eb9cfef96bbb27b7110/before.png)

__After__
![after](/uploads/c082884f225184d56a920adbc0a0a732/after.png)

## What are the relevant issue numbers?
#23960

See merge request !7405

Steps to reproduce:

1. Start with a repo with an image
2. Add a commit to delete the image
3. Add another commit to replace the image with another image

In a diff comparison, we really just compare about what the image was before the diff, not
the direct parent of the last commit. This MR fixes that.

Closes #3893, gitlab-org/gitlab-ee#678
Signed-off-by: Rémy Coutable <remy@rymai.me>

Use to_h to convert params to a hash

See merge request !7406

Fix typos and grammar errors

See the general Documentation guidelines http://docs.gitlab.com/ce/development/doc_styleguide.html

See merge request !7451

Improve naming convention in ci configuration module

## What does this MR do?

This MR improves the naming convention in CI configuration module to reflect the domain design better.

## What are the relevant issue numbers?

Related to #15060

See merge request !7448

Grapify subscription API

## What are the relevant issue numbers?

Related to #22928

See merge request !7380

Fix error links in help index page when access it with url `http://gitlab.example.com/help/` which have an extra slash 

Fixes #24349

See merge request !7396

Only turn on Sidekiq throttling if column exists

If the database has not been migrated properly, the initializer for Sidekiq will fail to start and cause the whole Rails server to crash. This change checks the existence for the column and allows Rails to start even if the setting has not been added as a database column.

Closes #24452

See merge request !7446

[ci skip]

Centralized all LDAP config logic in to `Gitlab::LDAP::Config`. We had varying configuration for devise/omniauth and other things. For example, `user_filter` was never taken in to account for devise/omniauth so a user object would always be created, even if the user did not match the user_filter. 

Fixes gitlab-org/gitlab-ce#21195, https://gitlab.com/gitlab-org/gitlab-ce/issues/15396 and gitlab-org/gitlab-ce#13296

See merge request !6606

Remove unneeded nil checks

See merge request !7437