Move part of admin area navigation from tabs into settings dropdown

Partly fix https://gitlab.com/gitlab-org/gitlab-ce/issues/18799 

See merge request !4796

Avoid autoload issue such as 'Mail::Parsers::AddressStruct'

This is mostly a shot in the dark but at least it shouldn't break anything.

Fixes #18810.

See merge request !4793

Remove Duplicated keys adding UNIQUE index to fingerprint

See merge request !4787

Fixed a couple of errors on import/export spotted in production

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/18828 and https://gitlab.com/gitlab-org/gitlab-ce/issues/18829

A couple of tiny bugs spotted after deploying in prod

See merge request !4782

Fix RangeError exceptions when referring to issues or merge requests outside of max database values

When using #XYZ in Markdown text, if XYZ exceeds the maximum value of a signed 32-bit integer, we get an exception when the Markdown render attempts to run `where(iids: XYZ)`. Introduce a method that will throw out out-of-bounds values.
    
Closes #18777

See merge request !4777

Grammar tweaks

## What does this MR do?

* Updates grammar in recent CI documentation.

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

## Why was this MR needed?

Because grammar.

## What are the relevant issue numbers?

Needed because of !4200 and !4201.

## Screenshots (if relevant)


See merge request !4772

Add merge request data to the progress information on Milestones pages.

## What does this MR do?

Adds data about merge requests to the Milestone show view. It previously only showed something like `3 issues: 2 open and 1 closed 20% complete`, now it shows `3 issues: 2 open and 1 closed 2 merge requests: 2 open and 0 merged 20% complete`.

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

I don't think so.

## Why was this MR needed?

The milestone progress % didn't accurately reflect the open/merged MRs.

## What are the relevant issue numbers?

Fixes #13980

## Screenshots (if relevant)

Before:

![Screen_Shot_2016-06-16_at_2.12.57_PM](/uploads/99a044ea918b23fe93cef3305c21086e/Screen_Shot_2016-06-16_at_2.12.57_PM.png)

After:

![Screen_Shot_2016-06-16_at_2.12.38_PM](/uploads/be17e723b9c9bbe33099d1f0e94192d0/Screen_Shot_2016-06-16_at_2.12.38_PM.png)

## Does this MR meet the acceptance criteria?

- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- [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)

cc: @jschatz1

See merge request !4719

New Project page improvements for mobile

## What does this MR do?

Redesigns the "Project path" fields on the New Project page.

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

Not that I know of, nothing I changed should break any other pages.

## Why was this MR needed?

The new project page was unusable on mobile because the project name text field didn't have enough space.

## What are the relevant issue numbers?

Fixes #18599.

## Screenshots (if relevant)

Before:

![Screen_Shot_2016-06-15_at_12.38.58_PM](/uploads/046a824b283e24266cabc9ea3dfb169c/Screen_Shot_2016-06-15_at_12.38.58_PM.png)

After:

![Screen_Shot_2016-06-15_at_12.37.19_PM](/uploads/6d01310192965b413bfedd9c8d2129f7/Screen_Shot_2016-06-15_at_12.37.19_PM.png)

![Screen_Shot_2016-06-15_at_12.37.28_PM](/uploads/3944a0f0ab04373ec92f7cafe90872df/Screen_Shot_2016-06-15_at_12.37.28_PM.png)

## Does this MR meet the acceptance criteria?

- [ ] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- [ ] Tests
  - [x] 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)
- [ ] 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)

cc: @jschatz1 @dzaporozhets 

See merge request !4687

Limit push email diff size

Restrict the size of diffs in push emails to 30 lines / 150 KB (whichever is smaller),
following https://gitlab.com/gitlab-org/gitlab_git/merge_requests/85.

Emails on push can get very large if they contain a lot of files that sneak under the single-file limit.

https://gitlab.com/gitlab-org/gitlab-ee/issues/490

See merge request !4566

Fix margin & padding on activity btn

## What does this MR do?
Fixes alignment of activity btn

## What are the relevant issue numbers?
Closes #18762 

## Screenshots (if relevant)
![Screen_Shot_2016-06-17_at_9.29.06_AM](/uploads/4ab9fb33d450dda72811a5ce2570b8c7/Screen_Shot_2016-06-17_at_9.29.06_AM.png)


See merge request !4750

Move admin->runners tab as subnav of overview tab

cc @annabeldunstone 

See merge request !4716

Fixed alignment of buttons in note forms

## What does this MR do?

Due to a CSS change on some buttons, the alignment of the save button on the note form went off. Also, it made no sense to have `.btn-grouped` as the button wasn't in a group.

## Screenshots (if relevant)

![Screen_Shot_2016-06-17_at_11.43.33](/uploads/5d9037a48ff6179fc906bdf0c6d5ff47/Screen_Shot_2016-06-17_at_11.43.33.png)

![Screen_Shot_2016-06-17_at_11.43.43](/uploads/8b130a25e8f73e79578d38f5f7aff4fb/Screen_Shot_2016-06-17_at_11.43.43.png)


See merge request !4740

Fixed tooltip placement on edit tags button

## What does this MR do?

Moves the placement of the tooltip to the body so not to affect the movement of the button.

## Screenshots (if relevant)

Old:

![tooltip-old](/uploads/9ecb9bb919578881994698cd8b1d1826/tooltip-old.gif)

New:

![tooltip-new](/uploads/66f90cf95c2ee4001bfa3c65b9de8c05/tooltip-new.gif)


See merge request !4737

Fixed size of buttons in branches list

## What does this MR do?

The buttons on the branch list were using `btn-xs` this MR removes that so the buttons are a normal size to match https://gitlab.com/gitlab-org/gitlab-ce/tags

## What are the relevant issue numbers?

#18677 

## Screenshots (if relevant)

![Screen_Shot_2016-06-17_at_10.38.31](/uploads/19fc173e3f549a84bb14517613403792/Screen_Shot_2016-06-17_at_10.38.31.png)

See merge request !4735

Aligns create merge request button vertically

## What does this MR do?

Based on https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/4644#note_12507178 I have vertically aligned the button correctly.

## Screenshots (if relevant)

Here is my awesome screenshot to show it is centered vertically 

![Screen_Shot_2016-06-17_at_10.17.19](/uploads/e7bf5bcc5b254ed4db376c16460d79a5/Screen_Shot_2016-06-17_at_10.17.19.png)

See merge request !4733

Ci scala example

## What does this MR do?

Add a scala CI example.

## Why was this MR needed?

Supersedes https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/2984

See merge request !4774

Hide tooltip manually

## What does this MR do?
Fixes an issue with tooltips not dissapearing  on Firefox after toggling label priority

## What are the relevant issue numbers?
Closes #18707

## Screenshots (if relevant)

**Test on Firefox**

![label-firefox](/uploads/09ed05f81b9861d666e5d9ad805fb501/label-firefox.gif)
## 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
  - [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 !4715

# Conflicts:
#	app/controllers/projects/todos_controller.rb

Ensure that group owner cannot request access to a project of their group

## What does this MR do?

It fixes two things:

- 91ad995d69e1a0f8991fd896f1d9febc109273fe Ensure that group owner cannot request access to a project of their group
- ec3ff061148d556757e7cd486cdc6083d77acf34 Ensure group/project owners can see their members' access_level (see the commit message for details)

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

Not really, these are pretty simple fixes.

## Why was this MR needed?

Because there was an issue created!

## What are the relevant issue numbers?

Fixes #18717.

## Does this MR meet the acceptance criteria?

- [x] CHANGELOG is not needed since the bug is only present in a 8.9 RC
- [x] 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 !4729

Avoid that GitHub import fails when retrieving Webhooks for non GitHub admins

Closes #18729 

See merge request !4723

API endpoints for award emoji

Closes #10884 

See merge request !4575

Implement custom notification level options

![Screen_Shot_2016-06-17_at_15.31.43](/uploads/3fc47d2f461b3e8b67bb8acaa304cf99/Screen_Shot_2016-06-17_at_15.31.43.png)

![Screenshot_from_2016-06-15_10-52-27](/uploads/88dbdd21d97e80ee772fe08fa0c9b393/Screenshot_from_2016-06-15_10-52-27.png)

part of #12758 

See merge request !4389

Fixed issue with assignee dropdown not selecting correctly

## What does this MR do?

Fixes an issue with assignee dropdown not selecting correctly.

See merge request !4762

Do not check repos without push events

Reduce false positives from automatic repository checks by skipping
projects without push events.

See merge request !4684

Ensure Todos counters doesn't count Todos for projects pending delete

Use `TodosFinder` instead of `current_user.todos` to filter projects
pending delete on Todos counters helpers.

Counters should not reflect the number of Todos displayed on the tabs.

Fixes #18633

See merge request !4663

Disable the unlink feature for SAML connected accounts (social login).

This disables the ability to manually unlink your SAML account, if you have one connected. In certain scenarios, the only allowed login mechanism can be SAML, and if you unlink your account you will be locked out of the system (configuration dependent).

Fixes #18613

See merge request !4662

Cache todo counters (pending/done)

See merge request !4438

Fix a 'wrong number of arguments' error

## What does this MR do?

Fixes #18745.

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

No.

## Why was this MR needed?

To fix #18745.

## What are the relevant issue numbers?

Fixes #18745.

## Does this MR meet the acceptance criteria?

- [ ] Tests
  - [ ] 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 !4757

Track method call times/counts as a single metric

This changes method call tracking so only a single metric is emitted regardless of the number of calls. This allows us to more accurately measure the total execution time of a method as well as the number of times a method is called. See 851e3ff7578973c2206628424eac3b951a3c656d for more details.

Method call tracking tracked calls individually meaning the end statistics may not always be accurate enough to get a good understanding of where time is spent.

See merge request !4754

Fix error when editing an issuable with a task list

Closes #18712

See merge request !4751

Filter out sensitive parameters of metrics data

See merge request !4748

Fixed styling of commit box in new MR

## What does this MR do?

Fixes an issue that caused the new merge request commit box to go all funny styled.

## What are the relevant issue numbers?

#18781 

## Screenshots (if relevant)

![Screen_Shot_2016-06-17_at_14.08.44](/uploads/b1e34b0c6bf67adc1be8748306e20b06/Screen_Shot_2016-06-17_at_14.08.44.png)

See merge request !4747

Fix error when CI job variables key used but not specified

## What does this MR do?

This MR fixes a an error when CI job variables specified, but not defined:

```yaml
image: ruby:2.2

test:
  variables:
  script:
     - rspec
```

## What are the relevant issue numbers?

Closes #18764  
Follow up discussion in: #18775 

## Does this MR meet the acceptance criteria?

- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- [x] 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] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

See merge request !4745

Properly support application/json in Container Registry

## What does this MR do?
When requesting tags a `application/json` is used by `docker/distribution`.

## Why was this MR needed?
Fixes regression introduced by https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/4669

## What are the relevant issue numbers?
Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/18736


See merge request !4742

Make sure that artifacts_file is nullified after removing artifacts

## What does this MR do?
Fixes a problem that `ExpireBuildArtifactsWorker` is executed for all previously removed artifacts.

## Why was this MR needed?
Currently the `Ci::Build::erase_artifacts!` doesn't ensure that data are saved to database.
The bang at end of this method lets you believe that it should do so.
This adds a missing `save` to this method.

## What are the relevant issue numbers?
None, yet.

## CHANGELOG
Since this is regression in feature introduce in RC4 no CHANGELOG entry is needed.

cc @grzesiek 


See merge request !4741

Customize all Devise mails

Continuing from https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/3354

See merge request !4297

Allow creating Personal Access Tokens through the website

Related to #2979 

- Allow a user to create personal access tokens, and use them to authenticate
- Refactor `API::Helpers` into `API::Helpers::Core` and `API::Helpers::Authentication`

# Tasks

- [ ]  #2979 (!3749)  - Personal Access Tokens
    - [x]  Basic Implementation
        - [x]  Add UI to add "Personal Access Tokens"
        - [x]  Reload `lib/api` on every request
        - [x]  Respect these tokens for API requests
        - [x]  Just a param or a header too?
        - [x]  Allow revoking tokens
        - [x]  Expire tokens
        - [x]  Left bar should have a "PAT" icon
        - [x]  Scopes?
        - [x]  Copy to Clipboard
        - [x]  Show active/inactive tokens separately
            - [x]  No need to check for expired/revoked in the appropriate places
        - [x]  Why does regular ApplicationController check for private token?
        - [x]  Support non-API requests
        - [x]  Revert (or work on) `lib/api` eager loading
    - [x]  Create MR
    - [x]  Refactoring
    - [x]  Fix tests
    - [x]  Write more tests
    - [x]  Add screenshots to MR
    - [x]  Add description of query performance to MR
    - [x]  Limit the number of queries in the `personal_access_tokens` page
    - [x]  Wait for CI to pass
    - [x]  Fix merge issues in schema.rb
    - [x]  Assign MR to endboss
    - [x]  Wait for feedback
    - [x]  Fix feedback
        - [x]  Wait for CI to pass
    - [x]  Assign to @rspeicher
    - [x]  Fix @rspeicher's comments
    - [x]  Wait for CI to pass
    - [x]  Assign back to @rspeicher
    - [x]  Write documentation and ping @axil
    - [x]  Wait for Axil to respond
    - [x]  Assign to endboss
    - [x]  Address Douwe's feedback
        - [x]  Use the `private_token` or `authentication_token` param instead of `personal_access_token`
        - [x]  Ditto for the header
    - [x]  Assign to endboss
    - [x]  Make sure CI is green
    - [x]  Address Douwe's feedback
        - [x]  Don't go through the `authenticate_user_from_private_token!` method, if a private token is supplied (or combine them)
        - [x]  In `authenticate_user_from_personal_access_token!` don't hit DB if `token_string` is `nil`
        - [x]  Use `current_user.personal_access_tokens.build` in the controller
        - [x]  Remove the "We aren't using `personal_access_token` as the root param" comment
        - [x]  `No need for = "...", we can just have the Inactive ... #{...} on the next line` in the view
        - [x]  Render dates in a (more) human format
        - [x]  CSS issue with table
        - [x]  Don't show the tokens in the UI indefinitely
        - [x]  How to implement scopes? Add-on to current impl? Doorkeeper?
    - [x]  Wait for @DouweM's comments about scopes
    - [x]  Address @DouweM's second review 
        - [x]  Try not using `native['innerHTML']`
        - [x]  use contexts for all "when ..."
        - [x]  Ensure consistency (styling) with other pages for "You don't have any tokens" message
        - [x]  "Actions" table column doesn't need a label
        - [x]  %td can be moved outside of the if/else statement
        - [x]  The header title should be "Profile Settings"
        - [x]  Can this be a `before_create`, so we don't need to use `generate`?
        - [x]  If it couldn't be revoked, will we show an error?
        - [x]  If it couldn't be saved, will we show an error?
    - [x]  Merge master
    - [x]  Update CHANGELOG entry
    - [x]  Add tests for form errors?
    - [x]  Post screenshots
    - [x]  Tag @jschatz1 for review
    - [x]  Wait for [build](https://gitlab.com/gitlab-org/gitlab-ce/commit/0dff6fd/builds) to pass
    - [x]  Respond to @jschatz1's comments
        - [x]  Hardcoded colors should be variables
        - [x]  Should not be allowed to chose a date in the past
        - [x]  Use the same table as in the Applications tab
        - [x]  button should say "Create Personal Access Token"
        - [x]  Float the revoke to the right on the `a`
        - [x]  Change revocation message. "Are you sure you want to revoke this certificate? This action cannot be undone."
        - [x]  Date stays selected and looks selected even though date is set as "never".
        - [x]  ~~hover on the calendar button shifts~~ (not caused by this MR - happens on `milestones#new` as well)
        - [x]  Don't use the panel for the created token
            - [x]  Use a normal flash for "Your new personal access token has been created"
            - [x]  Show the input (with the token) below it full width.
            - [x]  Put the "Make sure you save it - you won't be able to access it again." message near the input
        - [x]  Have the input highlight all on single click
    - [x]  Update screenshots
    - [x]  Merge master in + conflicts
    - [x]  Assign to @jschatz1 again
    - [x]  Respond to @jschatz1's comments
        - [x]  No button for clipboard, only link
        - [x]  text-danger
        - [x]  highlight fade on that area where the token was created
    - [x]  Make sure [build](https://gitlab.com/gitlab-org/gitlab-ce/commit/d754d99179f1ffe846fcc1d8e858163b39efc5dc/builds) is green
    - [x]  Assign to @jschatz1
    - [x]  Wait for [build](https://gitlab.com/gitlab-org/gitlab-ce/commit/faa0e3f7580bc38d4d12916b4589c64d6c2678a7/builds) to pass
    - [x]  Respond to @DouweM's feedback
        - [x]  move the redirect_to out of the if/else
        - [x]  certificate -> token
        - [x]  datepicker back to text field
        - [x]  combine the get_user_from_private_token and get_user_from_personal_access_token methods in ApplicationController
        - [x]  combine the get_user_from_private_token and get_user_from_personal_access_token methods in `lib/api/helpers`
        - [x]  don't need the new constants
    - [x]  Wait for [build](https://gitlab.com/gitlab-org/gitlab-ce/commit/9d7cda3ddce52baad9618466a5d00319b333be57/builds) to pass
    - [ ]  Wait for merge

# Screenshots
![Screen_Shot_2016-06-16_at_8.30.33_AM](/uploads/30a168964b7c5e0eb322705747829fb6/Screen_Shot_2016-06-16_at_8.30.33_AM.png)
![Screen_Shot_2016-06-16_at_8.30.44_AM](/uploads/7a8202885df6120071bbe81b215aaead/Screen_Shot_2016-06-16_at_8.30.44_AM.png)
![Screen_Shot_2016-06-16_at_8.31.02_AM](/uploads/6905c0848864e390138b771389c7a1b2/Screen_Shot_2016-06-16_at_8.31.02_AM.png)
![Screen_Shot_2016-06-16_at_8.31.29_AM](/uploads/0bc92369fb2f9bc335773f6abec421c3/Screen_Shot_2016-06-16_at_8.31.29_AM.png)

See merge request !3749

Export project functionality

This is a MR for the export functionality of https://gitlab.com/gitlab-org/gitlab-ce/issues/3050, which adds the ability to export single projects.

- [x] members
- DB data
  - [x] issues
  - [x] issue comments
  - [x] merge requests
  - [x] merge request diff
  - [x] merge request comments
  - [x] labels
  - [x] milestones
  - [x] snippets
  - [x] releases
  - [x] events
  - [x] commit statuses
  - [x] CI builds
- File system data
  - [x] Git repository
  - [x] wiki
  - [x] uploads
  - [ ] ~~CI build traces~~
  - [ ] ~~CI build artifacts~~
  - [ ] ~~LFS objects~~
- DB configuration
  - [x] services
  - [x] web hooks
  - [x] protected branches
  - [x] deploy keys
  - [x] CI variables
  - [x] CI triggers

See merge request !3114

Fix clipboard buttons on "Check out branch" modal.

Closes #18794 

See merge request !4760