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

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

Closes #18781

Use Git cached counters on project show page

See merge request !4711

Customize all Devise mails

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

See merge request !4297

[ci skip]

Remove JiraIssue model and replace references with ExternalIssue

This MR Removes unused JiraIssue class and replaces references with ExternalIssue

Closes #18203 

See merge request !4659

Add GFM autocomplete for labels

Closes #14637 

See merge request !4013

Fixed ordering in Project.find_with_namespace

This MR fixes the ordering of `Project.find_with_namespace` to ensure that it returns rows that match literally first.

Closes #18603

See merge request !4682

Use gitlab-git 10.2.0

Closes #18741

See merge request !4722

Reduce SQL query counts in IssueReferenceFilter

## What does this MR do?

This MR adds a preparation phase for reference filters that allows them to prepare/create data structures used while iterating over HTML nodes. In this particular case the preparation phase is used for issue references to greatly cut down the amount of queries executed to get projects/issues for Markdown references.

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

No.

## Why was this MR needed?

Rendering Markdown containing issue references would run at most two queries for every issue reference: one to get the project and one to get the issue from said project. When rendering Markdown with lots of issue references this would result in _a lot_ of queries being executed.

## What are the relevant issue numbers?

#18042

See merge request !4410

Added title attribute to entries in tree view

## What does this MR do?

Adds a title attribute to entries in the tree view. Moe useful when files have long names.

## What are the relevant issue numbers?

Closes #18353 


See merge request !4709

Added source branch text to dropdown toggle

## What does this MR do?

Previously, the dropdown toggle would default to "Select source branch", this changes that so that it defaults to the branch name and if that doesn't exist, it defaults to "Select source branch"

## Screenshots (if relevant)

![Screen_Shot_2016-06-07_at_12.20.10](/uploads/40d31e21297a99300050cf9f23bd7371/Screen_Shot_2016-06-07_at_12.20.10.png)

See merge request !4504

Fix project header alignment media query bug

## What does this MR do?
Fixes media query bug on project header

## Screenshots (if relevant)
![Screen_Shot_2016-06-15_at_3.22.20_PM](/uploads/3d84f8ffb88c316f317048e15ffea4f3/Screen_Shot_2016-06-15_at_3.22.20_PM.png)

See merge request !4689

Add bottom padding for merge request command line text

Because without bottom padding text is too close to the UI tabs - hard to navigate



See merge request !4681

Avoid a TypeError when initializing MergeRequest JS class with no arg

## What does this MR do?

Avoid a TypeError when initializing MergeRequest JS class with no arg.

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

No.

## Why was this MR needed?

Without this sane default you would get the following error when you
tried to instantiate a new MergeRequest object with no argument (i.e.
`new MergeRequest();`):
    
    TypeError: undefined is not an object (evaluating 'this.opts.action')

## What are the relevant issue numbers?

Fixes #13525.

## Does this MR meet the acceptance criteria?

- [x] No CHANGELOG since it's a trivial internal change
- [x] 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)
- [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 !4667

Fixed alignment of download dropdown

## What does this MR do?

Correctly aligns the download dropdown on merge requests

## Screenshots (if relevant)

![Screen_Shot_2016-06-14_at_14.47.06](/uploads/9381f25110e5573e56aa5c3f46786df5/Screen_Shot_2016-06-14_at_14.47.06.png)

See merge request !4646

Fixed last push event banner not being in container

## What does this MR do?

Adds the last push event content into a container with the correct class.

## What are the relevant issue numbers?

Closes #18567 

## Screenshots (if relevant)

![Screen_Shot_2016-06-14_at_13.17.41](/uploads/4afa3d2c73e59c5ffbd53869e49baa92/Screen_Shot_2016-06-14_at_13.17.41.png)

See merge request !4644

Fixed issue when opening a highlighted line diff

## What does this MR do?

With the new project nav being fixed, the diff page is scrolling the highlighted under the nav meaning you cant see what is highlighted. This corrects that by added the height of the new project nav into the offset.

See merge request !4597

Implements TemplateDropdown class to create custom template dropdowns

## What does this MR do?
Refactorize template dropdowns. This MR creates a base TemplateSelector class so it can be reused for multiple types of templates.

## 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
- [ ] 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 !4697

Shows build scroll buttons after build is complete

## What does this MR do?

Shows the build scroll buttons whenever there is a build trace. Previously they were only shown when the build was active.

## What are the relevant issue numbers?

Closes #18515 

## Screenshots (if relevant)

![Screen_Shot_2016-06-13_at_11.42.42](/uploads/6e0577f46a0cc7b4f2f13b17c85d97da/Screen_Shot_2016-06-13_at_11.42.42.png)

See merge request !4621

Besides when building the repository cache we cache 
those git counters too

Fix images in emails

Closes #18474. The confirmation email is actually the only one that uses the `image_tag` helper at the moment, but this will work for all of them:
```shell
$ ag image_tag -G mailer
app/views/layouts/devise_mailer.html.haml
13:              = image_tag('mailers/gitlab_header_logo.png', id: 'logo', alt: 'GitLab Wordmark')
24:                  = image_tag('mailers/gitlab_tanuki_2x.png', alt: 'GitLab Logo')
```

See merge request !4705

Lighten each logo path color instead of white

## What does this MR do?
Changes highlight/loading colors of tanuki from white to a lighter version of each path color

## Why was this MR needed?
Since the logo is no longer on the dark sidebar, the highlight color was getting lost against the light gray background

## What are the relevant issue numbers?
Closes #18521 

## Screenshots (if relevant)
![logo](/uploads/3743925862fa8e17d2fec426f7e4c853/logo.gif)

cc @jschatz1 @lbennett @dzaporozhets 

See merge request !4690

Banzai::Filter::ExternalLinkFilter use XPath

See merge request !4702

Closes #18353

Use gitlab_git 10.1.4

Towards https://gitlab.com/gitlab-org/gitlab-ce/issues/18690,
following https://gitlab.com/gitlab-org/gitlab_git/merge_requests/87 .

See merge request !4706

This reduces the number of queries executed in IssueReferenceFilter by
retrieving the various projects/issues that may be referenced in batches
_before_ iterating over all the HTML nodes.

A chunk of the logic resides in AbstractReferenceFilter so it can be
re-used by other filters in the future.

Improve pipeline status in case that pipeline has no jobs

## What does this MR do?

This MR resolves problem with pipeline status when there are no build in pipeline.

This can happen when builds were skipped - for example - by using `only`/`except` keyword in `.gitlab-ci.yml`.

## What are the relevant issue numbers?

Closes #17977

See merge request !4403

This ensures that Project.find_with_namespace returns a row matching
literally as the first value, instead of returning a random value.

The ordering here is _only_ applied to Project.find_with_namespace and
_not_ Project.where_paths_in as currently there's no code that requires
Project.where_paths_in to return rows in a certain order. Since this
method also returns all rows that match there's no real harm in not
setting a specific order either. Another reason is that generating all
the "WHEN" arms for multiple values in Project.where_paths_in becomes
really messy.

On MySQL we have to use the "BINARY" operator to turn a "WHERE" into a
case-sensitive WHERE as otherwise MySQL may still end up returning rows
in an unpredictable order.

Fixes gitlab-org/gitlab-ce#18603