License finder gem

Every time a gem is added to the Gemfile, or a gem is updated with a new dependency or change of license, LicenseFinder will check to ensure that the license in use has been whitelisted for use in the project. GPLv2 and GPLv3 libraries are not allowed to be linked-to from non-GPL projects (e.g. the MIT-licensed GitLab CE or proprietary EE), otherwise we're violating the license.

https://github.com/pivotal/LicenseFinder

See also: gitlab-com/operations#164

See merge request !3775

Fix missed colorize methods.

Fix #18250.

cc: @twk3 

See merge request !4495

Bump rouge to 1.11.0

See: https://github.com/jneen/rouge/blob/master/CHANGELOG.md

See merge request !4491

Use better_errors editor links in sherlock

Closes #18254. Uses the same editor configuration of `better_errors`
so that you don't have to configure things twice. Remember to have a
custom initializer that specifies your editor.

Example for atom. File `config/initializers/better_errors.rb`:
````ruby
if defined?(BetterErrors)
  BetterErrors.editor = "atm://open?url=file://%{file}&line=%{line}"
end
````

See merge request !4497

Remember to configure your `better_errors` editor to point to your program of preference

Add padding to bottom of wiki page, fix #12921.

## What does this MR do?
Adds padding to the bottom of the wiki page so it's not right up against the edge of the browser window.

## What are the relevant issue numbers?
#12921

## Screenshots (if relevant)

Before:

![Screen_Shot_2016-06-06_at_12.21.22_PM](/uploads/9710682a57f5e521253f17a65f896f4d/Screen_Shot_2016-06-06_at_12.21.22_PM.png)

After:

![Screen_Shot_2016-06-06_at_12.20.50_PM](/uploads/002068b072050e0f8146757a0386d30f/Screen_Shot_2016-06-06_at_12.20.50_PM.png)

cc: @jschatz1 

See merge request !4490

Make sure to mention the GNU Project and OSI-provided information regarding the GPL so no one tries to disagree with that decision.

Add gems and licenses that were previously missing. Approve a number of licenses after a bunch of research today.

Also add License Finder to CI (only runs on master).

In order to rehost all our gems in our own gem host, we need to have the legal rights to do so for every gem should they be taken down from RubyGems. License Finder automates checking of gems to ensure that we're in the clear legally.

Approved the MIT License because it essentially allows us to do "whatever" with those gems.

I am not a lawyer.

https://github.com/pivotal/LicenseFinder

Remove duplicated notification settings and add unique index

See merge request !4472

Fixed issue with activity links not being consistent

## What does this MR do?

Previously, links for opening an issue/merge request & commenting where different. Opening would only have a link on the number whereas commenting would have link on the text as well. This standardises it to include the type as well (ie. issue)

## What are the relevant issue numbers?

Closes #17621 

## Screenshots (if relevant)

![Screen_Shot_2016-06-01_at_12.12.09](/uploads/c778b007e6b6c068fcae30e34409ce98/Screen_Shot_2016-06-01_at_12.12.09.png)

See merge request !4400

Shows the edit comment button on mobile

## What does this MR do?

Shows the edit comment button on mobile.

## What are the relevant issue numbers?

Closes #17214 

## Screenshots (if relevant)

![Screen_Shot_2016-06-01_at_12.33.13](/uploads/d46b800c175a53821ea8e8af49c07641/Screen_Shot_2016-06-01_at_12.33.13.png)

See merge request !4402

Remove prev/next buttons on issues and merge requests

## What does this MR do?

Remove prev/next buttons on issues and merge requests sidebar

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

No

## Why was this MR needed?

The buttons were rarely used and added at least 1 query each on every page load which we could live without.

## What are the relevant issue numbers?

#18026

## Screenshots (if relevant)

Below is how it looks. Not sure if it's too much empty space. #17697 discusses a possible substitute for what to put there.

![Captura_de_pantalla_2016-06-06_a_las_11.09.26_a.m.](/uploads/7b379327aa6c608775f99bf47a9c3352/Captura_de_pantalla_2016-06-06_a_las_11.09.26_a.m..png)

![Captura_de_pantalla_2016-06-06_a_las_11.09.38_a.m.](/uploads/68bcae6754ed5ac48f1a6925fdd17d3f/Captura_de_pantalla_2016-06-06_a_las_11.09.38_a.m..png)

See merge request !4442

Add confidential issue notice in comment box.

## What does this MR do?

Adds a warning about confidential issues to the comment field when the issue is confidential.

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

I don't think so.

## Why was this MR needed?

It wasn't clear to users that they were commenting on a confidential issue, this makes it more explicit.

## What are the relevant issue numbers?

Fixes #15288 

## Screenshots (if relevant)

This is what it looks like at various screen sizes:

![Screen_Shot_2016-06-03_at_2.56.54_PM](/uploads/eb7f318bc19101f8514d7a4f10a77d73/Screen_Shot_2016-06-03_at_2.56.54_PM.png)

![Screen_Shot_2016-06-03_at_2.58.51_PM](/uploads/13674c3f1227b0d566b1d2aafc6712ed/Screen_Shot_2016-06-03_at_2.58.51_PM.png)

![Screen_Shot_2016-06-03_at_2.58.37_PM](/uploads/14ad419ed3ed86b7fbc080152e4030fa/Screen_Shot_2016-06-03_at_2.58.37_PM.png)

cc: @jschatz1 @dzaporozhets 

See merge request !4473

Notes are awardables

## What does this MR do?

Makes sure we can ⛈ comments/notes.

## What are the relevant issue numbers?
Follows up upon !2901, depends on !3785

Closes #3655 

## Screenshots (if relevant)
TODO



See merge request !4291

The buttons were rarely used and added at least 1 query each on every page load.

Fix comments on diff after LegacyDiffNote was extracted from Note

While Octokit auto pagination set the page size to the maximum 100, and
seek to not overstep the rate limit. When the rate limit is reached its
raises an exception, and stop doing new requests.

Here we use a custom pattern for traversing large lists, so we can
check if we’ll reach the rate limit and wait the API to reset the rate
limit before making new requests.

Extend specs for builds badge

## What does this MR do?

This MR extends specs for builds badge.

## Why was this MR needed?

We added an edge case to specs, while trying to reproduce problem described in #17549

## What are the relevant issue numbers?

#17549

See merge request !4401

Upgraded jQuery to version 2

## What does this MR do?

Upgrades jQuery to 2.2.1. 

Had to include the task_list JS file directly as it includes jQuery 1 directly https://github.com/github-archive/task_list/blob/master/app/assets/javascripts/task_list.coffee#L8 so when we change jQuery to `jquery2` it was including both jQuery 1 & 2.

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

For any JS errors

## What are the relevant issue numbers?

Closes #12440

See merge request !4384

Allow a U2F Device to be the Second Factor for Authentication

Parent Issue: #15337 

## TODO
- [ ] #15337 (!3905) FIDO/U2F 2FA using Yubikey
    - [x] Order a Yubikey?
    - [x] Do some reading to figure out what all this stuff means
    - [x] Look through the existing MR
    - [x] Browser support?
    - [x] Implementation
        - [x] User can register 2FA using their U2H device instead of authenticator
            - [x] Barebones flow
            - [x] Save the registration in the database
            - [x] Authentication flow
            - [x] First try after login/server start doesn't work
        - [x] User can log in using their U2F device
        - [x] Allow setting up authenticator if U2F is already set up (or vice versa)
        - [x] Change `two_factor_auths/new` to `show`
        - [x] `sign_requests` during registration? (Registering a device that has already been registered)
        - [x] 2FA skippable flow?
        - [x] Enforced 2FA flow (grace period?)
        - [x] Move the "Configure it Later" button to the right place
        - [x] Don't allow registration when the yubikey isn't plugged in
        - [x] Polish authentication flow
        - [x] Login should only show the 2FA method that's enabled
            - [x] Message to say that u2f only works on chrome, and it's recommended to enable otp as well.
        - [x] Index for key_handle
        - [x] Server-side errors while registering/logging in
        - [x] Handle non-chrome browsers
        - [x] Try to authenticate with a key that hasn't been registered (shouldn't work)
        - [x] Try the same key for multiple user accounts (should work)
        - [x] Fix existing tests
        - [x] Make sure CI is green
        - [x] Add tests
            - [x] Figure out how to fake the Yubikey
            - [x] Teaspoon tests for the React components
                - [x] Each device can only be registered once per user
            - [x] Feature specs
                - [x] Regular flows
                - [x] Test error cases
        - [x] Refactoring
            - [x] Refactor App ID
            - [x] Clean up the `show` action
        - [x] Annotate methods with definition of U2F
        - [x] Changelog
        - [x] Fix merge conflicts
        - [x] Verify flows
            - [x] Authenticator + no U2F
            - [x] U2F + no authenticator
            - [x] U2F + authenticator
            - [x] U2F + authenticator -> disable 2FA
            - [x] 2FA required with different grace periods
        - [x] Screenshots for MR
    - [x] Augment the [help docs](http://localhost:3000/help/profile/two_factor_authentication)
    - [x] Assign to endboss
    - [x] Ask for feedback on UI/UX
    - [x] Ask for feedback on copy
    - [x] Wait for review/merge
    - [x] Fix merge conflicts
    - [x] Wait for CI to pass
    - [x] Implement review comments/suggestions
        - [x] Move `TwoFactorAuthController#create_u2f` to a service
        - [x] Extra space before `Base64` in `u2f_registration` model
        - [x] Move `with/without_two_factor` scopes to class methods
        - [x] In `profiles/accounts/show`, add spaces at `{` and `}`
        - [x] Remove blank lines in `profiles/two_factor_auths/show`
        - [x] Fix typo in doc. "(universal 2nd factor )"
        - [x] Add "Added in 8.8" to doc
        - [x] In the doc, use 'Enable 2FA via mobile application' instead of 'Via Mobile Application'
        - [x] In the doc, use 'Enable 2FA via U2F device' instead of 'Via U2F Device
        - [x] Use "Two-Factor Authentication" everywhere
        - [x] Use `#icon` wrapper instead of `fa_stacked_icon`
        - [x] Check if `string` is enough for `key_handle` and `public_key`
        - [x] Separate `exercise` and `verify` phases of test (u2f_spec)
        - [x] Assert that `user_without_2fa` is _not_ in results (with_two_factor)
            - [x] Remove rubocop exception
        - [x] Refactor call to `User.with_two_factor.count` to not include `.length`
        - [x] Add a note that makes the "Disable" button/feature obvious
        - [x] Remove i18n
        - [x] Test in Firefox with addon (+ create new issue for support)
        - [x] Remove React
            - [x] Rewrite registration
            - [x] Switch underscore template to default style
            - [x] Rewrite authentication
            - [x] Move `register` haml to `u2f` dir
            - [x] Remove instance variables
            - [x] Fix tests
            - [x] Read SCSS guidelines
            - [x] Address @connorshea's comments regarding text style
            - [x] Make sure all classes and IDs are in line (add `js-` prefixes)
                - [x] Register
                - [x] Authenticate
            - [x] Refactoring?
        - [x] Include non-minifed version of bowser
        - [x] Audit log
        - [x] Look at the `browser` gem (and don't use bowser)
        - [x] Error message when on HTTP?
    - [x] Test on Mobile
    - [x] Fix merge conflicts
    - [x] Retest all flows
    - [x] Back to Rémy for review
    - [x] Make sure CI is green
    - [x] Wait for merge / more feedback
    - [x] Implement @rymai's changes
        - [x] JS/Coffeescript variables should be lowerCamelCase
        - [x] Spaces before/after `}` and `{` in HAML (and elsewhere)
        - [x] Rails view helpers in u2f HAML
        - [x] `%div.row.append-bottom-10`
        - [x] Wrap line in `without_two_factor` scope
        - [x] Exception-less flow in `U2F::CreateService`
    - [x] Fix merge conflicts
    - [x] Move service to model class method
    - [x] Fix teaspoon specs
    - [x] Address @rymai's suggestions about error handing
    - [x] Javascript error constants
    - [x] Fix merge conflicts
    - [x] One final review
        - [x] Test "registration with errors" flow
    - [x] Assign to Remy
    - [x] Wait for replies from @jschatz1
    - [x] Address @rymai's comments
        - [x] Omit `%div`
        - [x] Scope `$.find` globally
        - [x] Replace `find('#element-id).click` with `click_on('Element Text')
    - [x] Rebase master + conflicts
    - [x] Look at https://news.ycombinator.com/item?id=11690774
    - [x] Address @connorshea's comment regarding HTTPS on localhost
    - [x] Final sanity check
    - [x] Wait for [CI to pass](https://gitlab.com/gitlab-org/gitlab-ce/commit/c84179ad233529c33ee6ba8491cfea862c6cd864/builds)
    - [x] Address @rymai's next round of comments
        - [x] Interpolate `true` and `false` in DB scopes
        - [x] Why have `Gon::Base.render_data` thrice?
        - [x] `user_spec` should have correct spacing
        - [x] Use `arel_table[:id]` instead of `users.id`
        - [x] URL helper in `app/views/profiles/two_factor_auths/show.html.haml`
        - [x] Remove polyfill change
    - [x] Wait for [CI to pass](https://gitlab.com/gitlab-org/gitlab-ce/commit/0123ab8/builds)
    - [x] Address @jschatz1's comments
        - [x] Use `on('click', ...)` instead of `click(...)`
        - [x] Use `is` and `isnt` in coffeescript
        - [x] Use `and` and `or` in coffeescript
    - [x] Add `Gon::Base.render_data` to `devise_empty` (and other base layouts)
    - [x] Wait for [CI to pass](https://gitlab.com/gitlab-org/gitlab-ce/commit/401916397336174c582be3d3004a072f845d4b5f/builds)
    - [x] Wait for [build](https://gitlab.com/gitlab-org/gitlab-ce/commit/75955710ef9a5f0dcee04e8617028c0e3ea5bf50/builds) to pass
    - [x] Fix merge conflicts
    - [x] Inspect diff / workflow
    - [x] Assign back to @rymai
    - [x] Make sure [ci](https://gitlab.com/gitlab-org/gitlab-ce/commit/2c6316b29a9276ef44c7b4b39363a611bf5973a6/builds) has passed
    - [x] Fix merge conflicts (probably introduced by [devise upgrade](https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/4216)
    - [x] Wait for [CI](https://gitlab.com/gitlab-org/gitlab-ce/commit/a5ef48b7aa63d0d9e45b41643043b57208eaab9f/builds) to pass
    - [x] Respond to @rymai's comments
        - [x] Use `elsif`
        - [x] Check if we need `and return`
        - [x] Only fetch key handles from the DB
        - [x] No annotations to models?
        - [x] Align hash keys in model
    - [x] Wait for [build](https://gitlab.com/gitlab-org/gitlab-ce/commit/e0ef504734e7f14813c73bbb79f5c5f6fae3248c/builds) to pass
    - [ ] Wait for merge

## Screenshots

![Screenshot_2016-05-03_09.53.04](/uploads/1af3f277efa488dc107d36e6b4b07ca4/Screenshot_2016-05-03_09.53.04.png)
![Screenshot_2016-05-03_10.19.53](/uploads/2bfc67dfb96c0e005cce033d8b456813/Screenshot_2016-05-03_10.19.53.png)
![Screenshot_2016-05-03_10.19.56](/uploads/e912abedd5b1d07d7185cee9f204c5ff/Screenshot_2016-05-03_10.19.56.png)
![Screenshot_2016-05-03_10.20.04](/uploads/9350d5c98823d1f3d4e59517dfb8910a/Screenshot_2016-05-03_10.20.04.png)
![Screenshot_2016-05-03_10.31.15](/uploads/84473dc263e0643311a39006e649035f/Screenshot_2016-05-03_10.31.15.png)
![Screenshot_2016-05-03_10.31.22](/uploads/13ce43e0d7a565000af29984667eeb08/Screenshot_2016-05-03_10.31.22.png)
![Screenshot_2016-05-03_10.31.37](/uploads/b90fbb40dbf9bbd73af324f48ffdc948/Screenshot_2016-05-03_10.31.37.png)
![Screenshot_2016-05-03_10.36.48](/uploads/41a0fbc493c6fefeafd922b3ddf2a25e/Screenshot_2016-05-03_10.36.48.png)

See merge request !3905