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

Don't show 'Leave Project' to group members

## What does this MR do?

It hides the 'Leave Project' button to group members that are not explicitly a member of the project.

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

No.

## Why was this MR needed?

Because there was an issue opened!

## What are the relevant issue numbers?

Fixes #18724.

## 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] 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 !4739

Validate only and except regexp

## What does this MR do?
Adds a better validation for only and except which can contain regexps.

## Why was this MR needed?
Currently the RegexpError can be raised when processing next stage which leads to 500 in different places of code base.
This adds early check that regexps used in only and except are valid.

cc @grzesiek 

- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- [x] Tests
  - [x] Added for this feature/bug
  - [ ] 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 !4736

Fixed styling of clipboard button

Closes #18773 

See merge request !4728

Use Git cached counters on project show page

See merge request !4711

Allow customising of queries used for `update_column_in_batches`

This MR makes two changes to `add_column_with_default` and `update_column_in_batches`:

1. `add_column_with_default` no longer wraps the entire set of updates in a single transaction, preventing any locks from sticking around for the duration of the entire transaction
2. `update_column_in_batches` now takes a block which can be used to customise the queries. This uses Arel as messing with raw SQL strings is a total pain

In !4381 there's a need for updating existing rows/columns in a table in batches using a custom `WHERE` condition. Without the changes in this MR this would not be possible.

See merge request !4680

Fix permission checks in member row (backport from gitlab-org/gitlab-ee!460)

## What does this MR do?

It improves the check we use to display or not the members' access and controls in the members list.

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

No, I replaced an helper with just a permission check so I think it's a better solution.

## Why was this MR needed?

There were a spec failure in gitlab-org/gitlab-ee!460 because of the refactor done in the "request access" MR.

## What are the relevant issue numbers?

None.

## Does this MR meet the acceptance criteria?

- No CHANGELOG needed
- [x] Tests
  - [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 !4670

Added API endpoint for Sidekiq Metrics.

## What does this MR do?

It adds an API endpoint to gather metrics about Sidekiq, it's jobs, queues, and processes.

## Why was this MR needed?

There was no API endpoint for Sidekiq information.

## What are the relevant issue numbers?

Fixes #7171

## 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
- [x] Tests
  - [x] Added for this feature/bug
  - [x] All builds are passing

See merge request !4653

Fixed issue with user calendar colors

## What does this MR do?

Fixes an issue with the colors added onto the user contrib calendar. The calendar was change recently to remove a library which affected how the colors where generated.

## What are the relevant issue numbers?

Closes #18505 

## Screenshots (if relevant)

![Screen_Shot_2016-06-13_at_09.33.10](/uploads/f17451d2eb805e9d75d859cd1691e0bc/Screen_Shot_2016-06-13_at_09.33.10.png)

See merge request !4614

Add sorting dropdown to tag page

## What does this MR do?

Adds a sorting dropdown to the tags page just like the one on the branches page.

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

No

## Why was this MR needed?

Clients were asking for this

## What are the relevant issue numbers?

Closes #14918

## Screenshots (if relevant)

![Captura_de_pantalla_2016-06-01_a_las_4.07.58_p.m.](/uploads/4530683ddd91d3bdbdce77748fe63f87/Captura_de_pantalla_2016-06-01_a_las_4.07.58_p.m..png)

See merge request !4423

Use gitlab-git 10.2.0

Closes #18741

See merge request !4722

Banzai::Filter::UploadLinkFilter use XPath

See merge request !4703

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

[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

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

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

Hide the Todo button in the collapsed issuable sidebar.

## What does this MR do?

Fixes a bug where the "Add Todo" button was displayed in the collapsed sidebar.

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

This shouldn't remove any other elements from the collapsed sidebar.

## What are the relevant issue numbers?

None

## Screenshots (if relevant)

Before:

![Screen_Shot_2016-06-15_at_11.41.46_AM](/uploads/27a1ace58cf8c44ad96accd3d0b32f11/Screen_Shot_2016-06-15_at_11.41.46_AM.png)

After:

![Screen_Shot_2016-06-15_at_11.40.53_AM](/uploads/91a8585680fc482682d0efafdba4d599/Screen_Shot_2016-06-15_at_11.40.53_AM.png)

See merge request !4686

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

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