Move the last secret from .secret to config/secrets.yml, and delete
.secret if it exists.

.secret stores the secret token used for both encrypting login cookies
and for encrypting stored OTP secrets. We can't rotate this, because
that would invalidate all existing OTP secrets.

If the secret token is present in the .secret file or an environment
variable, save it as otp_key_base in secrets.yml. Now .secret can be
rotated without invalidating OTP secrets.

If the secret token isn't present (initial setup), then just generate a
separate otp_key_base and save in secrets.yml.

Update the docs to reflect that secrets.yml needs to be retained past
upgrades, but .secret doesn't.

Add advanced troubleshooting for debugging issues with the Docker registry



See merge request !5615

[ci skip]

Fix filter input alignment

## What does this MR do?
If you carefully observe the filter inputs on the [issues page](https://gitlab.com/gitlab-org/gitlab-ce/issues) and the [projects dashboard page](https://gitlab.com/dashboard/projects), you will notice that those input fields are actually a few pixels lower than the UI elements beside them (More so for the projects dashboard page than the issues page). This MR fixes that alignment issue so that they are aligned to the buttons on their right.

## Are there points in the code the reviewer needs to double check?
Shouldn't be

## Why was this MR needed?
Improves the existing UI

## What are the relevant issue numbers?
Closes #20559 

## Screenshots (if relevant)
Before
![Screen_Shot_2016-08-02_at_5.42.28_PM](/uploads/8530fc6c9ce20f28ae74b950bc1bd6be/Screen_Shot_2016-08-02_at_5.42.28_PM.png)

After
![Screen_Shot_2016-08-02_at_5.49.28_PM](/uploads/ec20e68045c2190aec52e5f059d1a3bc/Screen_Shot_2016-08-02_at_5.49.28_PM.png)

After (with color markings)
![Screen_Shot_2016-08-02_at_5.49.25_PM](/uploads/6e032b1ffb438018f6fadf294c3cebd3/Screen_Shot_2016-08-02_at_5.49.25_PM.png)

Before
![Screen_Shot_2016-08-02_at_5.41.19_PM](/uploads/11a3c30d0290328bb3298bc392facf9f/Screen_Shot_2016-08-02_at_5.41.19_PM.png)

After
![Screen_Shot_2016-08-02_at_5.49.47_PM](/uploads/f8e20346a19dc67cc3e54788dc0e72fb/Screen_Shot_2016-08-02_at_5.49.47_PM.png)

After (with color markings)
![Screen_Shot_2016-08-02_at_5.49.58_PM](/uploads/1839d5681ab2f3518609004511af86a6/Screen_Shot_2016-08-02_at_5.49.58_PM.png)

## Does this MR meet the acceptance criteria?

- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- 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 !5633

Move markdown doc to the right location



See merge request !5635

[ci skip]

Remove delay when hitting Reply... button on page with a lot of comments

Every time the "Reply..." button was hit, a new `GLForm` was instantiated (which is fine), which would then call `GitLab.GfmAutoComplete.setup()` without specifying which textarea we needed autocompletion on, which resulted in `GitLab.GfmAutoComplete.setup` iterating through every single textarea on the page. On a page with a lot of comments, where each comment would have its own textarea that will be used to edit the comment, this would take a long time and cause the whole page to hang for 2 seconds when a  "Reply..." button was clicked.

See merge request !5602

Convert image diff background image to CSS

## What does this MR do?
Replaces the `trans_bg.gif` image used for image diff background image with a CSS implementation of the same background image

## Are there points in the code the reviewer needs to double check?
None

## Why was this MR needed?
Uses CSS to replace the use of an image so that webpage rendering is slightly improved

## What are the relevant issue numbers?
Closes #20500 

## Screenshots (if relevant)
Before:
![Screen_Shot_2016-08-01_at_12.29.10_PM](/uploads/8269877c561c29e6b0ca988079ff3fc6/Screen_Shot_2016-08-01_at_12.29.10_PM.png)

After:
![Screen_Shot_2016-08-01_at_12.29.16_PM](/uploads/cc88848b9c0e044445d19b889fd79271/Screen_Shot_2016-08-01_at_12.29.16_PM.png)

## Does this MR meet the acceptance criteria?

- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- [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 !5598

Add simple identifier to public SSH keys

## What does this MR do?
Adds a simple identifier of user_name + hostname to public SSH keys

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

## Why was this MR needed?
To help people identify keys when they export them

## What are the relevant issue numbers?
#18866 

## 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
  - [ 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)
Closes #18866

See merge request !5614

Redirect to external issue tracker from `/issues`

Prior, in order to display the correct link to "Issues" in the project
navigation, we were performing a check against the project to see if it
used an external issue tracker, and if so, we used that URL. This was
inefficient.

Now, we simply _always_ link to `namespace_project_issues_path`, and
then in the controller we redirect to the external tracker if it's
present.

This also removes the need for the `url_for_issue` helper. Bonus! 🎉

See merge request !5608

[ci skip]

[ci skip]

Convert switch icon into icon font

## What does this MR do?
Converts the switch icon into the exchange icon from font awesome

## Are there points in the code the reviewer needs to double check?
Shouldn't be any

## Why was this MR needed?

*  Decreases an external resource for the repository compare page
*  Icon font provides a sharper image for displays with higher pixel resolutions

## What are the relevant issue numbers?
Closes #20508 

## Screenshots (if relevant)
Before:
![Screen_Shot_2016-08-01_at_3.06.06_PM](/uploads/6ad46cc6dff98ec534e1f5a0fe556fa7/Screen_Shot_2016-08-01_at_3.06.06_PM.png)

After:
![Screen_Shot_2016-08-01_at_3.06.10_PM](/uploads/3cb11c40cbba398f9986a4cc6b3a7e4c/Screen_Shot_2016-08-01_at_3.06.10_PM.png)

## Does this MR meet the acceptance criteria?

- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- [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 !5603

link the engineering workflow document from process and contributing

## What does this MR do?

Add links to process and contributing to the engineering workflow document. 

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

no.

## Why was this MR needed?

The engineering workflow document is very important to Inc developers, but was hard to find.

## What are the relevant issue numbers?

## Screenshots (if relevant)

## Does this MR meet the acceptance criteria?

not relevant

See merge request !5625

Allow branch names ending with .json for graph and network page

## What does this MR do?

Allow branch names to end with `.json` for graph and network page.

## Why was this MR needed?

Displaying branches ending on `.json` in repository view crashes because links to graph and network page can not be determined.

## What are the relevant issue numbers?

fixes #20462, #19585

See merge request !5579

Expand commit message width in repo view

## What does this MR do?
Expands the commit message width in repo view to take advantage of the unused white space (under the history href)

## Are there points in the code the reviewer needs to double check?
Just need to make sure there aren't any side effects

## Why was this MR needed?
To take advantage of the unused space on repo views

## What are the relevant issue numbers?
Closes #20225 

## Screenshots
Before:
![Screen_Shot_2016-07-27_at_11.10.22_AM](/uploads/1f2c604ac6d4ede2bac67179cfe77b20/Screen_Shot_2016-07-27_at_11.10.22_AM.png)

After:
![Screen_Shot_2016-07-27_at_11.08.55_AM](/uploads/34a36c884a06fd6cfd9b6512d1230196/Screen_Shot_2016-07-27_at_11.08.55_AM.png)

## Does this MR meet the acceptance criteria?
- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- Tests
  - [x] Added 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 !5494

Add and update vendored templates for 8.11

[ci skip]

See merge request !5626

[ci skip]

Fixed artifacts expire date in FF

## What does this MR do?

FireFox was trying to parse the date incorrectly so it would just show 'Past due'

## Screenshots (if relevant)

![Screen_Shot_2016-07-21_at_17.16.57](/uploads/938d39c648dc98540cd991cf552276dd/Screen_Shot_2016-07-21_at_17.16.57.png)

See merge request !5403

Speedup DiffNote#active? on discussions

See merge request !5597

Add es6 to teaspoon

## What does this MR do?

Adds the `es6` file extensions to teaspoon matchers so it can load those specs.

This also removes the current coffee matchers.

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

## Why was this MR needed?

We need to accept `.js.es6` specs.

## What are the relevant issue numbers?

## Screenshots (if relevant)

## 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
  - [ ] All builds are passing
- [ ] 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)

See merge request !5524

Resolve ""CI configuration" button when `.gitlab-ci.yml` is present"

## What does this MR do?
Adds `CI configuration` button to project overview page

## What are the relevant issue numbers?
Closes #20101

## Screenshots (if relevant)
![Screen_Shot_2016-07-28_at_11.51.32_AM](/uploads/499d942d203d287ae98b7589ef12673c/Screen_Shot_2016-07-28_at_11.51.32_AM.png)



See merge request !5558

Remove outdated notes from the update guide

## What does this MR do?

updates guides

See merge request !5624

Speedup DiffNote#active? on discussions, preloading noteables and avoid touching git repository to return diff_refs when possible

- Preloading noteable we share the same noteable instance when more than one 
discussion refers to the same noteable.
- Any other call to that object that is cached in that object will be for any 
discussion.
- In those cases where merge_request_diff has all the sha stored to build a diff_refs get that 
diff_refs using directly those sha instead accessing to the git repository to first get the 
commits and later the sha.

fix runner install link

## What does this MR do?

Fix link to GitLab CI Runner installation

## Why was this MR needed?

Link is broken

See merge request !5612

Revert "md5 and utf_encode js libraries"

## What does this MR do?

Remove two unused JavaScript libraries (`md5.js` and `utf8_encode.js`).

## Why was this MR needed?

Those libraries were not used anymore:

```
$ find app/ lib/ -name '*.js' -exec grep --perl-regexp --with-filename '(md5|utf8_encode)' {} \;
app/assets/javascripts/lib/utils/utf8_encode.js:function utf8_encode (argString) {
app/assets/javascripts/lib/utils/utf8_encode.js:  // *     example 1: utf8_encode('Kevin van Zonneveld');
app/assets/javascripts/lib/utils/md5.js:function md5 (str) {
app/assets/javascripts/lib/utils/md5.js:  // -    depends on: utf8_encode
app/assets/javascripts/lib/utils/md5.js:  // *     example 1: md5('Kevin van Zonneveld');
app/assets/javascripts/lib/utils/md5.js:  str = this.utf8_encode(str);
```


See merge request !5613

Instrument the Repository class

## What does this MR do?

This MR instruments the Repository class.

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

No.

## Why was this MR needed?

This class wasn't instrumented.

## Does this MR meet the acceptance criteria?

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

See merge request !5621

Since this isn't an ActiveRecord::Base descendant it wasn't
instrumented.

Add help document describing intended wiki linking behavior

Related to #16568
Closes #18019

- This documents the _intended_ behaviour of linking to wiki pages/files.

## TODO

- [x] Respond to @rymai's comments
    - [x] Use `succeed`
    - [x] Shouldn't this be <wiki_root>/miscellaneous.md here?
    - [x] what happens for file links that starts with a `/`?

See merge request !4372

Always compare with FETCH_HEAD in downtime_check

See merge request !5619