Reassign secret token when regenerating one

## What does this MR do?

This is an attempt to fix intermittent errors in out test suite.

```text
Failures:

  1) Gitlab::Shell memoized secret_token creates and links the secret token file
     Failure/Error: expect(File.read(secret_file).chomp).to eq(secret_token)
     
       expected: "690f959e206ab91acc54e1c605c7ff90"
            got: "cccb4e8df9360600271e61114d4e6e68"
     
       (compared using ==)
     # ./spec/lib/gitlab/backend/shell_spec.rb:47:in `block (3 levels) in <top (required)>'
```

It appears that `spec/lib/gitlab/backend/shell_spec.rb` tries to change the file that stores secret token, but `Gitlab::Shell` memoizes `@secret_token` on class level, so when it was already created by other tests (`spec/requests/api/internal_spec.rb` in this case), memoized token is not reassigned even if it was generated again with `ensure_secret_token!`.

See merge request !6844

Grapify todos API

## What does this MR do?

Add the Grape-DSL to the todos API.

## What are the relevant issue numbers?

Related to #22928

See merge request !6875

Extract project#update_merge_requests to its own worker from GitPushService

See merge request !6767

Resolve "Fix missing Glossary link"

## What does this MR do?

Fixes broken links in University.

## What are the relevant issue numbers?

Closes #23332

See merge request !6880

Grapify system hooks API

## What does this MR do?

Add the Grape-DSL to the system-hook API.

## What are the relevant issue numbers?

Related to #22928

See merge request !6861

Add more info on the new CI permissions model

From discussion in issue https://gitlab.com/gitlab-org/gitlab-ce/issues/22484

See merge request !6843

Refactor merge requests revisions docs

See merge request !6878

- A system note now appears on every push
- Replace dashes with underscores in images

[ci skip]

Link to review apps example from docs

Put a link in the example project of the Review Apps in dynamic environments
and to the list of CI examples.

See merge request !6873

[ci skip]

Do not run before_script, artifacts, cache in trigger_docs job

Fixes

See merge request !6866

Replace unique keyframes mixin with specific keyframe animation names

## What does this MR do?
Replaces `unique-keyframes` mixin with `include-keyframes` mixin

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

## Why was this MR needed?
Some users had GitLab hosted in a distributed environment that makes `unique-keyframes` a non-viable implementation. 
The randomized animation names from `unique-keyframes` was not being picked up by the different servers which resulted in 404 errors.

## Screenshots (if relevant)
None

## 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 [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [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)

## What are the relevant issue numbers?
Closes #22629

See merge request !6603

CE to EE merge check rake task

## What does this MR do?

This merge request adds a Rake task that checks whether the current branch can be merged cleanly to EE/master.

If not, it checks if a `<ce_branch>-ee` branch exists in EE, tries to merge it to EE/master and then tries to merge `ce_branch` to EE/master.

If the result of the check is that the current branch cannot be merged cleanly to EE/master, the job will fail, display troubleshooting steps, and a warning will be shown in the merge request.

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

Probably the steps I used to do the various checks, and also the steps I suggest to create an EE-specific branch.

## Why was this MR needed?

The goal is to catch as early as possible the possible conflicts a CE MR will cause when CE/master will be merged to EE/master. This way, the developer is warned that he/she should open a MR against EE before or as soon as the CE is merged. In the end, this should lower the work of the CE->EE merger.

## What are the relevant issue numbers?

Part of gitlab-org/gitlab-ee#715, hopefully.

See merge request !6746

Handle case where deployment ref no longer exists

## What does this MR do?

In 8.9, we didn't create keep-around refs for deployments. So it's possible that someone created a deployment (say, for testing), and then deleted the branch and all other references to that commit. That commit could then get GCed, and trying to view MRs on 8.11+ will show a 500. See https://gitlab.com/gitlab-org/gitlab-ce/issues/22655#note_16575020 for more details.

## Why was this MR needed?

If someone created a deployment on 8.9, then deleted all references to the commit for that deployment, we will throw an exception when checking if the deployment includes a commit.

Closes #22655.

See merge request !6855

Sort API mounts

## What does this MR do?

Sort the API mounts.

## Why was this MR needed?

The API mounts are unsorted.

See merge request !6831

Convert unicode emojis to images.

## Why was this MR needed?

For better cross platform interoperability with emojis.

Closes #22591

See merge request !6829

Also add a safeguard for non-CI env.
Signed-off-by: Rémy Coutable <remy@rymai.me>

Signed-off-by: Rémy Coutable <remy@rymai.me>

Use defined colour for a language when available

## What does this MR do?

This MR changes the colours of the different languages in the language graph.  It now uses the colour set in Linguist instead of the first six characters of the SHA256'd language name where possible.  If Linguist has no colour defined for a given language, it falls back to the old method of finding a colour.

I talked with @connorshea about creating this MR [on Twitter](https://twitter.com/connorjshea/status/784390886222286849) a few hours earlier. Here's also an older [tweet from May](https://twitter.com/nilsding/status/737018807223496708) where we discussed some possible improvements to the graph. 

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

Hopefully none ;)

## Why was this MR needed?

Aesthetics.

## Screenshots (if relevant)

Before:

![language_colours_before](/uploads/6b4bac784860da746d58708bdd6bba39/language_colours_before.png)

After:

![language_colours_after](/uploads/98818ebf48ffb47e6b785120e69b0b6c/language_colours_after.png)

## 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 [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [ ] 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 it does - rebase it please)
- [ ] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

## What are the relevant issue numbers?

- #12455

See merge request !6748

Keep-around refs for deployments were only introduced in 8.10, so any
deployment created in 8.9 could have a SHA pointing to a commit that no
longer exists in the repository. We can't do anything useful with those
deployments, so make `#includes_commit?` always return false for those.

Loosen requirement on request_store version

This gem follows semantic versioning and will not introduce breaking
changes in a minor version. See
https://github.com/steveklabnik/request_store#semantic-versioning

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/2868

See merge request !6853

Refactoring Issues Board

## What does this MR do?

This MR aims to minimize conflicts between the CE issues board feature with EE multiple boards feature.

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

## Why was this MR needed?

To avoid a lot of conflicts with EE multiple boards feature.

## 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)~~
- [x] API support added
- Tests
  - [X] Added for this feature/bug
  - [ ] All builds are passing
- [x] Conform by the [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [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)

## What are the relevant issue numbers?

https://gitlab.com/gitlab-org/gitlab-ee/issues/929

https://gitlab.com/gitlab-org/gitlab-ee/issues/1084

See merge request !6727

Use forked github-markup gem to enable python3 support with omnibus

## What does this MR do?
Changes the version of `github-markup` gem we are using, to be the forked one with the changes to enable python3 support.
The change is backward compatible with users using Python 2, and will only be running with Python 3 in Omnibus (with the help of a custom patch we apply there).

## Are there points in the code the reviewer needs to double check?
Make sure backward compatibility isn't broken for source installs.

## For the release manager

You need to make sure you pickup into stable this merge request as well (for omnibus): https://gitlab.com/gitlab-org/omnibus-gitlab/merge_requests/1015 as it's part of the fix, otherwise package will fail to build.

## Why was this MR needed?
We had some regressions with .rst rendering that were fixed, but still some issues with encoding persisted (this MR will fix that). See: https://gitlab.com/gitlab-org/gitlab-ce/issues/21696

## 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 [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [ ] 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)

## What are the relevant issue numbers?

* gitlab-org/gitlab-ce#21696
* gitlab-org/gitlab-ce#22748
* gitlab-com/support-forum#1097

See merge request !6659

GrapeDSL for variables



See merge request !6838

Merge branch '23234-deleting-a-milestone-removes-source-branch-deletion-options-of-associated-merge-requests' into 'master'

Maintain "force_remove_source_branch" options on Merge Request unless specified

## What does this MR do?

Fixes a problem where Merge Requests were losing the state associated with the flag to remove the source branch upon merge

* Closes #23234 
* Closes #23191
* Closes #19351

See merge request !6817

Keep a copy of gems needed by our releases as CI artifacts

This is meant as insurance in case a gem GitLab needs is ever removed
from rubygems.org. After we merge this, all future GitLab tags will
have a CI artifact archive containing all the gems (for all platforms)
specified in Gemfile.lock for that revision.

Only runs on tags (so we don't constantly create 50MB gem cache bundles).

See merge request !6617

This gem follows semantic versioning and will not introduce breaking
changes in a minor version. See
https://github.com/steveklabnik/request_store#semantic-versioning

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/2868

Add job to trigger a docs.gitlab.com build

## What does this MR do?

Add a job to build the docs site every time master tests pass.

## What are the relevant issue numbers?

https://gitlab.com/gitlab-com/doc-gitlab-com/issues/56

See merge request !6850

Implement second iteration of cycle analytics - Change in data measurement

Part of https://gitlab.com/gitlab-org/gitlab-ce/issues/22458

Measure everything that happened in the given time range, not only what's been pushed to production. With the exception of the staging and production stages.

- [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)
- Tests
  - [x] Added for this feature/bug
  - [x] All builds are passing
- [x] Conform by the [merge request performance guides](http://docs.gitlab.com/ce/development/merge_request_performance_guidelines.html)
- [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 it does - rebase it please)
- [ ] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

See merge request !6798

Fix secret names in HA docs

See https://gitlab.com/gitlab-org/gitlab-ee/issues/1110#note_16854559. I don't think this needs a CHANGELOG item really.

See merge request !6845