disable markdown in comments when referencing disabled features

fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/23548

This MR prevents the following references when tool is disabled:

- issues
- snippets
- commits - when repo is disabled
- commit range - when repo is disabled
- milestones

This MR does not prevent references to repository files, since they are just markdown links and don't leak
information.

See merge request !2011
Signed-off-by: Rémy Coutable <remy@rymai.me>

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

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

Replace issue access checks with use of IssuableFinder

Split from !2024 to partially solve https://gitlab.com/gitlab-org/gitlab-ce/issues/23867

⚠ - Potentially untested
💣 - No test coverage
🚥 - Test coverage of some sort exists (a test failed when error raised)
🚦 - Test coverage of return value (a test failed when nil used)
✅ - Permissions check tested

Using `visible_to_user` likely makes these security issues too. See [Code smells](#code-smells).

- [x] 🚦 app/finders/notes_finder.rb:15 [`visible_to_user`]
- [x] 🚥 app/views/layouts/nav/_project.html.haml:73 [`visible_to_user`] [`.count`]
- [x] ✅ app/services/merge_requests/build_service.rb:84 [`issue.try(:confidential?)`]
- [x] ✅ lib/api/issues.rb:112 [`visible_to_user`]
  - CHANGELOG: Prevented API returning issues set to 'Only team members' to everyone
- [x] ✅ lib/api/helpers.rb:126 [`can?(current_user, :read_issue, issue)`] Maybe here too?
- [x] ✅ lib/gitlab/search_results.rb:53 [`visible_to_user`]

- [ ] https://dev.gitlab.org/gitlab/gitlabhq/merge_requests/2024/diffs#b2ff264eddf9819d7693c14ae213d941494fe2b3_128_126
- [ ] https://dev.gitlab.org/gitlab/gitlabhq/merge_requests/2024/diffs#7b6375270d22f880bdcb085e47b519b426a5c6c7_87_87

See merge request !2031
Signed-off-by: Rémy Coutable <remy@rymai.me>

Fix missing access checks on issue lookup using IssuableFinder

Split from !2024 to partially solve https://gitlab.com/gitlab-org/gitlab-ce/issues/23867

⚠ - Potentially untested
💣 - No test coverage
🚥 - Test coverage of some sort exists (a test failed when error raised)
🚦 - Test coverage of return value (a test failed when nil used)
✅ - Permissions check tested

- [x] ✅ app/controllers/projects/branches_controller.rb:39
  - `before_action :authorize_push_code!` helpes limit/prevent exploitation. Always checks for reporter access so fine with
    confidential issues, issues only visible to team, etc.
- [x] 🚥 app/models/cycle_analytics/summary.rb:9 [`.count`]
- [x] ✅ app/controllers/projects/todos_controller.rb:19

- [x] Potential double render in app/controllers/projects/todos_controller.rb

- https://dev.gitlab.org/gitlab/gitlabhq/merge_requests/2024/diffs#cedccb227af9bfdf88802767cb58d43c2b977439_24_24

See merge request !2030
Signed-off-by: Rémy Coutable <remy@rymai.me>

Fix information disclosure in `Projects::BlobController#update`

It was possible to discover private project names by modifying `from_merge_request`parameter in `Projects::BlobController#update`. This fixes that.

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

https://gitlab.com/gitlab-org/gitlab-ce/issues/22869

See merge request !2023
Signed-off-by: Rémy Coutable <remy@rymai.me>

[ci skip]
Signed-off-by: Rémy Coutable <remy@rymai.me>

Fix for HackerOne XSS vulnerability in markdown

This is an updated blacklist patch to fix https://dev.gitlab.org/gitlab/gitlabhq/merge_requests/2007. No text is removed. Dangerous schemes/protocols and invalid URIs are left intact but not linked.

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/23153

See merge request !2015
Signed-off-by: Rémy Coutable <remy@rymai.me>

[ci skip]
Signed-off-by: Rémy Coutable <remy@rymai.me>

Use Hash rocket syntax to fix cycle analytics under Ruby 2.1

Refers to #23510

See merge request !6977

Fix Safari displaying NaN for selected due date

## What does this MR do?

1. Stops using `Date.parse` to parse selected due dates.
2. Refactors DueDateSelectors to be more maintainable and readable

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

**To review the actual fix, look here:** https://gitlab.com/gitlab-org/gitlab-ce/commit/4ad43ac3a12902d7ea01dc09f8a361b01c21a0ee. It would be difficult to pick out from the overall diff.

## Why was this MR needed?

In Safari, the due date selector was displaying 'NaN' when a date is selected, which was being returned by `Date.parse`. Because `Date.parse` is implemented differently across browsers it's generally recommended to favor implicit Date parsing with the `Date` constructor. For more background on this, [see MDN on Date.parse](https://developer.mozilla.org/en/docs/Web/JavaScript/Reference/Global_Objects/Date/parse).

Also, the code for DueDateSelector was pretty messy, and its logic was very tightly coupled, so I refactored it. None of the basic logic changed, I just broke it up into smaller pieces and made it more OO.

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/22984

See merge request !6797
Signed-off-by: Rémy Coutable <remy@rymai.me>

Fix broken rspec in compare text

!6910 changed the filter text from "Filter by branch/tag" to "Filter by Git revision"

See merge request !6926

Fix 500 error when creating mileston from group page

Part of https://gitlab.com/gitlab-org/gitlab-ce/issues/23378

See merge request !6920

Fix broken Spinach tests caused by changes in !6550

!6550 added dropdowns for the branch "from" and "to" fields, but these Spinach tests were not updated accordingly.

Partial fix to #23378

See merge request !6910

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

Loads GFM once for per page

## What does this MR do?

Currently the GFM init code is included every time there is a GFM form on the page. This changes that & only includes in once if any number of GFM forms are on the page.

## What are the relevant issue numbers?

#22827

See merge request !6840
Signed-off-by: Rémy Coutable <remy@rymai.me>

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

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

Fix JS bug with select2 because of missing `data-field` attribute in select box.

Fixes #23193

See merge request !6812
Signed-off-by: Rémy Coutable <remy@rymai.me>

Prevent flash alert text from being obscured when container is fluid

Fixes [a regression](https://gitlab.com/gitlab-org/gitlab-ce/commit/a2af7790) that causes the text within server-initiated flash *alerts* (not flash *notices*) to be obscured when `.container-fluid` is applied. It was reported in relation to a cherry-picking flash alert, but the problem occurs with all server-initiated flash alerts contained by a fluid container.

Note that as part of this fix, I combined some duplicate code and removed `.flash-text` & `.content-wrapper` selectors as they didn't seem to be necessary.

I manually tested JS-initiated Flash alerts to make sure this doesn't affect their appearance. I also grepped around for anything else that might depend on these styles. Everything checked out. But... can *you* see something this is going to break?

Affected users can't read flash alerts.

https://gitlab.com/gitlab-org/gitlab-ce/issues/22915

See merge request !6694
Signed-off-by: Rémy Coutable <remy@rymai.me>

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

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).

Make sure backward compatibility isn't broken for source installs.

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.

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

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

See merge request !6659
Signed-off-by: Rémy Coutable <remy@rymai.me>

Fixes long commit messages overflow viewport in file tree

## What does this MR do?
Fixes long commit messages breaking the table.
It adds back a max-width in `pixels` instead of `%`.

## Are there points in the code the reviewer needs to double check?
No.
## Why was this MR needed?
To fix the overflow of the commit message

## Screenshots (if relevant)
![max_width](/uploads/73af2ffbab29bf6e9bbd9287e9e142a0/max_width.png)

## 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
  - [ ] 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)
- [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?

Fixes #22544

See merge request !6573
Signed-off-by: Rémy Coutable <remy@rymai.me>

Prevent running GfmAutocomplete setup for each diff note

## What does this MR do?

Debounces GfmAutoComplete.setup.

## Why was this MR needed?

See https://gitlab.com/gitlab-org/gitlab-ce/issues/22704

Major lag on MR screens with many diff notes.

## 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
- Tests
  - [ ] 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 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-ce/issues/22704

See merge request !6569
Signed-off-by: Rémy Coutable <remy@rymai.me>

[ci skip]

[ci skip]

Add CHANGELOG entry for 8.12.6



See merge request !6816

Fix #23230: Update mailroom to 0.8.1 in Gemfile.lock

## What does this MR do?

Update mailroom to 0.8.1 in Gemfile.lock

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

## Why was this MR needed?
8.12.5 introduced a bug which put 2 different versions of mail_room in Gemfile.lock, probably due to a merge error.

## 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 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?
#23230 

Closes #23230

See merge request !6814

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

API: Share projects only with groups current_user can access

Aims to address the issues here: https://gitlab.com/gitlab-org/gitlab-ce/issues/23004

* Projects can be shared with non-existent groups
* Projects can be shared with groups that the current user does not have access to read

Concerns:

The new implementation of the API endpoint allows projects to be shared with a larger range of groups than can be done via the web UI.

The form for sharing a project with a group uses the following API endpoint to index the available groups: https://gitlab.com/gitlab-org/gitlab-ce/blob/494269fc92f61098ee6bd635a0426129ce2c5456/lib/api/groups.rb#L17. The groups indexed in the web form will only be those groups that the user is currently a member of.

The new implementation allows projects to be shared with any group that the authenticated user has access to view. This widens the range of groups to those that are public and internal.

See merge request !2005
Signed-off-by: Rémy Coutable <remy@rymai.me>

Don't send Private-Token headers to Sentry

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/22537

This bumps 'raven' (the Ruby gem we use to send errors to Sentry) to
version 2.0.2. We need 2.0.0 or newer to be able to sanitize HTTP
headers.

See merge request !2004
Signed-off-by: Rémy Coutable <remy@rymai.me>

Add a new gitlab:users:clear_all_authentication_tokens task

## What are the relevant issue numbers?

Part of #22537.

See merge request !6745
Signed-off-by: Rémy Coutable <remy@rymai.me>

Update mail_room gem

## What does this MR do?

Upgrades the mail_room gem from 0.8.0 to 0.8.1.

## Why was this MR needed?

mail_room throws an exception if the watching script joins a undefined thread. Release 0.8.1 adds a check to ensure that the thread exists before calling join.

Fixes gitlab-org/omnibus-gitlab#1619.

See merge request !6714
Signed-off-by: Rémy Coutable <remy@rymai.me>

Improve issue load time performance by avoiding ORDER BY in find_by call

See merge request !6724
Signed-off-by: Rémy Coutable <remy@rymai.me>

Resolve "NameError: undefined local variable or method `request' for #<Grape::Middleware::Error:0x007fc990..."

## What does this MR do?

Switches from `request` to `env` in an API helper method as the helpers are included in contexts lacking `request`.

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

I couldn't build a reproducer for this.

Closes #22820

See merge request !6615
Signed-off-by: Rémy Coutable <remy@rymai.me>