Ensure we don't show TODOS for projects pending delete

Joins the todos on the projects table in order to run the default scope. Also includes a where clause because the default scope is being removed soon.

An alternative approach, more like the Issues page, would be to filter down the list by passing user.authorized_projects into the where clause.

Or we could just be more defensive in the view when iterating.

Todos page throws 500 error for users with todos in a project pending deletion.

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/17813

cc\ @stanhu

See merge request !4300

[ci skip]

Fix 2FA-based login for LDAP users

The OTP input form is shared by both LDAP and standard logins, but when
coming from an LDAP-based form, the form parameters aren't nested in a
Hash based on the `resource_name` value.

Now we check for a nested `remember_me` parameter and use that if it
exists, or fall back to the non-nested parameters if it doesn't.

Somewhat confusingly, the OTP input form _does_ nest parameters under
the `resource_name`, regardless of what type of login we're coming from,
so that allows everything else to work as normal.

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/18185

See merge request !4493

Fixes missing number on generated ordered list

Closes #18102

See merge request !4437

Fix serious performance bug with rendering Markdown with InlineDiffFilter

Nokogiri's `node.replace` was being unnecessarily called for every text node in
the document due to a comparison bug. The code previously was comparing the
HTML representation of the full document against the text node, which would
always fail. Fix the comparison to just compare the modified text.

Closes #18011

See merge request !4392

Confidential notes data leak

Fixes part of https://gitlab.com/gitlab-org/gitlab-ee/issues/575

See merge request !1967

Fix wiki project clone address error

_Note: Originally opened at !4407 by @chujinjin._

---

fix wiki project clone address error in Wiki Git Access View, show as below:

![image](/uploads/5e3bf6d1418c42862a885319c31bc3cf/image.png)

Fixes #17643.

See merge request !4429

Use downcased path to container repository as this is expected path by Docker

Docker Engine requires path to be lowercase. This makes all container registry paths to be show and used downcased instead of mixed case.

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/17959

See merge request !4420

Use project that belongs to pipeline in view

This MR makes project in pipelines view match the one that pipeline has been created for.

Closes #17943

See merge request !4376

Pass the "Remember me" value to the 2FA token form

Prior, if a user had 2FA enabled and checked the "Remember me" field,
the setting was ignored because the OTP input was on a new form and the
value was never passed.

Closes #18000

See merge request !4369

Add Application Setting to configure Container Registry token expire delay (default 5min)

This adds an option to configure Container Registry token expire delay. The default is set to 5mins (something that is also used by Docker Hub).

What is left:
* [x] Write test to check the expire_delay

Fixes: https://gitlab.com/gitlab-org/gitlab-ce/issues/17890

@stanhu I think that this should land in patch release of 8.8.

See merge request !4364

Merge branch 'make-container-registry-authentication-service-compatible-with-older-docker' into 'master'

Make authentication service for Container Registry to be compatible with < Docker 1.11

This removes the usage of `offline_token` which is only present when using `Docker 1.11.x` instead we relay on `scope`. This should make it compatible with any client starting from 1.6 (I did test only 1.8 and up).

Right now we return 403 if unauthorized user doesn't have access to anything. In all other cases we return token, but with empty `access`, which simply disallow requested action.

See merge request !4363

Fix import URL migration error

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/17956

See merge request !4321

Fix 404 page when viewing TODOs that contain milestones or labels in different projects

A user viewing the TODOs page will see a 404 if there are mentioned milestones or labels in multiple different projects. This is likely a caching bug and only occurs
when Markdown rendering occurs across multiple projects, which is why it's so tricky to reproduce. This is what I think is happening:
    
1. LabelReferenceFilter#references_in encounters label ~X for ProjectA and finds the label in the DB as id = 1.
2. LabelReferenceFilter.references_in yields [1, 'X', nil, ...]
3. Since project_ref is nil, AbstractReferenceFilter#project_from_ref_cache caches nil => ProjectA.
4. LabelReferenceFilter#references_in encounters label ~Y for ProjectB and finds the label in the DB as id = 2.
5. LabelReferenceFilter.references_in yields [2, 'Y', nil, ...]
6. AbstractReferenceFilter#project_from_ref_cache lookups nil and returns ProjectA. It was supposed to be ProjectB.
7. A is the wrong project, so the label lookup fails.
   
This MR expands the `project_ref` to the right value as soon as we have it to avoid this caching bug.
    
Closes #17898


See merge request !4312

Ensure project name is present on page

## What does this MR do?
Fixes a failing spec




See merge request !4307

Fixed JS error when trying to remove discussion form

## What does this MR do?

Fixes a JS error which was caused by an ID of the form not matching what was returned by the JSON. Instead of checking that, it gets the current form from the ajax success event.

This would only happen on outdated discussions because the ID of the discussion form ends with `-false` because it isn't active. However, the note is added to an active discussion so the ID returned actually ends in `-true` & therefore the JS couldn't find the correct form.

## What are the relevant issue numbers?

Closes #17778

See merge request !4303

Fix gitlab importer issue

Fixed credentials not being called correctly - probably some bad refactoring or search & replace... 

Fixes https://gitlab.com/gitlab-org/gitlab-ee/issues/565

See merge request !4301

Fixed issue with button color when no CI enabled

## What does this MR do?

Fixes an issue with the color of the merge button when no CI is setup.

## What are the relevant issue numbers?

Closes #17844

## Screenshots

![Screen_Shot_2016-05-25_at_09.58.44](/uploads/87aac74c5e2f8bfd2831e99c5915856d/Screen_Shot_2016-05-25_at_09.58.44.png)

See merge request !4287

Move tags to column in generic_commit_status

Part of https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/4249    

cc @ayufan 



See merge request !4277

Improve design of Pipeline view

## What does this MR do?

Improves current design of Pipelines view when there is multiple stages.
This makes the statuses clickable and makes the view more compact.

## Screenshots (if relevant)

![Screen_Shot_2016-05-21_at_01.20.40](/uploads/dd031b7af7005c7a61f3165fefa8b7c9/Screen_Shot_2016-05-21_at_01.20.40.png)

cc @DouweM @markpundsack @rspeicher @marin 

See merge request !4230

Fixed potential issue with 2 ci status polling events happening

Possible cause for double notifications was if the request was slow & then you changed page whilst this request was happening it would finish on another page & then launch another interval - this stops that issue.

Also passed in the CI status as an option value rather than waiting for the first ajax request to finish

See merge request !3869

[ci skip]

Fix concurrent request when updating build log in browser

If you have a slow internet connection the trace will not be updated correctly. We need to check if our request is the latest one.

Fixes: https://gitlab.com/gitlab-org/gitlab-ce/issues/17535

See merge request !4183