Fix faulty deployment refs

In the 8.13 RC cycle, so before the release, there was a time in which
references in git where stored by id instead of iid. This could be fixed
by time, if the iid catches up with the id, it overwrites it. But in the
mean time we have wrong refs in the folder.

This commit fixes that. For all projects we have deployments we'll find
the ones where the ref has a higher number than the iid is now and calls
`#create_ref` on the corresponding deployment.

Fixes gitlab-com/infrastructure#683

cc @ayufan 

One worry: I tested this locally, couldn't find a way to do automate this.

See merge request !7352

Add logging for rack attack events

Patch for issue: https://gitlab.com/gitlab-org/gitlab-ce/issues/15612 and partial patch for https://gitlab.com/gitlab-com/support/issues/119.

Also related: https://gitlab.com/gitlab-org/gitlab-ce/issues/22527 

Adds logging for throttle and blacklist rack attack events to the production log.

@stanhu @MrChrisW

See merge request !7585

Fix typo in Build page JavaScript

## What does this MR do?

fixes #24614

See merge request !7563

Fix broken commit metadata loading for large repository trees

## What does this MR do?

Fixes a regression introduced in !7208 in which a call to `ajaxGet()` would fail when loading metadata for large repository trees.

This call produced no errors in the console because it is contained in a sort of `eval` block in jQuery.  This is an ugly, easily broken method for loading data asynchronously whose problems were exemplified by this issue.  I'm opening a separate issue (#24660) to alter this implementation.

## Why was this MR needed?

The failing AJAX call was causing metadata to stop loading, and the `timeago` functionality to stop running due to script failure.

## Screenshots (if relevant)

![Screen_Shot_2016-11-18_at_2.03.13_PM_copy](/uploads/ab0c11d5c405c01d8e45818b3ca96f23/Screen_Shot_2016-11-18_at_2.03.13_PM_copy.png)

## Does this MR meet the acceptance criteria?

- [ ] All builds are passing
- [ ] Branch has no merge conflicts with `master` (if it does - rebase it please)

## What are the relevant issue numbers?

Closes #24652

See merge request !7588

makes compare previous version link easily clickable

## What does this MR do?
This MR does a minor fix about `Compare previous link` which is not easily clickable when long commit list are expanded

## Are there points in the code the reviewer needs to double check?
NR
## Why was this MR needed?
For better UX and make browse easy

## Screenshots (if relevant)

**Before:**
![BrRs](/uploads/11e60ef150a9035ae94d6ed69c3038b5/BrRs.gif)

**After**
![2016-11-19_02.02.42](/uploads/961bac1ddcdc4338ac72bc690c52b7f1/2016-11-19_02.02.42.gif)

## Does this MR meet the acceptance criteria?

- [ ] [Changelog entry](https://docs.gitlab.com/ce/development/changelog.html) 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
  - [x] All builds are passing
- [ ] 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)

## What are the relevant issue numbers?


Closes #24658

See merge request !7587

Resolve "Margins look weird in Project page with pinned sidebar in project stats bar"

## What does this MR do?
Fixes the margins of the project buttons in small screens and when the sidebar is pinned.

Both top and left margin were not aligned with the rest of the page.

## Screenshots (if relevant)
![Screen_Shot_2016-11-18_at_16.39.01](/uploads/9213cbbfba5fd4a57716c09d1807d2ea/Screen_Shot_2016-11-18_at_16.39.01.png)
![margins](/uploads/86bfad4fb48e67224e8bc8f9b8e38520/margins.gif)

## Does this MR meet the acceptance criteria?

- [x] [Changelog entry](https://docs.gitlab.com/ce/development/changelog.html) 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 it does - 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 #24070

See merge request !7580

Fix focus state in preview tab

## What does this MR do?
Fixes the focus border in the preview tab by modifying the `line-height`, keeping the same height 🤸 

## Screenshots (if relevant)
![Screen_Shot_2016-11-18_at_18.35.36](/uploads/3ef96699194704f030cc8d2b5132226c/Screen_Shot_2016-11-18_at_18.35.36.png)

## Does this MR meet the acceptance criteria?

- [ ] [Changelog entry](https://docs.gitlab.com/ce/development/changelog.html) 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 it does - 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 #24641

See merge request !7581

Precalculate authorized projects in database

## What does this MR do?
It caches user's authorized projects in database instead of using multiple unions, which should simplify and speed-up things since this operation (getting authorized projects) is used a lot.

## Are there points in the code the reviewer needs to double check?
Did we miss a scenario where we need to refresh the list of projects?

## 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 [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)
- [x] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

## What are the relevant issue numbers?
#23150 

See merge request !6839

Adds MR ID to changelog entry

Removes changelog entry

Fixes after review

Closes #23150

Less intrusive system note

## What does this MR do?
This MR is for making system notes less intrusive by implementing proposed design
 
## Are there points in the code the reviewer needs to double check?
System notes are reusing in issues, commits and MR discussions. May need to double check to make sure that the design is not breaking anywhere

## Why was this MR needed?
This merge request solve issue #19797 

## Screenshots (if relevant)
**Before:**
![merge-request-before](/uploads/91953598087a613078d80333a43815a7/merge-request-before.png)
**After**
![2016-11-15_17.41.46](/uploads/c809ba53cc34ee83bb439ed741dc39f3/2016-11-15_17.41.46.gif)

## 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)
- [ ] API support added
- 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)
- [x] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

## What are the relevant issue numbers?
#19797, #23129

See merge request !6755

Slash command for mattermost

Closes  #22540

## Does this MR meet the acceptance criteria?

- [x] [Changelog entry](https://docs.gitlab.com/ce/development/changelog.html) added
- [ ] [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)


See merge request !7438

Use `Gitlab.config.gitlab.host` over `'localhost'`

Use `Gitlab.config.gitlab.host` over `'localhost'`

This would fix long standing failures running tests on
my development machine, which set `Gitlab.config.gitlab.host`
to another host because it's not my local computer. Now I
finally cannot withstand it and decided to fix them once and
for all.

See merge request !7562

Improved Ruby code in autocomplete user search

## What does this MR do?

Improves the Ruby code for finding users in the assignee dropdown based on the Ruby review.

See merge request !7576

Improve consistency of empty todo list messages

- They all now end with punctuation
- Not everyone enjoys, or can even drink, coffee
- The "High five!" message had no context for why we were high-fiving
- "Henceforth" is one word

[ci skip]

See merge request !7572

add parsing support for incoming html email

## What does this MR do?
Fixes #18388 by adding support for parsing HTML email

## Are there points in the code the reviewer needs to double check?
The new class, Gitlab::Email::HTMLParser, which needs to translate the HTML content to text and also delete replies, as they are not necessarily in the correct format to be caught by EmailReplyParser. The solution I found that should work for any HTML-formatted email is to remove all `<table>` and `<blockquote>` tags. Actual `<table>` elements (to be interpreted by markdown) should already be encoded with e.g. `&lt;table&gt;` - the only failure mode is if there is an *actual* HTML table in the content itself, which we wouldn't be able to support easily anyways.

The gem `html2text` traverses the HTML tree and outputs text - and markdown in the case of HTML links or images.

See merge request !7397

Resolve "spec/lib/gitlab/backend/shell_spec.rb causes other specs to fail"

## What does this MR do?

It ensures we rely on `Gitlab::Shell`'s public API and not on its internal. Since `Gitlab::Shell` is caching the value of its token, the only way to get the correct token is to call `Gitlab::Shell.secret_token`, not to read the `Gitlab.config.gitlab_shell.secret_file` file!

Fixes #24599

See merge request !7557

Adds changelog entry

Fix margins with pinned sidebar

Fix scss linter errors

Adds MR ID to changelog entry

Document how to prevent artifacts from passing to next stage

See merge request !7575

[ci skip]

Remove title from skipped status svg

Closes #24617

See merge request !7570

Add CI example for Play/Scala apps with deployment to Heroku

Replaces https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/3204

See merge request !7574

[ci skip]

Add environment info to builds page

![Screen_Shot_2016-11-02_at_5.44.01_PM](/uploads/3443d9518997147d1e6f41830e3774ff/Screen_Shot_2016-11-02_at_5.44.01_PM.png)

Closes #23205

See merge request !7251

Pass correct tag target to post-receive hook when creating tag via UI

Fixes #24437

See merge request !7556

- They all now end with punctuation
- Not everyone enjoys, or can even drink, coffee
- The "High five!" message had no context for why we were high-fiving
- "Henceforth" is one word

[ci skip]

In the 8.13 RC cycle, so before the release, there was a time in which
references in git where stored by id instead of iid. This could be fixed
by time, if the iid catches up with the id, it overwrites it. But in the
mean time we have wrong refs in the folder.

This commit fixes that. For all projects we have deployments we'll find
the ones where the ref has a higher number than the iid is now and calls
`#create_ref` on the corresponding deployment.

Fix migration missing ignored transaction method

Adds missing `disable_ddl_transaction!` to migration

See merge request !7569

Add JIRA remotelinks and prevent duplicated closing messages

implements #13232  
closes #20479   

See merge request !7413

Fix misaligned buttons on admin builds page

## What does this MR do?
Fix misaligned buttons on admin builds page

## Are there points in the code the reviewer needs to double check?
No

## Why was this MR needed?
Because buttons are misaligned.

## Screenshots (if relevant)
![fix-admin-ci-table](/uploads/49472f7a12f868556e1bf482c9f837c4/fix-admin-ci-table.gif)

## Does this MR meet the acceptance criteria?

- [x] [Changelog entry](https://docs.gitlab.com/ce/development/changelog.html) 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 it does - 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 #24371

See merge request !7424