Fix creation of Ci::Commit object which can lead to pending, failed in some scenarios

## What does this MR do?

If we use a new `project.ci_commits` it will add it to array, and some other services which can do a save on a project can lead to a scenario when `ci_commit` will be saved, where it should not be.

## What are the relevant issue numbers?

https://gitlab.com/gitlab-com/support-forum/issues/717 https://gitlab.com/gitlab-com/support-forum/issues/715 https://gitlab.com/gitlab-org/gitlab-ce/issues/17596 https://gitlab.com/gitlab-com/support-forum/issues/714 https://gitlab.com/gitlab-org/gitlab-ce/issues/13402

cc @rymai 


See merge request !4214

Move generator templates to generator_templates/



See merge request !4217

Create a todo on failing MR build

Implements #14067. I worked on this with @DouweM (any mistakes are mine).

When a build fails for a commit, create a todo for the author of the merge request that commit is the HEAD of. If the commit isn't the HEAD commit of any MR, don't do anything. If there already is a todo for that user and MR, don't do anything.

Current limitations:
- This isn't configurable by project.
- The author of a merge request might not be the person who pushed the breaking commit.
- I haven't tested this with a working CI setup, just with the unit tests below and by modifying my DB directly.


See merge request !3177

Syntax-highlight diffs in push emails

![image](/uploads/8ecbabc65382214b8de63aae24f66cea/image.png)

Based on:
https://gitlab.com/gitlab-org/gitlab-ee/merge_requests/151



See merge request !4147

Update 'after_script' introduction note

Related to gitlab-org/gitlab-ci-multi-runner#1321

See merge request !4205

Add pipeline view

This is continuation of https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/3653

cc @DouweM @grzesiek 

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/17551
Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/15625


See merge request !3703

Removed outdated comment from migration helpers

[ci skip]

See merge request !4213

Since we eager load everything in lib/ putting ERB code in .rb files
will result in syntax errors. By moving the templates to
./generator_templates we can work around this.

Resolve "Wrong sorting of commit order in MR view?"

!4052 fixed this for the most obvious cases, but there were still some problems.

Here's my test case: I have a branch where I was suffering from an unfortunate
issue. Every other commit I made had its commit date set to one day before it
should have been. (Perhaps my system clock was misbehaving.)

```shell
for i in {1..10}
do
  echo $i > $i
  git add $i
  GIT_COMMITTER_DATE=`date -v -$((i % 2))d` git commit -m $i
done
```

The git CLI still gives me the commits in the right order, but I can see that
the timestamps alternate between two values:

```shell
$ git log --format='%h %ct %p %s' master...HEAD
f0c3108 1463646313 3d38a13 10
3d38a13 1463559913 67f419b 9
67f419b 1463646313 74330c0 8
74330c0 1463559913 56361d7 7
56361d7 1463646313 ba1b60c 6
ba1b60c 1463559913 f91497d 5
f91497d 1463646313 79c5e57 4
79c5e57 1463559913 b953cef 3
b953cef 1463646313 12fc411 2
12fc411 1463559913 835715b 1
```

Unfortunately, GitLab didn't like this _at all_. Here's what the commits on my
MR from that branch looked like:
![image](/uploads/fdc38e932eeedcb77de9ec4b50ad1476/image.png)

That's because we were sorting the commits by date, which is safe if they are in
that order anyway. If they aren't, then because Ruby's sorting isn't stable, we
lose even the ordering among the correctly-ordered commits with the same
timestamp.

After these changes (and reloading the MR's diff), this looks like:
![image](/uploads/b09fb0f51359c1c89484e713e859512b/image.png)

The commits view was also wrong, but in a slightly different way. In table form:

| View | Before | After |
| --- | --- | --- |
| Commit list | 10, 8, 6, 4, 2, 9, 7, 5, 3, 1 | 10, 9, 8, 7, 6, 5, 4, 3, 2, 1 |
| MR commits | 10, 2, 8, 4, 6, 5, 7, 3, 9, 1 | 10, 9, 8, 7, 6, 5, 4, 3, 2, 1 |

Closes #12724

See merge request !4208

Fixed project settings alert colors

In another MR, the class name was changed making all the alert messages have no background color

![Screen_Shot_2016-05-16_at_15.41.23](/uploads/58c9cb8016c4cdd0b7a02609554d3598/Screen_Shot_2016-05-16_at_15.41.23.png)![Screen_Shot_2016-05-16_at_15.41.15](/uploads/03e0a9f6d2b6c583cef79efbb3fc73cc/Screen_Shot_2016-05-16_at_15.41.15.png)![Screen_Shot_2016-05-16_at_15.41.31](/uploads/41481ab2a4069def0e44c4bb8784fbb3/Screen_Shot_2016-05-16_at_15.41.31.png)

See merge request !4161

Project variables UI

![Screen_Shot_2016-04-27_at_09.01.23](/uploads/cb9b1ac42aa734cfd3271c03dfaccc12/Screen_Shot_2016-04-27_at_09.01.23.png)

![Screen_Shot_2016-04-27_at_09.01.29](/uploads/4f317014d60f205a0e29497ad20f8a2e/Screen_Shot_2016-04-27_at_09.01.29.png)

Closes #14091

See merge request !3942

Replace animate.css with a smaller subset of animations.

As discussed in #15667. This saves ~50KB uncompressed.

cc: @jschatz1 

See merge request !3937

Fix broken documentation links

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/15249

- [x] `/help/ui`- This is working for me
- [x] `/help/ci/examples/deployment/README.md` - Fixed
- [x] `/help/ci/api/projects.md` - Fixed
- [x] `/help/markdown/LICENSE` - Cannot do much to fix it, added a note.
- [x] `/help/ci/ssh/README.md` - Cannot find this link referenced anywhere.

See merge request !3903

Fixed advice on invalid permissions on upload path

When running the checks, my upload path has wrong permissions, the advice could not fix it because it does not change the permission of this directory (only sub-directories).
```
Uploads directory setup correctly? ... no
  Try fixing it:
  sudo find /home/git/gitlab/public/uploads -type d -not -path /home/git/gitlab/public/uploads -exec chmod 0700 {} \;
  For more information see:
  doc/install/installation.md in section "GitLab"
  Please fix the error above and rerun the checks.
```

Executing this instead fixed the error :
```
sudo chmod 700 /home/git/gitlab/public/uploads
```

See merge request !2948

Added helper methods for database migrations

These helpers can ultimately be used to write migrations that don't
require downtime.

See #15464 for more information.

See merge request !3860

Fix warning messages with SVG ALLOWED_ELEMENTS

Define the right module names so that Rails autoloading and eager loading will work properly.

Eliminates "warning: already initialized constant Gitlab::Sanitizers::SVG::ALLOWED_ELEMENTS"

See merge request !4207

Changing the confidentiality of an issue now creates a new system note

Closes #15236.

See merge request !4189

Revert "Merge branch 'issues/15127' into 'master'"

This reverts merge request !3647


See merge request !4212

This reverts merge request !3647

It's possible to construct a commit graph where the output of `git log`
isn't in timestamp order. Grouping the commits in the list by date then
gives dramatically wrong results. Instead, go for the more pragmatic
approach: use the commits in the order they're given, and just show the
date line each time the date changes. This means that the same date
header can show up multiple times, but at least the ordering is
preserved.

Eliminates "warning: already initialized constant Gitlab::Sanitizers::SVG::ALLOWED_ELEMENTS"

fix #15127 ActiveJob::DeserializationError thrown

`send_devise_notification` pre-maturely enqueued the task when the user instance
has not yet been committed into the database, causing a record-not-found in the
other sidekiq process.

`devise-async` has already been taking care of asynchronous mail sending, we just
need to run it inside queue `mailers` instead of `mailer` to enable it.

The implementation of `devise-async` enqueues the task in `after_commit` hook
which is the right way to do it.

See merge request !3647

Mask credentials from URL when the import of project has failed.

REF: #17560 

See merge request !4185

Remove unused Project scopes

Closes #17635.

See merge request !4204

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

Fix changelog for 7.9.3

Closes #1484 

See merge request !4202

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

fix example urls for (dis)associating runners to projects



See merge request !2993

doc: fix git lfs workaround for using http instead of https

the url should only point to `info/lfs` instead of `info/lfs/batch/objects`

See merge request !2713