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"