See #1871

Signed-off-by: Dmitriy Zaporozhets <dmitriy.zaporozhets@gmail.com>

Partial fix #2202

Signed-off-by: Dmitriy Zaporozhets <dmitriy.zaporozhets@gmail.com>

Closes #2116
Closes https://github.com/gitlabhq/gitlabhq/issues/9502

Closes #1359

Closes #1804

HTML span elements only apply to a single line, and in the case of multi-line
comments, the highlighting was dropped as a result. Ensure that each line has
the proper styling to fix this.

Closes #1577

Closes https://github.com/gitlabhq/gitlabhq/issues/9500

Add gitlab-shell to error message to give user a clue that something may be wrong there.

Ran into this in #2082. User was told that repositories were created when they were
not due to hooks symlink being wrong.

- Updated CHANGELOG

Closes #745

Closes #1724

Steps to reproduce:
1. Create a project with a README
2. In the actual remote, type: `git symbolic-ref HEAD refs/heads/nowhere`
3. Check that HEAD is gone via `git ls-remote .`
4. Go to the projects page and see the Error 500

Closes https://github.com/gitlabhq/gitlabhq/issues/9484

Starting with migration `20150717130904` commit count is stored in the
database. For existing projects it defaults to `0` and is updated to the
correct value when commits are pushed.

The newly introduced rake task updates the commit count for all projects
which have not been updated yet.

Refs !986, !989, #2040.

On the first load, the merge request tabs would be requested in JSON format to render
the HTML. This would cause the "Reload with full diff" button to create a link to diff.json.

Closes #2041