Flush repository caches before renaming projects

This should hopefully solve gitlab-org/gitlab-ce#13790. Once I know the exact steps to reproduce the problem I should be able to confirm this.

cc @dblessing @inem

See merge request !2974

Add Todos documentation

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/13884

See merge request !3064

Don't show "Welcome to GitLab" when the search didn't return any projects

Fixes #13785. /cc @pixdrift

### Before

![Screen_Shot_2016-03-02_at_10.55.02](/uploads/b6b6ead2143d01e374ad296e72182d79/Screen_Shot_2016-03-02_at_10.55.02.png)

### After

![Screen_Shot_2016-03-02_at_12.12.33](/uploads/6e16c44e69039c534ea0fc3373c6060b/Screen_Shot_2016-03-02_at_12.12.33.png)

See merge request !3059

Tag deletion doesn't use AJAX anymore

See merge request !2986

Fix permissions for deprecated CI build status badge

This fixes permissions for deprecated status badge, being unavailable even if project is public.

Closes #13324

See merge request !3030

Show days remaining instead of elapsed time for Milestone.

Closes #13623

See merge request !2978

Fix import from gitlab.com fails

_Originally opened at !2896 by @kazsw._

- - -

Fixes #12652

CGI.escape encodes '/' by default.
Second argument can be removed.

See merge request !2988

Fix help keyboard shortcut for relative URL setups

Fixes gitlab-org/gitlab-ce#12751

See merge request !3016

Fix relative URL

See https://github.com/gitlabhq/gitlabhq/issues/10053

 1. Same configuration way for relative URL like with Omnibus
 2. Loading the relative configuration from Rakefile as Rails do not load initializers for `asset:precompile`

First point has another positive side effect: no collisions (due to git controlled `application.rb`) any more during the upgrades of source based installations and relative url configuration

 - [x] tests on the source based installation
 - [x] tests on the centos&ubuntu omnibus packages

Fixes: gitlab-org/gitlab-ce#13730, gitlab-org/gitlab-ce#13727, gitlab-org/omnibus-gitlab#1143 and https://github.com/gitlabhq/gitlabhq/issues/10053

See merge request !2979

Fix issue with overlap of sidebar links.

Thanks @iamphill for the help with this one. 

![Screen_Shot_2016-03-01_at_10.19.52_AM](/uploads/f203fde79ae397ad18f23c4108f1c306/Screen_Shot_2016-03-01_at_10.19.52_AM.png)

cc @iamphill @alfredo1 @dzaporozhets @rymai 

See merge request !3043

Don't show any "2FA required" message if it's not actually required

Prior, if the user had enabled and then disabled 2FA, they would be
shown a "You must enable Two-factor Authentication for your account."
message when going back to re-activate it, even if 2FA enforcement was
disabled.

See merge request !3014

Improve implementation to check read access to forks and add pagination.

Fixes #13648

The following optimizations where made:

- Pagination was added.
- Code to check for read permissions to forks was optimized, in the past we were doing too many queries for each project.

See merge request !2991

Don't repeat labels listed on Labels tab.

Fixes #13622

See merge request !2924

Brings back missing "Gitlab" text on the logo

Closes #13851 

See merge request !2989

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

For !2927 

See merge request !3011

Branded appearance to CE

Closes #11489

The difference with the EE version is only that there is no distinction between light and dark logos, though this wasn't used anyway. If this is fine, I'll create a MR on EE too.

TODO:
- [x] Copy docs
- [x] Make new screenshots
- [ ] Remove Custom Welcome message feature?

@rymai: I was unsure what labels to add to ping you, so I just ping you like this 😉

/cc @DouweM

See merge request !2927

Update Rails to 4.2.5.2

See https://groups.google.com/forum/#!msg/rubyonrails-security/ddY6HgqB2z4/we0RasMZIAAJ
and https://groups.google.com/forum/#!msg/rubyonrails-security/ly-IH-fxr_Q/WLoOhcMZIAAJ

See merge request !3020

See https://groups.google.com/forum/#!msg/rubyonrails-security/ddY6HgqB2z4/we0RasMZIAAJ
and https://groups.google.com/forum/#!msg/rubyonrails-security/ly-IH-fxr_Q/WLoOhcMZIAAJ

Created helper class to hide content in issue sidebar when collapsed

![Screen_Shot_2016-02-25_at_10.38.39](/uploads/ca49cc230edf7e71b7726e905f523092/Screen_Shot_2016-02-25_at_10.38.39.png)

Closes #13764

See merge request !2968

Fix order in Gemfile.lock

See merge request !2969

Does not create a Todo when commenting on commit or project snippet

Closes #13733

See merge request !2964

Move "I should see Crowd login form" feature to a view spec

We were doing all kinds of code gymnastics to "enable" Crowd in the
feature spec and this would sometimes cause a transient failure.

Really what it's testing is if the Crowd login form shows when Crowd's
enabled, so this is much better suited to a view spec.

See merge request !2963

Sidebar overlaps content when screen is below 1200px.

When screen is below 1200px, the sidebar overlaps.
When screen is above 1200px, the sidebar pushes content out.
z-index change to make sure hamburger stays on top.
Fixes #12717
![screensize](/uploads/9a21fa06d583a49d6ebbf1ada34c6792/screensize.gif)

![screensize-small](/uploads/7c25f46e962248a40840562a01c83f8f/screensize-small.gif)

Also sorry I couldn't get the collapse button in the screen cap. It's there.

See merge request !2620

Changed padding & background color for highlighted notes

Closes #12453

![Screen_Shot_2016-02-23_at_11.18.59](/uploads/19150d884fd1175fe0df5f6daee64206/Screen_Shot_2016-02-23_at_11.18.59.png)

See merge request !2937

Fixed revert button tooltip placement causing movement

Before:

![moving-tooltip](/uploads/65cb9a41e8b8114fd8ee10d68cfd8206/moving-tooltip.gif)

After:

![moving-tooltip](/uploads/a1c36eb5735dc7592c49f6b5cb1469b5/moving-tooltip.gif)

See merge request !2910

Fix group projects styles

Makes new project button visible when no projects are available.
Fixes #13193

![Screen_Shot_2016-02-04_at_1.08.27_PM](/uploads/36be9d5892506e7d1abcf4eb2a622e12/Screen_Shot_2016-02-04_at_1.08.27_PM.png)

![Screen_Shot_2016-02-04_at_1.07.48_PM](/uploads/fa257a1965017ff1274572dc66fccf90/Screen_Shot_2016-02-04_at_1.07.48_PM.png)

![Screen_Shot_2016-02-04_at_1.07.28_PM](/uploads/326f6fdac24b56e8408efd0d11dc2805/Screen_Shot_2016-02-04_at_1.07.28_PM.png)

cc @creamzy @skyruler

See merge request !2714

Fixed issue with content in the issue sidebar disappearing

Closes #13626

See merge request !2919

Revert "Remove newrelic gem. Closes #12860"

This reverts commit 53176717.

Conflicts:
	Gemfile.lock

See merge request !2943

Show Crowd login even when sign-in is disabled

Fixes #13176.

See merge request !2749

Does not raise an error when Todo  is already marked as done

Closes #13681

See merge request !2926

Update sentry-raven to 0.15.6

Fixes a few bugs, most notably (for our purposes): https://github.com/getsentry/raven-ruby/pull/450

See merge request !2947

Set of UI fixes

* Improve wiki pages
* Improve profile pages

cc @skyruler

See merge request !2758

Restrict permissions on public/uploads

Based on https://gitlab.com/gitlab-org/omnibus-gitlab/merge_requests/631

See merge request !2764

Issues can be dragged & dropped into empty milestone lists

This is also possible with MRs. Also fixed an issue where MRs weren't sortable

Fixes #13668

![milestone](/uploads/aada0f48ce8b1407cce920eef3f4d5f3/milestone.gif)

See merge request !2935