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

Add bottom margin for flash container on login page
Signed-off-by: Dmitriy Zaporozhets <dmitriy.zaporozhets@gmail.com>

cc @jschatz1 @skyruler 

Fixes #13935 

See merge request !3040

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

Replace Gollum `[[_TOC_]]` tag with result of TableOfContentsFilter

Closes #2494

See merge request !2952

Only validate avatar cropping values when avatar is present AND changed

Closes #13905

See merge request !3018

Properly check for a pre-existing error in `User#namespace_uniq`

Rails adds an empty error to the Errors object even if you just call
`#[]` on it:

```
[1] pry(main)> u = User.last
[2] pry(main)> u.errors.keys
=> []
[3] pry(main)> u.errors[:username].present?
=> false
[4] pry(main)> u.errors.keys
=> [:username]
```

See merge request !3017

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

Precompile assets before all spinach tests

Try to fix failing tests.

cc @jschatz1 

See merge request !3041

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

Changed # to ! on merge requests on activity view

Closes #9082

![Screen_Shot_2016-02-23_at_11.59.55](/uploads/87b859ae63282ae24025168404beb158/Screen_Shot_2016-02-23_at_11.59.55.png)

See merge request !2938

Batch size >1000 does not pay off

We did a small experiment to see how a full scan of the Redis keys on
gitlab.com speeds up as we increase the batch size. The values on the
right are time in seconds for a full scan (no delete operations).

```
count: 10);      284.500529021
count: 100);      86.21216934
count: 1_000);    60.931676195
count: 10_000);   60.96355610
count: 100_000);  62.378172541
```

It looks like 1,000 is a good number.

See merge request !2970

Explain why we mangle blob content types

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/9079

See merge request !2956

Closes #9082

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 !3019

Brings back missing "Gitlab" text on the logo

Closes #13851 

See merge request !2989

include contributions from forked projects on profile calendar

Shows contributions from forked projects in the calendar

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/3612

See merge request !2918

Add commit message to slack script

Ass suggested by @rdavila, this adds the current commit message as of HEAD to the slack script.

See merge request !3027

Add link to triggers doc in variables section

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/13901

See merge request !3025

[ci skip]

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

Closes #13905

Rails adds an empty error to the Errors object even if you just call
`#[]` on it:

```
[1] pry(main)> u = User.last
[2] pry(main)> u.errors.keys
=> []
[3] pry(main)> u.errors[:username].present?
=> false
[4] pry(main)> u.errors.keys
=> [:username]
```

Fixes padding loss after editing a diff comment

Also applies .timeago() to comment datetimes when diff page is entered directly.

Also fixes the vertical position of the comment count icon.

See merge request !3012

initializers are not loaded during the rake task assets:precompile,
so assets generation runs without relative url configuration in Rails
and produces broken assets.

in order to have it the same way like in omnibus

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.

Prior, if the user enabled 2FA, then disabled it and came back some time
after the grace period expired, they would be forced to enable 2FA
immediately.

Revert "Merge branch 'issue_5854' into 'master'"

This reverts merge request !2992

cc @rdavila 

See merge request !3013

Fix for project paths ending in .wiki

This prevents `Git operation was rejected by pre-receive hook` when
an actual project ending with .wiki is thought to be a wiki by the
`Internal` API.

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/13742

See merge request !2960

This reverts merge request !2992

Add commit message to JIRA's notification payload.

Closes #5854 

See merge request !2992