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Closes #1268
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Disable reference generation in preformatted/code blocks
### Summary
If a user adds text in code or preformatted text via Markdown or HTML that contains `#XXX`, the system adds a note that issue `XXX` was mentioned. This is particularly annoying because we often list gdb backtrace dumps into our issues, and many issues get mentioned as a result. For example:
```
(gdb) bt
#0 0x00000000004004c4 in second () at main.cc:6
#1 0x00000000004004d2 in first () at main.cc:11
#2 0x00000000004004dd in main () at main.cc:17
(gdb)
```
### Steps to reproduce
1. In an issue, write the above text using Markdown or HTML tags (e.g. `<code>`, `<pre>`).
2. Observe that [issue 1](https://gitlab.com/gitlab-org/gitlab-ce/issues/1) and [issue 2](https://gitlab.com/gitlab-org/gitlab-ce/issues/2) have a note that says they were mentioned.
### Expected behavior
Everything enclosed in the code blocks should be ignored as references.
### Observed behavior
Issues get referenced unnecessarily.
### Fix
I've made `reference_extractor.rb` strip out HTML and Markdown blocks before processing. I considered running the raw text through the entire Markdown processor, but this seems overkill and perhaps could lead to some unintended side effects.
See merge request !365
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Change permissions on backup files - #2
Use more restrictive permissions for backup tar files and for the db, uploads, and repositories directories inside the tar files. See #1894. Now the backup task recursively `chmod`s the `db/`, `uploads/`, and `repositories/` folders with 0700 permissions, and the tar file is created as 0600.
This is a followup to !1703, which was reverted because it broke Rspec tests. The test failures were due to the rake task changing directories and not changing back, which I fixed with this commit.
cc @sytse
See merge request !1716
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Use more restrictive permissions for backup tar files and for the db,
uploads, and repositories directories inside the tar files.
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This reverts commit 516bcabbf42d60db2ac989dce4c7187b2a1e5de9.
Conflicts:
Gemfile
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Fixed rake task gitlab:cleanup:block_removed_ldap_users
Maybe not the most elegant solution, but it works for us.
This closes issue gitlab-org/gitlab-ce#955.
See merge request !338
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Backup repo with tar instead of git bundle
Fixes gitlab/gitlab-ee#246
See merge request !1723
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Fewer Git constants, more Git helpers.
See merge request !1727
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Return `true` from `non_restricted_level?` when the
`restricted_visibility_levels` setting is nil.
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List new commits for newly pushed branch in activity view.
When someone pushes commits, I want to see them, regardless if it's a new or existing branch. If it's a new branch, we compare with the default branch (usually master).

See merge request !1711
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Fix invalid Atom feeds when using emoji, horizontal rules, or images
This is a fix for issues #880, #723, #1113.
Markdown must be rendered to XHTML, not HTML, when generating summary content for Atom feeds. Otherwise, content-less tags like *img* and *hr* are not terminated and make the Atom XML invalid. Such tags are generated when issue descriptions, merge request descriptions, comments, or commit messages use emoji, horizontal rules, or images.
To pass this option through from the relevant Haml templates to the proper place in the `gfm()` method, a new method `gfm_with_options()` is introduced. It reuses the options dictionary passed to `markdown()` and interprets options `xhtml` and `parse_tasks` from it (the latter was a convenient replacement for `gfm_with_tasks()`). `xhtml` is already interpreted by Redcarpet::Render::HTML, but that alone was not sufficient, because the post-processing in `gfm()` would convert its XHTML tags back to HTML.
I found no way of passing additional optional options to the existing `gfm()` method without requiring updates to existing callers and without getting in the way of the existing optional arguments, but maybe someone who knows more about Ruby than I can think of one.
Thorough review appreciated since this is the first time I have used Ruby.
See merge request !344
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Fixes issues #880, #723, #1113: Markdown must be rendered to XHTML, not HTML, when generating summary content for Atom feeds. Otherwise, content-less tags like <img> and <hr>, generated when issue descriptions, merge request descriptions, comments, or commit messages use emoji, horizontal rules, or images, are not terminated and make the Atom XML invalid.
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This reverts commit c42262b43b009af990e5769840391862d64a1c2d, reversing
changes made to c6586b1283a94c8f08bc669f4d8a9384b263073e.
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Change permissions on backup files
Use more restrictive permissions for backup tar files and for the db, uploads, and repositories directories inside the tar files. See #1894. Now the backup task recursively `chmod`s the `db/`, `uploads/`, and `repositories/` folders with 0700 permissions, and the tar file is created as 0600.
cc @sytse
See merge request !1703
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Use more restrictive permissions for backup tar files and for the db,
uploads, and repositories directories inside the tar files.
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Restricted visibility levels - bug fix and new feature
This allows admin users to override restricted visibility settings when creating and updating projects and snippets, and moves the restricted visibility configuration from gitlab.yml to the web UI. See #1903.
## Move configuration location
I added a new section to the application settings page for restricted visibility levels. Each level has a checkbox, styled with Bootstrap to look like a toggle button. A checked box means that the level is restricted. I added a glowing text shadow and changed the background color for checked buttons because the default styles made it hard to distinguish between checked and unchecked. This image shows the new section with the "Public" box checked:

## Allow admins to override
To allow admin users to override the restricted visibility levels, I had to remove the `visibility_level` validation from the `Project` class. The model doesn't know about the `current_user`, which should determine whether the restrictions can be overridden. We could use the creator in the validation, but that wouldn't work correctly for projects where a non-admin user is the creator and an admin tries to change the project to a restricted visibility level.
The `Project::UpdateService` and `Project::CreateService` classes already had code to determine whether the current user is allowed to use a given visibility level; now all visibility level validation is done in those classes. Currently, when a non-admin tries to create or update a project using a restricted level, these classes silently set the visibility level to the global default (create) or the project's existing value (update). I changed this behavior to be more like an Active Model validation, where using a restricted level causes the entire request to be rejected.
Project and personal snippets didn't have service classes, and restricted visibility levels weren't being enforced in the model or the controllers. The UI disabled radio buttons for restricted levels, but that wouldn't be difficult to circumvent. I created the `CreateSnippetService` and `UpdateSnippetService` classes to do the same restricted visibility check that the project classes do. And since I was dealing with snippet visibility levels, I updated the API endpoints for project snippets to allow users to set and update the visibility level.
## TODO
* [x] Add more tests for restricted visibility functionality
cc @sytse @dzaporozhets
See merge request !1655
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Conflicts:
db/schema.rb
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Bug fixes and new tests for the restricted visibility changes.
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Add new service classes to create and update project and personal
snippets. These classes are responsible for enforcing restricted
visibility settings for non-admin users.
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Allow admins to use restricted visibility levels when creating or
updating projects.
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Add checkboxes to the application settings page for restricted
visibility levels, and remove those settings from gitlab.yml.
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Unblock user if they were unblocked in AD.
Fixes problem with !1687.
See merge request !1694
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Execute hooks and services when branch or tag is created or deleted through web interface.
Fixes #2095.
Split up into commits to make it easier to see why what was changed :)
See merge request !1692
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Add blue theme to GitLab
See merge request !1682
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Allow smb:// links in Markdown text.
As requested by Sam McLeod at https://gitlab.com/gitlab-org/gitlab-ce/issues/1184
See merge request !1669
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Fix code preview theme setting for comments, issues, merge requests, and snippets
User color scheme was not being used: default white color scheme was always chosen. Also, default background for code in notes was always overriding the user color scheme.
Closes #1139
See merge request !357
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snippets.
Also preserve code preview color scheme in events dashboard.
Assign default colors to all code blocks shown as <pre class="code highlight [color_scheme]">
Closes #1139
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Generate valid json
This patch helps to be compatible to other programing languages as it improves the validation of hook data. It seems only ruby can handle 'nil' as value while other json decode function will fatal.
See merge request !182
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