Use relative links in `doc`, fix broken generated HTML links

Links like (doc/web_hooks/web_hooks.md) work in the GitLab source code
web interface, but the HTML generator produces broken links in the `doc`
subdirectories:
http://doc.gitlab.com/ce/hooks/doc/web_hooks/web_hooks.html
instead of the right one
http://doc.gitlab.com/ce/web_hooks/web_hooks.html
in
http://doc.gitlab.com/ce/hooks/custom_hooks.html.

Fixes #14338

[ci skip]
Signed-off-by: Anatoly Borodin <anatoly.borodin@gmail.com>

doc/hooks/custom_hooks.md

@@ -2,7 +2,7 @@
 
 **Note: Custom git hooks must be configured on the filesystem of the GitLab
 server. Only GitLab server administrators will be able to complete these tasks.
-Please explore [webhooks](doc/web_hooks/web_hooks.md) as an option if you do not have filesystem access. For a user configurable Git Hooks interface, please see [GitLab Enterprise Edition Git Hooks](http://doc.gitlab.com/ee/git_hooks/git_hooks.html).**
+Please explore [webhooks](../web_hooks/web_hooks.md) as an option if you do not have filesystem access. For a user configurable Git Hooks interface, please see [GitLab Enterprise Edition Git Hooks](http://doc.gitlab.com/ee/git_hooks/git_hooks.html).**
 
 Git natively supports hooks that are executed on different actions.
 Examples of server-side git hooks include pre-receive, post-receive, and update.

doc/release/security.md

@@ -15,7 +15,7 @@ Please report suspected security vulnerabilities in private to <support@gitlab.c
 1. Verify that the issue can be reproduced
 1. Acknowledge the issue to the researcher that disclosed it
 1. Inform the release manager that there needs to be a security release
-1. Do the steps from [patch release document](doc/release/patch.md), starting with "Create an issue on private GitLab development server"
+1. Do the steps from [patch release document](../release/patch.md), starting with "Create an issue on private GitLab development server"
 1. The MR with the security fix should get a 'security' label and be assigned to the release manager
 1. Build the package for GitLab.com and do a deploy
 1. Build the package for ci.gitLab.com and do a deploy

doc/security/two_factor_authentication.md

@@ -6,7 +6,7 @@ password to login, they'll be prompted for a code generated by an application on
 their phone.
 
 You can read more about it here:
-[Two-factor Authentication (2FA)](doc/profile/two_factor_authentication.md)
+[Two-factor Authentication (2FA)](../profile/two_factor_authentication.md)
 
 ## Enabling 2FA
 

doc/workflow/importing/import_projects_from_bitbucket.md

 # Import your project from Bitbucket to GitLab
 
-It takes just a few steps to import your existing Bitbucket projects to GitLab. But keep in mind that it is possible only if Bitbucket support is enabled on your GitLab instance. You can read more about Bitbucket support [here](doc/integration/bitbucket.md).
+It takes just a few steps to import your existing Bitbucket projects to GitLab. But keep in mind that it is possible only if Bitbucket support is enabled on your GitLab instance. You can read more about Bitbucket support [here](../../integration/bitbucket.md).
 
 * Sign in to GitLab.com and go to your dashboard
 

doc/workflow/protected_branches.md

@@ -12,7 +12,7 @@ A protected branch does three simple things:
 
 You can make any branch a protected branch. GitLab makes the master branch a protected branch by default.
 
-To protect a branch, user needs to have at least a Master permission level, see [permissions document](doc/permissions/permissions.md).
+To protect a branch, user needs to have at least a Master permission level, see [permissions document](../permissions/permissions.md).
 
 ![protected branches page](protected_branches/protected_branches1.png)