New doc site needs indexes.

doc/README.md

 ## The GitLab Documentation covers the following subjects
 
 + [API](api/README.md)
-+ [API](api/)
-+ [API](api)
-+ [API](/api/)
-+ [API](/api)
++ [Development](development/README.md)
++ [Install](install/README.md)
++ [Integration](external-issue-tracker/README.md)
++ [Legal](legal/README.md)
++ [Markdown](markdown/markdown.md)
++ [Permissions](permissions/permissions.md)
++ [Public access](public_access/public_access.md)
++ [Raketasks](raketasks/README.md)
++ [Release](release/README.md)
++ [Security](security/README.md)
++ [System hooks](system_hooks/system_hooks.md)
++ [Update](update/README.md)
++ [Web hooks](web_hooks/web_hooks.md)
++ [Workflow](workflow/workflow.md)

doc/development/README.md

++ [Architecture](architecture.md)
++ [Shell commands](shell_commands.md)

doc/install/README.md

++ [Installation](installation.md)
++ [Requirements](requirements.md)
++ [Structure](structure.md)
++ [Database MySQL](database_mysql.md)

doc/legal/README.md

++ [Corporate contributor license agreement](corporate_contributor_license_agreement.md)
++ [Individual contributor license agreement](individual_contributor_license_agreement.md)

doc/raketasks/README.md

++ [Backup restore](backup_restore.md)
++ [Cleanup](cleanup.md)
++ [Features](features.md)
++ [Maintenance](maintenance.md)
++ [User management](user_management.md)
++ [Web hooks](web_hooks.md)

doc/release/README.md

++ [Monthly](monthly.md)
++ [Security](security.md)

doc/security/README.md

++ [Password length limits](password_length_limits.md)
++ [Rack attack](rack_attack.md)

doc/update/README.md

++ [The indivual upgrade guides](https://gitlab.com/gitlab-org/gitlab-ce/tree/master/doc/update)
++ [Uprader](upgrader.md)
++ [Ruby](ruby.md)
++ [Patch versions](patch_versions.md)
++ [MySQL to Postgress](mysql_to_postgress.md)