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→How to change the navigation
The navigation system is setup through a special type called an 'interface message'. (The interface message system is also used for many other aspects of the Mediawiki system.) This means that you don't actually have to change 'code' to affect the menu. You can simply edit a special page in the mediawiki system. Edits to this page get stored in the database like every other page edit which provides built-in versioning etc. However, it can also mean that pushing changes from a development machine to a server can be more challenging than pushing 'code' changes.
In any case, to change the nav, you will want to edit the '''MediaWiki:Sidebar''' page. (e.g. http://example.com/wiki/index.php/MediaWiki:Sidebar) The right to edit this page is normally restricted to administrators, so if you want to delegate the responsibility for this, you will want to look at the user permissions system. There are rules and conventions which apply here, and you can [[MediaWikimw:Manual:Navigation_bar | find more help in the documentation]]. In case you are going to change the location of blocks like the '''search''' box or '''toolbox''' (which normally show up in the sidebar) by making a custom theme, you'll want to coordinate those changes with the sidebar.
== How to make your own skin ==