Thread:Project:Support desk/How to make no follow link to pages where user may see the page code?/reply (18)

As said on the manual page, overwriting old files is not recommended, as it can cause problems with old files remaining there that are not part of the new installation. This also reminds you to download new versions of your existing extensions.

The most convenient way is to install on a new folder, and then switch the published directory of the server to the new location. Uploads can also be put outside of the MediaWiki installation files so you don't need to move/copy them.