If you do not have any modded files on your site you can upload the files from the upgrade package without a second glance, go to Admin Panel -> System Admin, click on Upgrade and hit the button. If you have some modded files on your site, then check if any of the files in the upgrade package corresponds with the modded files, port the modifications to the upgraded version and upload that one (a program like WinMerge is excellent for comparing files and porting code modifications). Then follwo the same upgrade procedure via the Admin Panel.
You do the same for the upgrade from 12 to 13.
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