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If you are using the shallow numbering CSS (this is the default), and you want to hide the "Chapter" prefix, use the following rules in your customization CSS:

For the TOC:

*[class ~= "map/topicmeta"] > *[class ~= "topic/navtitle"]:before {
    display:none !important; 

For the titles in the content, change the content of the title :before (this example just uses the chapter number):

*[class ~= "topic/topic"][is-chapter]:not([is-part]) > *[class ~= "topic/title"]:before {
    content: counter(chapter) ". " !important;