In general, site-wide customizations are achieved by updating:
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The site configuration themeconfig.json file (your customized version of the siteconfig.json file). This controls which sections of the site pages are visible, such as the Resources and Disqus widgets, and how some of them operate. For detailed information on this file, see: Customize the Magellan site configuration.
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The application CSS file that controls aspects of a site: themestyles.css files, which is a customized version of the mainstyles.css file. For details on the CSS files to change, see: Change Magellan CSS files
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The application CSS file that controls site content: contentstyles.css. Definitions for all the styles used in Author-it are included in this file. Any specific customizations to these styles and topic content, images, links should be included in this CSS file.