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To convert PDF files to HTML5 from the command line, ensure that Java is installed on your machine along with the required Java build file (jar). Start by organizing your PDF files in one folder and create an empty folder for the HTML output. Open the command line, then type: `java -jar` followed by dragging and dropping the jar file, then the folder containing the PDFs, and finally the empty output folder. This process converts the PDFs, generating HTML files in the output folder. You can view the converted files in a browser using a fully featured viewer that supports page loading, zooming, and layouts, or you can examine individual pages to create a custom solution.