How do I run the software directly from the jar?

You can run the PDF to HTML5 conversion program directly from the jar - for example if you wanted to use it from some other language or script.

To run it, use:

java -cp %jpedalDir%/jpedal.jar org/jpedal/examples/javafx/ExtractPagesAsJavaFX PDFFileORDirectory outputDir

PDFFileORDirectory is the location of the PDF files to convert, and outputDir is where to place the converted files. If a directory does not exist it will be created. You may also want to enable JAI and increase the memory used.

Here is my test example:

java -Xmx512M -Dorg.jpedal.jai=true -cp C:/jpedal.jar org/jpedal/examples/javafx/ExtractPagesAsJavaFX /Users/markee/PDFs/ /Users/markee/javafx/

How do I include the software in my Java code?

There is a documented Java PDF to HTML5 example written which is included in the jar.