Some intruduction
Use a unique name for each label in your subproject, for example '\section uppaalport_labelname Title'.
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As shown in this line, at this point -> Section Heading you can make references by using the \ref command.
Use the command \section and \subsection in your manual to make the layout of your manual. Do not use \mainpage or \page command.
You can put images into the manual with the \image command.