FPDoc can work with a project file. This is an XML file which can contain specifies global options, and which contains the definition for one or more packages, for which it lists input files and description files etc. The project file is described in more detail in chapter 4, page 108.
This option expects an argument, the name of the project file to use.
Example:
fpdoc --project=rtl-project.xml --format=html --package=rtl