You can open Ortelius from the command line or from other applications and add the following arguments:

/folder:C\:flash\myprojet\
The project folder where the actionscript classes are placed.

/destination:C\:flash\mydoc
The folder where the documentation file are placed. If theres allready a project in the folder it opens this project and add the additional classes from the project.

/name:C\:flash\myprojet\mydoc
The name of the project