Note that this feature is not available in latest released pasdoc version, 0.10.0. You must download and compile pasdoc yourself or use DevelopmentSnapshots to use this feature.
Checkbox Store only relative paths in project file on PasDocGui:
If this is checked (the default), all paths (like Pascal units filenames, include files paths, output path, filenames of introduction and css files) are stored with relative paths inside *.pds file. This means that you can freely move your saved *.pds file within your filesystem and you can share this file with other developers (e.g. you can put it inside some CVS repository). You only should keep the relative paths valid – e.g. when you move your *.pds file, you want to move also the Pascal source files referenced inside this file.