The Orbiter configuration user manual pdf is the OrbiterConfig.pdf file found in the Doc folder, gattispilot.
But as to the main question (if I interpret correctly), if you're looking for a vessel that uses every feature available in a configuration file, you'll rarely find it. Main reason being is that if you have a vessel so complex that it uses all features, you probably want to use a different tool to get even more additional features. Examples are Spacecraft4, GenericVessel, Multistage2015, programming in LUA, programming in C++, vesselbuilder, etc.
But of the vessels included in stock Orbiter, the Carina probe (Config\Vessels\Carina.cfg) is probably your best bet.
And as the config parameters are so simple, many definitions are very similar. For example, the attachment definition is very similar to the docking definition, so it should be pretty straightforward to do.