If you'r brave enough, you want to start your new file from scratch :

PuppetSoul will ask you for a path.

Then :

• Empty will create a full empty file. Nothing in it.
• 'Fill with common Monks' will create a file with the usual needed Monks for a usual rig :

As you can learn in the Monks section, the PUPinit and PUPclean are needed for a usual rig. Refer to this section to know why

The spine is just here to show you where to put your construction, Feel free to delete it.