I would suggest following this chronology:

• installation
• working locally
• working with others
• reference

Hence, the chapters would be:

• Introduction
• why pijul
• Installing
• Getting Started
  • Pijul identities
• working locally
  • channels
  • splitting and combining changes
  • conflicts
  • exchange patch between repositories (needed ???)
• working with others
  • creating a Nest account
  • upload public keys
  • create repository
  • contribute to a project
• Reference
• configuration

I would propose to drop the Theory (diff) chapter.