Full Chapter Index

The full specification covers 48 chapters across 6900+ lines. Below is the complete chapter index with scope descriptions.

For access to the full specification, contact dev@rotifer.dev or file an issue in the rotifer-spec repository.

Core Architecture

#	Chapter	Scope
1	Problem Statement	Three systemic challenges
2	Design Principles	Three axioms + environment-independence
3	URAA Architecture	Five-layer stack (L0–L4)
4	Gene & Genome Standard	Phenotype, genome, controller genes, versioning
5	Fitness Model	F(g) + V(g) dual-metric, diversity factor
6	Agent Identity	Sovereign identity, key management
7	Core Mechanisms	Trust anchor, sandbox, hot-loading

Propagation & Competition

#	Chapter	Scope
8	Propagation Dynamics	Gene discovery, SIR propagation model
24	Evolutionary Dynamics	Population genetics, exploration budgets, seasonal resets
33	Arena Mechanism Design	Evolutionary game theory, incentive compatibility, anti-Sybil

Security & Trust

#	Chapter	Scope
9	Security Model	9 attack categories, defense matrix
10	Privacy Model	Selective disclosure, opaque gene calibration
28	Agent Identity & Keys	Identity/key separation, atomic key rotation, recovery
32	Agent Ethics & Accountability	Five-layer accountability chain, ethical boundaries
37	Regulatory Adapter Interface	Risk classification, compliance data export

Composition & Execution

#	Chapter	Scope
15	Gene Composition Algebra	4 core operators (Seq, Par, Cond, Try), gradual type system
34	Composition Algebra Safety	Semi-formal proofs — Progress, Preservation, Termination
42	Streaming Gene Model	Three-layer hybrid architecture for streaming
11	Rotifer IR	Cross-binding intermediate representation

Agent Lifecycle

#	Chapter	Scope
16	Agent Lifecycle	4-state core machine (INIT → ACTIVE → DORMANT → TERMINATED)
38	Agent Memory Model	Knowledge genes for structured memory, migration
46	Gene Lifecycle	6-state machine (Draft → Published → Active → Deprecated → Archived → Tombstoned)

Interoperability & Scale

#	Chapter	Scope
12	Binding Interface	Platform-agnostic RotiferBinding facade
25	Cross-Binding State Migration	Atomic three-phase migration protocol
41	Cross-Binding Arena Federation	Cross-platform competition
45	Cross-Binding Semantic Consistency	SemanticProfile 5-dimension declaration

Governance & Verification

#	Chapter	Scope
14	Protocol Governance	Self-evolving governance with PAP proposal standard
26	Formal Verification	Property classification, proof formats, verifier interface
43	Formal Protocol Model	TLA+/Alloy dual-language modeling, Lean 4 proofs
47	Gene Testing Framework	4-layer test pyramid (T1–T4), publishing gates

Multi-Agent & Communication

#	Chapter	Scope
22	Multi-Agent Coordination	Capability broadcast, cross-agent task protocol
48	Agent Communication Primitives	5 interaction modes

Additional Chapters

#	Chapter	Scope
13	Use Cases	Application scenarios
17	Observability	3-layer telemetry, time-travel replay
18	Gene Attribution & Lineage	Derivation tracking, lineage graph
19	Human-Agent Interaction	Override protocol, privileged entities
20	Conformance Testing	3-level compliance (Core/Standard/Full)
21	Protocol Profiles	Full/Constrained, binary phenotype
23	Contribution Metrics	Portable contribution proofs
27	Protocol Versioning	Semantic versioning, feature flags
29	Cross-Protocol Interop	ProtocolAdapter, trust degradation
30	Data Sovereignty	4-class data taxonomy, DataPolicy
31	Fault Tolerance	Layered fault tolerance, checkpoints
35	Protocol Bootstrap	Seed + culture genesis model
36	Agent Cognitive Accessibility	Layered explainability, audit mode
39	Emergent Behavior Detection	Observatory genes, 3 emergence categories
40	Performance Framework	Performance baselines, memory quotas
44	Scalability Analysis	Scalability contracts, 3-level cache

Glossary

Term	Definition
Gene	Atomic unit of agent capability — modular, transferable, fitness-evaluable
Phenotype	Structured metadata declaration describing a gene’s interface and properties
Genome	Ordered collection of genes assembled into an agent’s capability set
Arena	Competitive environment where genes in the same domain are ranked by fitness
Fitness F(g)	Continuous evaluation score combining performance, reliability, efficiency, adoption, composability, and diversity
Binding	Platform-specific implementation of the protocol (Cloud, Edge, TEE, Web3, etc.)
Rotifer IR	Environment-agnostic intermediate representation for cross-binding gene portability
Trust Anchor	L0 mechanism enforcing immutable security constraints — the only non-evolving component
HLT	Horizontal Logic Transfer — inter-agent gene sharing analogous to biological HGT
Synthesizer	Abstract interface for gene creation (LLM, template, rule-based, manual, or hybrid)
Observatory Gene	Special gene at L4 that monitors for emergent behaviors across agent populations