mkdocs.yml

site_name: TNFR Python Engine
site_description: Canonical documentation for the TNFR Python Engine
site_url: https://fermga.github.io/TNFR-Python-Engine/
repo_url: https://github.com/fermga/TNFR-Python-Engine
repo_name: fermga/TNFR-Python-Engine
docs_dir: build/docs-source
site_dir: site
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  - Contributor and agent instructions: AGENTS.md
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# BEGIN GENERATED DOCS NAVIGATION
  - "Technical documentation":
      - "Documentation map": docs/README.md
      - "Usage guides":
          - "CLI and SDK": docs/CLI_AND_SDK.md
          - "Research evidence and frozen source restoration": docs/guides/RESEARCH_EVIDENCE.md
          - "Regional and relational SDK": docs/guides/REGIONAL_AND_RELATIONAL.md
          - "Native relational execution and observations": docs/guides/relational/RELATIONAL_EXECUTION.md
          - "Native relational capture, memory and continuous proofs": docs/guides/relational/RELATIONAL_CAPTURE_AND_MEMORY.md
          - "Shared observations, information and finite-sample bounds": docs/guides/relational/OBSERVATION_AND_INFORMATION.md
          - "Normalized-sine comparison, inference and forecasts": docs/guides/relational/SINE_COMPARISON_AND_INFERENCE.md
          - "Sine response, constitutive comparisons and hidden memory": docs/guides/relational/SINE_RESPONSE_AND_MEMORY.md
          - "Sine pattern geometry, formation and recovery": docs/guides/relational/SINE_PATTERNS.md
          - "Conservative sine saddle preparations and certificates": docs/guides/relational/SINE_SADDLE_CERTIFICATES.md
          - "Conservative sine regional and collective dynamics": docs/guides/relational/SINE_REGIONAL_DYNAMICS.md
          - "Retained sine pair state, identification and pulses": docs/guides/relational/SINE_PAIR_DYNAMICS.md
          - "Observational interfaces": docs/STRUCTURAL_INTERFACE_THEORY.md
          - "Optional Torch backend": docs/TORCH_BACKEND.md
      - "Contracts and diagnostics":
          - "API contracts": docs/API_CONTRACTS.md
          - "Relational dynamics": docs/contracts/RELATIONAL_DYNAMICS.md
          - "Native relational execution and observations": docs/contracts/relational/RELATIONAL_EXECUTION.md
          - "Native relational capture, memory and continuous proofs": docs/contracts/relational/RELATIONAL_CAPTURE_AND_MEMORY.md
          - "Shared observations, information and finite-sample bounds": docs/contracts/relational/OBSERVATION_AND_INFORMATION.md
          - "Normalized-sine comparison, inference and forecasts": docs/contracts/relational/SINE_COMPARISON_AND_INFERENCE.md
          - "Sine response, constitutive comparisons and hidden memory": docs/contracts/relational/SINE_RESPONSE_AND_MEMORY.md
          - "Sine pattern geometry, formation and recovery": docs/contracts/relational/SINE_PATTERNS.md
          - "Conservative sine saddle preparations and certificates": docs/contracts/relational/SINE_SADDLE_CERTIFICATES.md
          - "Conservative sine regional and collective dynamics": docs/contracts/relational/SINE_REGIONAL_DYNAMICS.md
          - "Retained sine pair state, identification and pulses": docs/contracts/relational/SINE_PAIR_DYNAMICS.md
          - "Operator events": docs/contracts/OPERATOR_EVENTS.md
          - "Structural fields": docs/STRUCTURAL_FIELDS_TETRAD.md
# END GENERATED DOCS NAVIGATION
# BEGIN GENERATED THEORY NAVIGATION
  - "Theory and research":
      - "Reading routes and implementation map": theory/README.md
      - "Research program":
          - "TNFR research program": theory/RESEARCH_PROGRAM.md
      - "State and laws":
          - "Conceptual core, dependencies and worked examples": theory/CONCEPTUAL_CORE.md
          - "Fundamental theory": theory/FUNDAMENTAL_THEORY.md
          - "Parameter foundations": theory/NODAL_PARAMETER_FOUNDATIONS.md
          - "Native C5 foundation account and dynamic capacity": theory/nodal/NATIVE_FOUNDATIONAL_ACCOUNT.md
          - "Relation foundations": theory/nodal/RELATION_FOUNDATIONS.md
          - "Pressure premises": theory/nodal/PRESSURE_CONSTITUTIVE_SCOPE.md
          - "Joint parameter response": theory/nodal/JOINT_PARAMETER_RESPONSE.md
          - "Glossary": theory/GLOSSARY.md
      - "Organized objects and retained identity":
          - "Emergence and ontology": theory/EMERGENT_ONTOLOGY.md
          - "Acquired native organization and regional response": theory/nodal/NATIVE_ACQUIRED_RESPONSE.md
          - "Scale, geometry and collective-state index": theory/TNFR_SCALE_GEOMETRY_AND_BRIDGE.md
          - "Resonance foundations": theory/nodal/RESONANCE_FOUNDATIONS.md
          - "Global pulse, emergence and resonance: hypothesis audit": theory/nodal/GLOBAL_PULSE_HYPOTHESIS.md
          - "Operators, autonomous occurrence and pulse closure": theory/nodal/OPERATOR_PULSE_CLOSURE.md
      - "Operators, grammar and support events":
          - "Structural operators": theory/STRUCTURAL_OPERATORS.md
          - "Unified grammar": theory/UNIFIED_GRAMMAR_RULES.md
          - "Diagnostic and grammar scope": theory/DIAGNOSTIC_AND_GRAMMAR_SCOPE.md
          - "Relational support events": theory/nodal/RELATIONAL_SUPPORT_EVENTS.md
      - "Diagnostics and geometry":
          - "Structural observation families and reconstruction": theory/MINIMAL_STRUCTURAL_DEGREES.md
          - "Coherence profiles and observation limits": theory/COHERENCE_OBSERVATION_FOUNDATIONS.md
          - "Structural conservation diagnostics": theory/STRUCTURAL_CONSERVATION_THEOREM.md
          - "Stability and dynamics diagnostics": theory/STRUCTURAL_STABILITY_AND_DYNAMICS.md
          - "Extended fields": theory/EXTENDED_FIELDS_AND_DERIVED_QUANTITIES.md
      - "Form, phase and coherent patterns":
          - "Inherited form dynamics": theory/nodal/INHERITED_FORM_DYNAMICS.md
          - "Phase-to-form exchange": theory/nodal/PHASE_FORM_EXCHANGE.md
          - "Primitive phase closure": theory/nodal/PRIMITIVE_PHASE_CLOSURE.md
          - "Derived form phase": theory/nodal/DERIVED_FORM_PHASE.md
          - "Relational law and chapter index": theory/nodal/RELATIONAL_EXCHANGE_ADMISSION.md
          - "Relational coefficient and capacity identification": theory/nodal/RELATIONAL_RESPONSE_IDENTIFICATION.md
          - "Sine law and constitutive information boundaries": theory/nodal/SINE_CONSTITUTIVE_INFORMATION.md
          - "Free relative-phase access between organized children": theory/nodal/ORGANIZED_FREE_PHASE_PROBE.md
          - "Reciprocal form-resource envelope": theory/nodal/RECIPROCAL_FORM_RESOURCE_ENVELOPE.md
          - "Information from a small phase preparation": theory/nodal/ORGANIZED_SMALL_RESOURCE_INFORMATION.md
      - "Native formation and composition":
          - "Native local recovery and regional interaction": theory/nodal/RELATIONAL_RECOVERY_AND_INTERACTION.md
          - "Native phase domains and capture": theory/nodal/RELATIONAL_DOMAIN_AND_CAPTURE.md
          - "Native validated transit and preparation controls": theory/nodal/RELATIONAL_FORMATION_CONTROLS.md
          - "Relational pattern composition": theory/nodal/RELATIONAL_PATTERN_COMPOSITION.md
          - "Effective mediated connections": theory/nodal/RELATIONAL_EFFECTIVE_CONNECTIONS.md
          - "Native formation and its obstructions": theory/nodal/RELATIONAL_NATIVE_FORMATION.md
      - "Formed sine classes and collective interfaces":
          - "Smooth-sine pattern dynamics": theory/nodal/SINE_PATTERN_DYNAMICS.md
          - "Repeated probes of formed sine classes": theory/nodal/SINE_FORMED_CLASS_MAINTENANCE.md
          - "Contact of actually formed sine classes": theory/nodal/SINE_FORMED_CLASS_CONTACT.md
          - "Reduced ports of formed sine classes": theory/nodal/SINE_REDUCED_CLASS_PORTS.md
          - "Network composition of reduced sine ports": theory/nodal/SINE_REDUCED_PORT_COMPOSITION.md
          - "Acquired mediator class and a transmitted form response": theory/nodal/SINE_CLASS_MEDIATED_RESPONSE.md
          - "Effective memory of an acquired sine-class mediator": theory/nodal/SINE_CLASS_MEDIATED_MEMORY.md
          - "Two-probe superposition on an acquired sine composite": theory/nodal/SINE_CLASS_NONLINEAR_SUPERPOSITION.md
          - "Finite separation of a nonlinear class-mediated response": theory/nodal/SINE_CLASS_NONLINEAR_PROTOCOL.md
          - "Organization dependence of nonlinear interaction": theory/nodal/SINE_CLASS_NONLINEAR_ORGANIZATION.md
          - "Complete cubic-amplitude mediator response": theory/nodal/SINE_CLASS_CUBIC_RESPONSE.md
          - "Spatial observation of nonlinear class interaction": theory/nodal/SINE_CLASS_SPATIAL_OBSERVATION.md
          - "Feasible amplitudes for class discrimination": theory/nodal/SINE_CLASS_AMPLITUDE_FEASIBILITY.md
          - "Independent full-law class comparison protocol": theory/nodal/SINE_CLASS_COMPARISON_PROTOCOL.md
          - "Repeated joined class interaction": theory/nodal/SINE_CLASS_REPEATED_INTERACTION.md
          - "Nonlinear collective interface": theory/nodal/SINE_CLASS_COLLECTIVE_INTERFACE.md
          - "Changed-input collective prediction": theory/nodal/SINE_CLASS_CHANGED_INPUT_PREDICTION.md
          - "Independent changed-input full-law protocol": theory/nodal/SINE_CLASS_COLLECTIVE_FORWARD_PROTOCOL.md
          - "Causal composition of acquired sine-class interfaces": theory/nodal/SINE_CLASS_INTERFACE_COMPOSITION.md
          - "Causal nonadditivity of distinct neighbor interventions": theory/nodal/SINE_CLASS_NEIGHBOR_NONADDITIVITY.md
          - "Independent distinct-neighbor protocol": theory/nodal/SINE_CLASS_NEIGHBOR_FORWARD_PROTOCOL.md
          - "Nonlinear excess storage and loss": theory/nodal/SINE_CLASS_STORAGE_EXCESS.md
          - "Uniform tracking of reduced sine ports": theory/nodal/SINE_PORT_RELAXATION.md
          - "Form tracking by ordered heat comparison": theory/nodal/SINE_PORT_FORM_TRACKING.md
      - "Conservative organization, pulses and memory":
          - "Exact and controlled form-phase reductions": theory/nodal/SINE_FORM_PHASE_REDUCTION.md
          - "Conservative regional formation and its barriers": theory/nodal/SINE_REGIONAL_FORMATION.md
          - "Collective phase families and live contact feedback": theory/nodal/SINE_COLLECTIVE_PHASE_DYNAMICS.md
          - "Canonical contact between maintained weighted stars": theory/nodal/SINE_WEIGHTED_STAR_CANONICAL_CONTACT.md
          - "Finite registration and collective identity after contact": theory/nodal/SINE_WEIGHTED_STAR_FINITE_IDENTITY.md
          - "Conservative source preparation and finite retention": theory/nodal/SINE_CONSERVATIVE_PREPARATION.md
          - "Native reduction and memory index": theory/nodal/RELATIONAL_PATTERN_MEMORY.md
          - "Native mediated pattern dynamics": theory/nodal/RELATIONAL_MEDIATOR_DYNAMICS.md
          - "Sine environmental state and causal memory": theory/nodal/SINE_ENVIRONMENTAL_MEMORY.md
          - "Return-path geometry and collective response": theory/nodal/RELATIONAL_RETURN_PATH_GEOMETRY.md
          - "Retained phase records and finite contact readout": theory/nodal/RELATIONAL_PHASE_MEMORY.md
          - "Sine relative state, recovery and conservative identity": theory/nodal/SINE_PATTERN_RECOVERY.md
      - "Transport, memory and clocks":
          - "EPI diffusion stability": theory/TNFR_DIFFUSION_STABILITY_THEOREM.md
          - "Directed nonnormal dynamics": theory/TNFR_DIRECTED_NONNORMAL_DYNAMICS.md
          - "Derived EPI memory": theory/DERIVED_EPI_MEMORY.md
          - "Capacity and localization": theory/CAPACITY_LOCALIZATION_BALANCE.md
          - "Cycle support dynamics": theory/CYCLE_SUPPORT_DYNAMICS.md
          - "Cycle memory relaxation": theory/CYCLE_MEMORY_RELAXATION.md
          - "Forced support balance": theory/FORCED_SUPPORT_BALANCE.md
          - "Forced regional response and environmental readouts": theory/nodal/FORCED_REGIONAL_RESPONSE.md
          - "Forced-source closure and phase clocks": theory/nodal/FORCED_SOURCE_AND_CLOCK.md
          - "Conditional phase locking and circulation geometry": theory/nodal/FORCED_PHASE_LOCKING.md
          - "Winding generation and native writer boundaries": theory/nodal/FORCED_WINDING_AND_WRITERS.md
          - "Geometric identity and capacity-feedback bounds": theory/nodal/FORCED_GEOMETRIC_IDENTITY.md
          - "REMESH fixed-delay models": theory/REMESH_INFINITY_DERIVATION.md
          - "Sufficient unordered pair state": theory/nodal/SINE_PAIR_STATE.md
          - "Internal replica pulses and their perturbations": theory/nodal/SINE_REPLICA_PULSE.md
          - "Collective prediction and temporal error allowances": theory/nodal/SINE_COLLECTIVE_PREDICTION.md
          - "Phase and joint form-phase grouping": theory/nodal/SINE_PAIR_GROUPING.md
          - "Pair geometry under alternative reciprocal mobility": theory/nodal/SINE_PAIR_MOBILITY.md
          - "Pair actions, regional exchange and cancellation": theory/nodal/SINE_PAIR_INTERACTION.md
          - "One admitted collective word": theory/nodal/SINE_PAIR_WORD.md
          - "Collective Resonance and internal geometry": theory/nodal/SINE_PAIR_RESONANCE.md
          - "Collective Coupling and support-law admission": theory/nodal/SINE_PAIR_COUPLING.md
          - "Actual contact between maintained organizations": theory/nodal/SINE_ORGANIZATION_CONTACT.md
          - "Stationary and energy geometry of the actual contact": theory/nodal/SINE_CONTACT_STATIONARY_GEOMETRY.md
          - "Phase-nearest UM contact, maintenance and finite exchange": theory/nodal/SINE_PROXIMITY_CONTACT.md
      - "Organized sources and parent dynamics":
          - "Constitutive freedom of organized patterns": theory/nodal/ORGANIZED_PATTERN_CONSTITUTIVE_FREEDOM.md
          - "Constitutive inheritance through organized interfaces": theory/nodal/ORGANIZED_PATTERN_CONSTITUTIVE_INHERITANCE.md
          - "Carried prediction through a reciprocal composite interaction": theory/nodal/ORGANIZED_COMPOSITE_RECIPROCITY.md
          - "Composite relaxation, effective interaction and marked-pair identity": theory/nodal/ORGANIZED_COMPOSITE_RELAXATION.md
          - "Regional contact transport and hidden-profile information": theory/nodal/ORGANIZED_REGIONAL_TRANSPORT.md
          - "Predictive repeated organized composition": theory/nodal/REPEATED_ORGANIZED_COMPOSITION.md
          - "Parent registration acquired from organized children": theory/nodal/ORGANIZED_PARENT_ACQUISITION.md
          - "Restoring response of an acquired organized parent": theory/nodal/ORGANIZED_PARENT_RESTORING_RESPONSE.md
          - "Continuous form actuation of the acquired-parent phase event": theory/nodal/ORGANIZED_PARENT_CONTINUOUS_ACTUATION.md
          - "Constructive continuous realization of the acquired-parent phase event": theory/nodal/ORGANIZED_PARENT_CONSTRUCTIVE_ACTUATION.md
          - "Collective actuation with unresolved fine state": theory/nodal/ORGANIZED_PARENT_COLLECTIVE_ACTUATION.md
          - "Autonomous exchange with a finite auxiliary reservoir": theory/nodal/ORGANIZED_PARENT_RESERVOIR_EXCHANGE.md
          - "Retained reservoir information and local organized equilibria": theory/nodal/ORGANIZED_PARENT_RESERVOIR_MEMORY.md
          - "Complete port inherited from an organized C9 source": theory/nodal/ORGANIZED_SOURCE_PORT.md
          - "State-guard sensitivity of the organized word": theory/nodal/ORGANIZED_SOURCE_GUARD_SENSITIVITY.md
          - "Sufficient hybrid state on the organized child-swap sector": theory/nodal/ORGANIZED_SOURCE_CHILD_QUOTIENT.md
          - "Exact organized-source state modulo a global child exchange": theory/nodal/ORGANIZED_SOURCE_CHILD_ORBIT.md
          - "Full-state capture and collective registration of the organized source": theory/nodal/ORGANIZED_SOURCE_CAPTURE.md
      - "Collective winding and contact response":
          - "Acquisition of an outer winding by five acquired C9 organizations": theory/nodal/ORGANIZED_OUTER_WINDING.md
          - "Alternative-law outer acquisition": theory/nodal/ORGANIZED_ALTERNATIVE_OUTER_ACQUISITION.md
          - "Alternative-law finite interaction": theory/nodal/ORGANIZED_ALTERNATIVE_CONTACT.md
          - "Dynamical cancellation on ideal organized contact": theory/nodal/ORGANIZED_CONTACT_DYNAMIC_CANCELLATION.md
          - "Fine preparation and hidden contact response": theory/nodal/ORGANIZED_CONTACT_PREPARATION_SENSITIVITY.md
          - "Finite probe response of the acquired outer organization": theory/nodal/ORGANIZED_OUTER_RESPONSE.md
          - "Observing outer winding with unknown child phase origins": theory/nodal/ORGANIZED_OUTER_OBSERVATION.md
          - "Observing outer winding on one continuing organization": theory/nodal/ORGANIZED_SEQUENTIAL_OBSERVATION.md
          - "External interaction of an acquired collective organization": theory/nodal/ORGANIZED_EXTERNAL_INTERACTION.md
          - "Finite interaction across relative phase origins": theory/nodal/ORGANIZED_EXTERNAL_REGISTRATION.md
          - "Joint preparation resources for finite interaction": theory/nodal/ORGANIZED_JOINT_RESOURCES.md
      - "Organized observation and predictive information":
          - "Finite coupling across normalized interfaces": theory/nodal/ORGANIZED_INTERFACE_FACTORIZATION.md
          - "Conserved charge observations": theory/nodal/ORGANIZED_CHARGE_OBSERVATION.md
          - "Complete-state electrical realization": theory/nodal/ORGANIZED_ELECTRICAL_REALIZATION.md
          - "Actual-source electrical comparison": theory/nodal/ORGANIZED_ELECTRICAL_SOURCE.md
          - "Operational electrical identification": theory/nodal/ORGANIZED_ELECTRICAL_IDENTIFICATION.md
          - "Finite input on the actual five-child organization": theory/nodal/ORGANIZED_ELECTRICAL_ACTUATION.md
          - "Observing collective winding with finite form inputs": theory/nodal/ORGANIZED_FINITE_OBSERVATION.md
          - "Five-child electrical observation protocol": theory/nodal/ORGANIZED_ELECTRICAL_PROTOCOL.md
          - "Collective response inherited from constituents": theory/nodal/ORGANIZED_CONSTITUENT_MEMORY.md
          - "Finite collective prediction with frozen variances": theory/nodal/ORGANIZED_COMPRESSED_MEMORY.md
          - "Preparation-aware collective initialization": theory/nodal/ORGANIZED_MEMORY_INITIALIZATION.md
          - "Computable post-observation prediction": theory/nodal/ORGANIZED_COMPUTABLE_PREDICTION.md
          - "Predictive sufficiency of joint observations": theory/nodal/ORGANIZED_OBSERVED_PREDICTION.md
          - "Admission of an observation-based forecast": theory/nodal/ORGANIZED_OBSERVED_FORECAST.md
          - "Constitutive law and unknown initialization": theory/nodal/ORGANIZED_LAW_OBSERVATION.md
          - "Current discrimination under uncertainty": theory/nodal/ORGANIZED_ROBUST_CURRENT.md
          - "Physical feasibility of organized current observation": theory/research/ORGANIZED_ELECTRICAL_FEASIBILITY.md
          - "Collective state and matrix response": theory/nodal/ORGANIZED_EFFECTIVE_LAW.md
          - "Loaded finite-window collective observation": theory/research/ORGANIZED_FINITE_WINDOW_DESIGN.md
          - "Integrated sensor response during recovery": theory/research/ORGANIZED_RECOVERY_OBSERVATION.md
      - "Collective maintenance and assembly":
          - "Organized identity under continued external contact": theory/nodal/ORGANIZED_CONTACT_MAINTENANCE.md
          - "Composition error of simultaneous contact responses": theory/nodal/SINE_CONTACT_COMPOSITION.md
          - "Organized identity under weak external contact": theory/nodal/ORGANIZED_WEAK_CONTACT_MAINTENANCE.md
          - "Alternative-law weak-contact registration and capture": theory/nodal/ORGANIZED_ALTERNATIVE_WEAK_CONTACT.md
          - "Constitutive transition of collective registration": theory/nodal/ORGANIZED_CONSTITUTIVE_TRANSITION.md
          - "A marked interaction of a critical parent": theory/nodal/CRITICAL_PARENT_INTERACTION.md
          - "Collective boundary constraints and the scope of restoration": theory/nodal/COLLECTIVE_BOUNDARY_CONSTRAINTS.md
          - "Reflection obstruction for full-fine contact identity": theory/nodal/ORGANIZED_CONTACT_REFLECTION_OBSTRUCTION.md
          - "Full-fine stationary contact and marked chambers": theory/nodal/ORGANIZED_CONTACT_STATIONARY_SEARCH.md
          - "Composition-compatible constitutive laws": theory/nodal/COMPOSITION_COMPATIBLE_CONSTITUTIVE_LAWS.md
          - "Oriented-interface profile inheritance": theory/nodal/ORIENTED_INTERFACE_PROFILE_INHERITANCE.md
          - "Network-wide organized compatibility": theory/nodal/ORGANIZED_NETWORK_COMPATIBILITY.md
          - "Capture of the acquired three-object assembly": theory/nodal/ACQUIRED_ORGANIZED_NETWORK_CAPTURE.md
          - "Identity-preserving assembly work": theory/nodal/ORGANIZED_ASSEMBLY_WORK.md
          - "Joint acquisition on preexisting fine support": theory/nodal/ORGANIZED_JOINT_ACQUISITION.md
          - "Locally unprepared receiver mechanism": theory/nodal/ORGANIZED_RECEIVER_MECHANISM.md
          - "Controlled slow receiver admission": theory/nodal/ORGANIZED_RECEIVER_SLOW_ADMISSION.md
          - "Source-preserving receiver enclosure": theory/nodal/ORGANIZED_RECEIVER_ENCLOSURE.md
          - "Regional work and winding retention": theory/nodal/ORGANIZED_REGIONAL_RETENTION.md
      - "Constitutive barriers and source preparation":
          - "Constitutive identity barriers and work": theory/nodal/CONSTITUTIVE_IDENTITY_BARRIERS.md
          - "Constitutive receiver source and comparison": theory/nodal/CONSTITUTIVE_RECEIVER_COMPARISON.md
          - "Preparation information and acquired modes": theory/nodal/SINE_PREPARATION_MODE_SELECTION.md
          - "Preparation paths, capture and forced phase passage": theory/nodal/SINE_PREPARATION_PATH_SELECTION.md
          - "Terminal restrictions on the same preparation path": theory/nodal/SINE_PREPARATION_PATH_LIMITS.md
          - "Source-specific capture through the actual phase passage": theory/nodal/SINE_PREPARATION_PATH_CAPTURE.md
          - "Constitutive robustness of source-path capture": theory/nodal/SINE_PREPARATION_PATH_ROBUSTNESS.md
      - "Sine contact, observation and inference":
          - "Two-port compatibility of sine classes": theory/nodal/SINE_TWO_PORT_COMPATIBILITY.md
          - "Finite transit of two-port sine classes": theory/nodal/SINE_TWO_PORT_TRANSIT.md
          - "Prepared capture of two-port sine classes": theory/nodal/SINE_TWO_PORT_CAPTURE.md
          - "Supplied probe of the acquired two-port composite": theory/nodal/SINE_TWO_PORT_PROBE.md
          - "Interior phase probe of acquired two-port deformation": theory/nodal/SINE_TWO_PORT_DIPOLE.md
          - "Two-port geometry from a calibrated local response": theory/nodal/SINE_TWO_PORT_INFERENCE.md
          - "Geometry and gain from two successive phase inputs": theory/nodal/SINE_TWO_PULSE_INFERENCE.md
          - "Geometry, sensor gain and a declared uncertain clock": theory/nodal/SINE_CLOCK_INFERENCE.md
          - "Finite curvature from one additional reading": theory/nodal/SINE_FINITE_CURVATURE_INFERENCE.md
          - "Clock drift, sampled exposure and robust mean-rate inference": theory/nodal/SINE_CLOCK_DRIFT_INFERENCE.md
          - "Finite-aperture observations and mean-clock inference": theory/nodal/SINE_APERTURE_INFERENCE.md
          - "Finite-noise and horizon resolution for the four boxcar observations": theory/nodal/SINE_APERTURE_RESOLUTION.md
      - "Localized transport and organization":
          - "Finite transport of a localized identity": theory/nodal/LOCALIZED_IDENTITY_TRANSPORT.md
          - "Source resources for localized mobile identities": theory/nodal/LOCALIZED_TRANSPORT_SOURCES.md
          - "Prepared mobile encounter and interaction observation": theory/nodal/LOCALIZED_MOBILE_INTERACTION.md
          - "Certified observation of a mobile encounter": theory/nodal/LOCALIZED_MOBILE_RESPONSE.md
          - "Geometry and formation of localized organization": theory/nodal/LOCALIZED_ORGANIZATION_GEOMETRY.md
          - "Localized formation compatibility": theory/nodal/LOCALIZED_FORMATION_COMPATIBILITY.md
          - "Same-band source and regional work": theory/nodal/LOCALIZED_SINGLE_BAND_WORK.md
          - "Localized retention mechanisms": theory/nodal/LOCALIZED_RETENTION_MECHANISMS.md
      - "Model-specific operator and hierarchy studies":
          - "Native operator dynamics": theory/NATIVE_OPERATOR_DYNAMICS.md
          - "Native collective calculus": theory/NATIVE_COLLECTIVE_CALCULUS.md
          - "Aggregate operators and native transitions": theory/NATIVE_AGGREGATE_OPERATORS.md
          - "Collective IL/OZ pressure handoff": theory/nodal/SINE_COLLECTIVE_PRESSURE_HANDOFF.md
          - "Pressure-completion compatibility": theory/nodal/SINE_PRESSURE_COMPLETION.md
          - "Complete form-capacity actions": theory/nodal/SINE_FORM_CAPACITY_ACTION.md
          - "Directional maintenance": theory/nodal/SINE_DIRECTIONAL_MAINTENANCE.md
          - "Collective identity through form-capacity action": theory/nodal/SINE_COLLECTIVE_IDENTITY_TRANSITION.md
          - "Collective Reception": theory/nodal/SINE_COLLECTIVE_RECEPTION.md
          - "Collective Transition": theory/nodal/SINE_COLLECTIVE_TRANSITION.md
          - "Collective Mutation admission": theory/nodal/SINE_COLLECTIVE_MUTATION_ADMISSION.md
          - "Collective Mutation action": theory/nodal/SINE_COLLECTIVE_MUTATION_ACTION.md
          - "Collective hierarchy": theory/nodal/SINE_COLLECTIVE_HIERARCHY.md
          - "Hierarchy-to-contact composition": theory/nodal/SINE_HIERARCHY_CONTACT.md
          - "Maintained-source birth obstruction": theory/nodal/SINE_ORGANIZED_BIRTH_OBSTRUCTION.md
          - "Capacity and temporal access": theory/nodal/SINE_CAPACITY_TEMPORAL_ACCESS.md
          - "Local capacity and joint temporal admission": theory/nodal/SINE_LOCAL_CAPACITY_ADMISSION.md
          - "Acquired local-capacity history": theory/nodal/SINE_LOCAL_HISTORY_ACQUISITION.md
          - "THOL birth on a certified maintained parent": theory/nodal/SINE_MAINTAINED_PARENT_THOL.md
          - "Default UM on the retained THOL successor": theory/nodal/SINE_MAINTAINED_PARENT_UM.md
          - "Maintained-parent SHA closure and changed law": theory/nodal/SINE_MAINTAINED_PARENT_CLOSURE.md
          - "Finite preparation families for the held sine law": theory/nodal/SINE_PREPARATION_ROBUSTNESS.md
          - "Connected child's temporal capability": theory/nodal/SINE_CHILD_TEMPORAL_READINESS.md
          - "Child OZ and observation timing": theory/nodal/SINE_CHILD_GRAMMAR_TIMING.md
          - "Acquired-child THOL and word completion": theory/nodal/SINE_CHILD_THOL_ADMISSION.md
          - "Stationary geometry of the proposed UM successor": theory/nodal/SINE_SUCCESSOR_STATIONARY_GEOMETRY.md
          - "Principal-chamber minimum exclusion": theory/nodal/SINE_SUCCESSOR_PRINCIPAL_REDUCTION.md
          - "Successor motion and sufficient state": theory/nodal/SINE_SUCCESSOR_NONSTATIONARY.md
          - "Collective Recursivity": theory/nodal/SINE_COLLECTIVE_RECURSIVITY.md
          - "Coupling and winding": theory/COUPLING_WINDING_PERSISTENCE.md
          - "Coherent pattern contact": theory/COHERENT_PATTERN_CONTACT.md
          - "THOL pressure feedback": theory/THOL_PRESSURE_FEEDBACK.md
          - "THOL birth and transport": theory/THOL_BIRTH_AND_TRANSPORT.md
          - "Child coupling feedback": theory/CHILD_COUPLING_FEEDBACK.md
      - "Auxiliary models and physical comparisons":
          - "Variational and exchange models": theory/TNFR_VARIATIONAL_PRINCIPLE.md
          - "Dissipative/open-system models": theory/DISSIPATIVE_AND_OPEN_SYSTEMS.md
          - "Gauge and polarization constructions": theory/GAUGE_SYMMETRY_AND_UNIFICATION.md
          - "Physical correspondence atlas and emergence boundaries": theory/PHYSICAL_REGIME_CORRESPONDENCES.md
      - "Arithmetic and applications":
          - "Number theory": theory/TNFR_NUMBER_THEORY.md
          - "Structural observability — R1": theory/TNFR_STRUCTURAL_OBSERVABILITY.md
          - "Arithmetic dynamics — R2": theory/TNFR_ARITHMETIC_DYNAMICS.md
          - "CRT composition — R3": theory/TNFR_CRT_FRACTALITY.md
          - "p-adic dynamics — R4": theory/TNFR_PADIC_DYNAMICS.md
          - "Algebraic number fields — R5": theory/TNFR_ALGEBRAIC_NUMBER_FIELDS.md
          - "Additive dynamics — R6": theory/TNFR_ADDITIVE_DYNAMICS.md
          - "Arithmetic pressure — R7": theory/TNFR_ARITHMETIC_PRESSURE.md
          - "Arithmetic operators — R8": theory/TNFR_ARITHMETIC_OPERATORS.md
          - "Riemann scope": theory/TNFR_RIEMANN_RESEARCH_NOTES.md
      - "Research, measurement and parked evidence":
          - "Passive transport protocol": theory/research/PASSIVE_TRANSPORT_PROTOCOL.md
          - "Regional phase/amplitude protocol": theory/research/PHASE_AMPLITUDE_MEASUREMENT_PROTOCOL.md
          - "Chemical observation and predictive information": theory/research/CHEMICAL_OBSERVATION_ADMISSION.md
          - "Physical admission of the delayed digital-PLL realization": theory/research/DPLL_PHYSICAL_ADMISSION.md
          - "TCLab comparison boundary": theory/research/TCLAB_EXPLORATORY_PROTOCOL.md
          - "Parked C6 evidence boundary": theory/C6_RESEARCH_MECHANISM_AUDIT.md
          - "Relative-coupling observation admission": theory/research/RELATIVE_COUPLING_PROBE.md
      - "Research navigation":
          - "Theory-to-execution map": theory/THEORY_TO_EXECUTION.md
          - "Bibliographic methods for TNFR foundations": theory/BIBLIOGRAPHIC_METHODS.md
      - "Published guide routes":
          - "Retired nodal research strategy": theory/NODAL_RESEARCH_STRATEGY.md
          - "Retired five-stage execution plan": theory/research/FIVE_STAGE_EXECUTION_PLAN.md
# END GENERATED THEORY NAVIGATION
      - Historical archive: theory/research/archive/README.md
      - Retired programme boundaries: theory/research/archive/RETIRED_PROGRAMME_BOUNDARIES.md
  - Examples: examples/README.md
  - Benchmarks: benchmarks/README.md
  - Applications:
      - Scope and retained projects: applications/README.md
      - Basic primality utility: applications/primality-test/README.md
  - Development:
      - Testing: TESTING.md
      - Contributing: CONTRIBUTING.md
      - Security: SECURITY.md
      - Workflows: .github/WORKFLOWS.md
      - Repository scripts: scripts/README.md