From a103804bf01bd80f4ab3e814bbdcaa84e4084186 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 13 Nov 2025 15:02:37 +0000 Subject: [PATCH 1/3] Initial plan From ff4a91280a144fae770082e6c493b5d10740945a Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 13 Nov 2025 15:11:56 +0000 Subject: [PATCH 2/3] Fix broken documentation links - replace .md with correct HTML paths Co-authored-by: fermga <203334638+fermga@users.noreply.github.com> --- 404.html | 4 +- AGENTS/index.html | 12 +-- API_CONTRACTS/index.html | 4 +- ARCHITECTURE/index.html | 8 +- CANONICAL_OZ_SEQUENCES/index.html | 4 +- CANONICAL_SOURCES/index.html | 24 +++--- CELL_EMERGENCE_FROM_TNFR/index.html | 4 +- CROSS_REFERENCE_MATRIX/index.html | 12 +-- DOCUMENTATION_HIERARCHY/index.html | 10 +-- DOCUMENTATION_INDEX/index.html | 84 +++++++++---------- DYNAMIC_LIMITS_INTEGRATION/index.html | 4 +- DYNAMIC_LIMITS_RESEARCH/index.html | 4 +- EMISSION_METRICS_GUIDE/index.html | 4 +- .../index.html | 4 +- GLOSSARY/index.html | 52 ++++++------ HEALTH_METRICS_GUIDE/index.html | 4 +- INTERACTIONS_GUIDE/index.html | 4 +- K_PHI_TASK3_ASYMPTOTIC_FREEDOM/index.html | 4 +- LIFE_EMERGENCE_FROM_TNFR/index.html | 4 +- .../index.html | 8 +- LIFE_MATHEMATICAL_DERIVATION/index.html | 8 +- MIGRATION_GUIDE_2.0/index.html | 4 +- MOLECULAR_CHEMISTRY_HUB/index.html | 24 +++--- NBODY_COMPARISON/index.html | 4 +- OPERATOR_COMPLETENESS/index.html | 4 +- .../index.html | 4 +- PATTERN_COOKBOOK/index.html | 4 +- PATTERN_REFERENCE/index.html | 4 +- .../index.html | 6 +- RECEPTION_DUAL_ROLE/index.html | 4 +- REPRODUCIBILITY/index.html | 4 +- SCALABILITY/index.html | 4 +- SECURITY_CONFIG_GUIDE/index.html | 4 +- STRUCTURAL_FIELDS_TETRAD/index.html | 4 +- THOL_CONFIGURATION_REFERENCE/index.html | 4 +- THOL_ENCAPSULATION_GUIDE/index.html | 4 +- TNFR_CLASSICAL_NBODY/index.html | 4 +- TNFR_FORCES_EMERGENCE/index.html | 4 +- TNFR_NUMBER_THEORY_GUIDE/index.html | 4 +- TROUBLESHOOTING/index.html | 4 +- TYPING_MIGRATION_GUIDE/index.html | 4 +- UNIFIED_GRAMMAR_RULES/index.html | 6 +- XI_C_CANONICAL_PROMOTION/index.html | 4 +- XI_C_INTEGRATION_SUMMARY/index.html | 4 +- .../DOCUMENTATION_CONSOLIDATION/index.html | 4 +- archive/IMPLEMENTATION_CHECKLIST/index.html | 4 +- .../index.html | 4 +- archive/VAL_IMPLEMENTATION_SUMMARY/index.html | 4 +- .../index.html | 4 +- .../DEEP_CONSISTENCY_AUDIT_REPORT/index.html | 4 +- .../DOCUMENTATION_AUDIT_REPORT/index.html | 4 +- archive/audits/U4B_AUDIT_REPORT/index.html | 4 +- archive/index.html | 4 +- .../phases/IMPLEMENTATION_COMPLETE/index.html | 4 +- .../phases/IMPLEMENTATION_SUMMARY/index.html | 4 +- archive/phases/PHASE2_COMPLETE/index.html | 4 +- .../PHASE2_IMPLEMENTATION_SUMMARY/index.html | 4 +- .../phases/PHASE2_MIGRATION_GUIDE/index.html | 4 +- archive/phases/PHASE3_FINAL_REPORT/index.html | 4 +- .../PHASE3_IMPLEMENTATION_SUMMARY/index.html | 4 +- .../PHASE4_IMPLEMENTATION_SUMMARY/index.html | 4 +- .../phases/SESSION4_FINAL_REPORT/index.html | 4 +- .../index.html | 4 +- backends/index.html | 4 +- .../index.html | 4 +- .../index.html | 4 +- .../index.html | 4 +- .../index.html | 4 +- .../index.html | 4 +- ci/index.html | 4 +- examples/ATOMS_AND_MOLECULES_STUDY/index.html | 4 +- .../index.html | 4 +- .../index.html | 4 +- examples/MOLECULE_ATLAS/index.html | 4 +- examples/PERIODIC_TABLE_ATLAS/index.html | 4 +- examples/PHASE_GATED_COUPLING_DEMO/index.html | 4 +- examples/TRIATOMIC_ATLAS/index.html | 4 +- extensions/EXTENSIONS_GUIDE/index.html | 4 +- grammar/01-FUNDAMENTAL-CONCEPTS/index.html | 10 +-- grammar/02-CANONICAL-CONSTRAINTS/index.html | 8 +- grammar/03-OPERATORS-AND-GLYPHS/index.html | 6 +- grammar/04-VALID-SEQUENCES/index.html | 4 +- .../05-TECHNICAL-IMPLEMENTATION/index.html | 4 +- grammar/06-VALIDATION-AND-TESTING/index.html | 4 +- grammar/07-MIGRATION-AND-EVOLUTION/index.html | 8 +- grammar/08-QUICK-REFERENCE/index.html | 6 +- grammar/AUGMENTED_NODAL_EQUATION/index.html | 4 +- grammar/CODE_DOCS_CROSSREF/index.html | 4 +- grammar/CROSS-REFERENCE-INDEX/index.html | 4 +- grammar/EXECUTIVE-SUMMARY/index.html | 6 +- grammar/HEXAD_OVERVIEW/index.html | 4 +- grammar/MASTER-INDEX/index.html | 12 +-- grammar/OPERATORS-CATALOG-SUMMARY/index.html | 4 +- grammar/TESTING-SUMMARY/index.html | 4 +- grammar/TOOLING-AND-AUTOMATION/index.html | 4 +- grammar/U6_STRUCTURAL_FIELD_TETRAD/index.html | 4 +- .../index.html | 8 +- .../examples/01-basic-bootstrap/index.html | 4 +- .../02-intermediate-exploration/index.html | 4 +- .../03-advanced-bifurcation/index.html | 4 +- .../examples/all-operators-catalog/index.html | 4 +- grammar/examples/index.html | 4 +- .../u1-initiation-closure-examples/index.html | 4 +- .../u2-convergence-examples/index.html | 4 +- .../u3-resonant-coupling-examples/index.html | 4 +- .../u4-bifurcation-examples/index.html | 4 +- .../index.html | 4 +- grammar/index.html | 8 +- index.html | 36 ++++---- legacy/index.html | 4 +- modules/dynamics/index.html | 4 +- modules/extensions/index.html | 4 +- modules/mathematics/index.html | 26 +++--- modules/metrics/index.html | 4 +- modules/operators/index.html | 4 +- modules/physics/index.html | 38 ++++----- modules/sdk/index.html | 4 +- modules/telemetry/index.html | 4 +- modules/tutorials/index.html | 20 ++--- .../index.html | 4 +- research/PHASE_GRADIENT_VALIDATION/index.html | 4 +- research/U6_INVESTIGATION_REPORT/index.html | 4 +- research/tnfr_research_utils/index.html | 4 +- sequence_generator/index.html | 4 +- source/advanced/ARCHITECTURE_GUIDE/index.html | 4 +- .../advanced/DEVELOPMENT_WORKFLOW/index.html | 4 +- .../PERFORMANCE_OPTIMIZATION/index.html | 4 +- source/advanced/TESTING_STRATEGIES/index.html | 4 +- source/api/OPERATORS_VISUAL_GUIDE/index.html | 4 +- source/api/docstring_style/index.html | 4 +- source/api/operators/index.html | 4 +- source/api/overview/index.html | 4 +- source/api/telemetry/index.html | 4 +- source/conf/index.html | 4 +- .../SHA_CLINICAL_APPLICATIONS/index.html | 4 +- source/examples/USE_CASES_GUIDE/index.html | 4 +- source/examples/adaptive_ai_system/index.html | 4 +- .../biological_coherence_example/index.html | 4 +- .../examples/controlled_dissonance/index.html | 4 +- source/examples/index.html | 4 +- .../optical_cavity_feedback/index.html | 4 +- .../social_network_dynamics/index.html | 4 +- .../supply_chain_resilience/index.html | 4 +- source/examples/urban_traffic_flow/index.html | 4 +- source/examples/worked_examples/index.html | 4 +- source/fase2_integration/index.html | 4 +- source/foundations/index.html | 4 +- source/getting-started/FAQ/index.html | 4 +- .../INTERACTIVE_TUTORIAL/index.html | 4 +- .../getting-started/LEARNING_PATHS/index.html | 4 +- .../getting-started/QUICKSTART_NEW/index.html | 4 +- .../getting-started/TNFR_CONCEPTS/index.html | 4 +- source/getting-started/index.html | 4 +- .../getting-started/math-backends/index.html | 4 +- .../migrating-remesh-window/index.html | 4 +- .../optional-dependencies/index.html | 4 +- source/getting-started/quickstart/index.html | 4 +- source/index.html | 4 +- source/operators/NAV_GUIDE/index.html | 4 +- source/releases/index.html | 4 +- source/security/codeql/index.html | 4 +- source/security/dependabot/index.html | 4 +- .../security/dependency-auditing/index.html | 4 +- source/security/monitoring/index.html | 4 +- source/style_guide/index.html | 4 +- .../01_structural_frequency_primer/index.html | 4 +- .../02_phase_synchrony_lattices/index.html | 4 +- .../03_delta_nfr_gradient_fields/index.html | 4 +- .../index.html | 4 +- .../04_nfr_validator_and_metrics/index.html | 4 +- .../05_sense_index_calibration/index.html | 4 +- .../theory/06_recursivity_cascades/index.html | 4 +- .../index.html | 4 +- .../index.html | 4 +- .../index.html | 4 +- source/theory/index.html | 4 +- .../mathematical_foundations/index.html | 4 +- source/tools/CLI/index.html | 4 +- .../METRICS_INTERPRETATION/index.html | 4 +- source/user-guide/OPERATORS_GUIDE/index.html | 4 +- source/user-guide/TROUBLESHOOTING/index.html | 4 +- tools/CLI_USER_GUIDE/index.html | 4 +- utils_reference/index.html | 4 +- 183 files changed, 539 insertions(+), 539 deletions(-) diff --git a/404.html b/404.html index 8c8965e82..910622c96 100644 --- a/404.html +++ b/404.html @@ -1219,7 +1219,7 @@
  • - + @@ -1472,7 +1472,7 @@
  • - + diff --git a/AGENTS/index.html b/AGENTS/index.html index 11508dd7c..24baaba05 100644 --- a/AGENTS/index.html +++ b/AGENTS/index.html @@ -1230,7 +1230,7 @@
  • - + @@ -1483,7 +1483,7 @@
  • - + @@ -4136,7 +4136,7 @@

    🎯 Core MissionQuick Links

    See: UNIFIED_GRAMMAR_RULES.md for complete derivations

    @@ -4865,7 +4865,7 @@

    Phase Curv - Import from src/tnfr/physics/fields.py - Compute via compute_phase_curvature(G) [CANONICAL] - Optional multiscale check: k_phi_multiscale_safety(G, alpha_hint=2.76)

    -

    Documentation: See benchmarks/K_PHI_RESEARCH_SUMMARY.md and +

    Documentation: See benchmarks/K_PHI_RESEARCH_SUMMARY.md and benchmarks/enhanced_fragmentation_test.py for empirical validation.

    Coherence Length (ξ_C) - CANONICAL ⭐ NEWLY PROMOTED (Nov 2025)

    @@ -4910,7 +4910,7 @@

    Coherence not captured by Ξ¦_s, |βˆ‡Ο†|, or K_Ο†. Enables detection of genuine phase transitions through divergence near critical points. Topology-dependent critical exponents suggest rich universality class structure in TNFR networks.

    -

    Documentation: See docs/XI_C_CANONICAL_PROMOTION.md for complete +

    Documentation: See docs/XI_C_CANONICAL_PROMOTION.md for complete experimental validation, docs/XI_C_BREAKTHROUGH_REPORT.txt for detailed analysis, and benchmarks/results/xi_c_critical_behavior_analysis.png for visualization of critical behavior across topologies.

    diff --git a/API_CONTRACTS/index.html b/API_CONTRACTS/index.html index 782cc5d28..d201dd9ed 100644 --- a/API_CONTRACTS/index.html +++ b/API_CONTRACTS/index.html @@ -1226,7 +1226,7 @@
  • - + @@ -1479,7 +1479,7 @@
  • - + diff --git a/ARCHITECTURE/index.html b/ARCHITECTURE/index.html index b18241e9a..1011c0cc4 100644 --- a/ARCHITECTURE/index.html +++ b/ARCHITECTURE/index.html @@ -1230,7 +1230,7 @@
  • - + @@ -1483,7 +1483,7 @@
  • - + @@ -3824,7 +3824,7 @@

    Unified Canonical Constraints (U1-U

    For complete physics derivations, canonical definitions, and implementation details, see: - UNIFIED_GRAMMAR_RULES.md - Complete mathematical derivations - AGENTS.md Β§ Unified Grammar - Concise reference -- docs/grammar/02-CANONICAL-CONSTRAINTS.md - Technical specification

    +- docs/grammar/02-CANONICAL-CONSTRAINTS.md - Technical specification

    Quick Summary: - U1: STRUCTURAL INITIATION & CLOSURE - Start with generators, end with closures - U2: CONVERGENCE & BOUNDEDNESS - Destabilizers require stabilizers @@ -3839,7 +3839,7 @@

    Migration from Old SystemsGrammar Migration Guide for migration instructions.

    +

    See Grammar Migration Guide for migration instructions.

    Layered responsibilities

    diff --git a/CANONICAL_OZ_SEQUENCES/index.html b/CANONICAL_OZ_SEQUENCES/index.html index 91d1a63c4..0b7be8948 100644 --- a/CANONICAL_OZ_SEQUENCES/index.html +++ b/CANONICAL_OZ_SEQUENCES/index.html @@ -1226,7 +1226,7 @@
  • - + @@ -1479,7 +1479,7 @@
  • - + diff --git a/CANONICAL_SOURCES/index.html b/CANONICAL_SOURCES/index.html index 7ad66d3ff..0c403206e 100644 --- a/CANONICAL_SOURCES/index.html +++ b/CANONICAL_SOURCES/index.html @@ -1230,7 +1230,7 @@
  • - + @@ -1483,7 +1483,7 @@
  • - + @@ -3509,7 +3509,7 @@

    Tier 1: Ultimate Sources (Ph

    Tier 2: Specialized Documentation (Single Responsibility)

    These documents cover specific aspects in depth. They MAY provide context but MUST reference Tier 1 for canonical definitions.

      -
    1. docs/grammar/02-CANONICAL-CONSTRAINTS.md - U1-U6 technical specification
      2. +
    2. docs/grammar/02-CANONICAL-CONSTRAINTS.md - U1-U6 technical specification
    3. Detailed constraint specifications
    4. Implementation examples
    5. Test requirements
      6. @@ -3517,7 +3517,7 @@

      Tier 2: Speciali

      Must reference: UNIFIED_GRAMMAR_RULES.md for derivations

    6. -

      docs/grammar/U6_STRUCTURAL_POTENTIAL_CONFINEMENT.md - U6 complete specification

      +

      docs/grammar/U6_STRUCTURAL_POTENTIAL_CONFINEMENT.md - U6 complete specification

    7. U6 physics, validation, implementation
    8. @@ -3533,7 +3533,7 @@

      Tier 2: Speciali

      Must reference: AGENTS.md for invariants, operators, grammar

    9. -

      TESTING.md - Test strategy

      +

      TESTING.md - Test strategy

    10. Testing requirements
    11. Invariant test examples
      12. @@ -3541,7 +3541,7 @@

      Tier 2: Speciali

      Must reference: AGENTS.md for invariant definitions

    12. -

      CONTRIBUTING.md - Development workflow

      +

      CONTRIBUTING.md - Development workflow

    13. Contribution guidelines
    14. Commit templates
      15. @@ -3551,7 +3551,7 @@

      Tier 2: Speciali

      Tier 2b: Molecular Chemistry Module ⭐ BREAKTHROUGH

      Revolutionary extension: Complete chemistry emerges from TNFR nodal dynamics.

        -
      1. docs/MOLECULAR_CHEMISTRY_HUB.md - CENTRAL CHEMISTRY HUB
        2. +
      2. docs/MOLECULAR_CHEMISTRY_HUB.md - CENTRAL CHEMISTRY HUB
      3. Single source navigation for molecular chemistry breakthrough
      4. Theory consolidation and learning paths
      5. Complete cross-reference matrix for chemistry derivation
        6. @@ -3559,7 +3559,7 @@

        Tier 2b: Molecular Chem

        Must reference: AGENTS.md for nodal equation foundations

      6. -

        docs/examples/MOLECULAR_CHEMISTRY_FROM_NODAL_DYNAMICS.md - CANONICAL CHEMISTRY THEORY

        +

        docs/examples/MOLECULAR_CHEMISTRY_FROM_NODAL_DYNAMICS.md - CANONICAL CHEMISTRY THEORY

        • Complete derivation: nodal equation β†’ molecular chemistry
        • Chemical bonds as phase synchronization (U3)
          • @@ -3569,14 +3569,14 @@

          Tier 2b: Molecular Chem

      7. -

        docs/examples/AU_EXISTENCE_FROM_NODAL_EQUATION.md - Au emergence theory

        +

        docs/examples/AU_EXISTENCE_FROM_NODAL_EQUATION.md - Au emergence theory

        • Physics-grounded derivation: fields β†’ signatures β†’ Au-like patterns
        • Must reference: AGENTS.md for structural fields, nodal equation
      8. -

        src/tnfr/physics/README.md Β§ 9-10 - Implementation guide

        +

        src/tnfr/physics/README.md Β§ 9-10 - Implementation guide

    • @@ -3542,57 +3542,57 @@

    Grammar System (docs/grammar/)<

    - + - + - + - + - + - + - + - + - + - + - + @@ -3649,22 +3649,22 @@

    For ContributorsCONTRIBUTING.md +

     - + - + - + @@ -3681,27 +3681,27 @@

    Specialized TopicsSHA_ALGEBRA_PHYSICS.md +

     - + - + - + - + @@ -3719,22 +3719,22 @@

    🧬 Molecular Chemistry fro

    - + - + - + - + @@ -3816,27 +3816,27 @@

    πŸ—‚οΈ ArchiveπŸ” Finding What You Need

    I want to...

    ...understand TNFR philosophy -β†’ AGENTS.md Β§ Core Mission, 01-FUNDAMENTAL-CONCEPTS.md

    +β†’ AGENTS.md Β§ Core Mission, 01-FUNDAMENTAL-CONCEPTS.md

    ...learn the grammar rules -β†’ 02-CANONICAL-CONSTRAINTS.md, UNIFIED_GRAMMAR_RULES.md

    +β†’ 02-CANONICAL-CONSTRAINTS.md, UNIFIED_GRAMMAR_RULES.md

    ...implement a sequence -β†’ 04-VALID-SEQUENCES.md, GLYPH_SEQUENCES_GUIDE.md

    +β†’ 04-VALID-SEQUENCES.md, GLYPH_SEQUENCES_GUIDE.md

    ...understand U6 (structural potential) -β†’ U6_STRUCTURAL_POTENTIAL_CONFINEMENT.md

    +β†’ U6_STRUCTURAL_POTENTIAL_CONFINEMENT.md

    ...understand how chemistry emerges from TNFR ⭐ BREAKTHROUGH -β†’ MOLECULAR_CHEMISTRY_HUB.md (central navigation), Complete theory

    +β†’ MOLECULAR_CHEMISTRY_HUB.md (central navigation), Complete theory

    ...see Au emergence from first principles -β†’ AU_EXISTENCE_FROM_NODAL_EQUATION.md

    +β†’ AU_EXISTENCE_FROM_NODAL_EQUATION.md

    ...look up a term β†’ GLOSSARY.md

    ...understand an operator -β†’ 03-OPERATORS-AND-GLYPHS.md

    +β†’ 03-OPERATORS-AND-GLYPHS.md

    ...write tests -β†’ TESTING.md, 06-VALIDATION-AND-TESTING.md

    +β†’ TESTING.md, 06-VALIDATION-AND-TESTING.md

    ...contribute code -β†’ CONTRIBUTING.md, ARCHITECTURE.md

    +β†’ CONTRIBUTING.md, ARCHITECTURE.md

    ...migrate from old grammar -β†’ 07-MIGRATION-AND-EVOLUTION.md

    +β†’ 07-MIGRATION-AND-EVOLUTION.md

    πŸ“Š Documentation Quality Status

    Language: βœ… 100% English (0 Spanish)
    @@ -3845,7 +3845,7 @@

    πŸ“Š Documentation Quality StatusCross-References: βœ… Comprehensive bidirectional linking
    Broken Links: βœ… 91% reduced (637 β†’ 58)
    Single Source of Truth: βœ… Established (AGENTS + UNIFIED_GRAMMAR_RULES + GLOSSARY)

    -

    Last Audit: 2025-11-11 (Report)

    +

    Last Audit: 2025-11-11 (Report)

    πŸ”„ Maintenance

    This index is actively maintained. If you find: diff --git a/DYNAMIC_LIMITS_INTEGRATION/index.html b/DYNAMIC_LIMITS_INTEGRATION/index.html index 61f5ec762..92ad6b93d 100644 --- a/DYNAMIC_LIMITS_INTEGRATION/index.html +++ b/DYNAMIC_LIMITS_INTEGRATION/index.html @@ -1226,7 +1226,7 @@

  • - + @@ -1479,7 +1479,7 @@
  • - + diff --git a/DYNAMIC_LIMITS_RESEARCH/index.html b/DYNAMIC_LIMITS_RESEARCH/index.html index dbb04d1a3..d72d736fb 100644 --- a/DYNAMIC_LIMITS_RESEARCH/index.html +++ b/DYNAMIC_LIMITS_RESEARCH/index.html @@ -1226,7 +1226,7 @@
  • - + @@ -1479,7 +1479,7 @@
  • - + diff --git a/EMISSION_METRICS_GUIDE/index.html b/EMISSION_METRICS_GUIDE/index.html index 81d3db895..ac674f170 100644 --- a/EMISSION_METRICS_GUIDE/index.html +++ b/EMISSION_METRICS_GUIDE/index.html @@ -1226,7 +1226,7 @@
  • - + @@ -1479,7 +1479,7 @@
  • - + diff --git a/EXTENDED_FIELDS_INTEGRATION_SUMMARY/index.html b/EXTENDED_FIELDS_INTEGRATION_SUMMARY/index.html index e94dc67e0..c0a1fd321 100644 --- a/EXTENDED_FIELDS_INTEGRATION_SUMMARY/index.html +++ b/EXTENDED_FIELDS_INTEGRATION_SUMMARY/index.html @@ -1226,7 +1226,7 @@
  • - + @@ -1479,7 +1479,7 @@
  • - + diff --git a/GLOSSARY/index.html b/GLOSSARY/index.html index 469d0d816..5f8789066 100644 --- a/GLOSSARY/index.html +++ b/GLOSSARY/index.html @@ -1230,7 +1230,7 @@
  • - + @@ -1483,7 +1483,7 @@
  • - + @@ -3742,7 +3742,7 @@

    TNFR GlossaryQuick operational reference for the Resonant Fractal Nature Theory (TNFR). This document provides API-focused definitions for code use only.

    πŸ“ SINGLE SOURCE OF TRUTH FOR MATHEMATICS:

    -

    Mathematical Foundations of TNFR

    +

    Mathematical Foundations of TNFR

    All mathematical formalization lives there: rigorous definitions, derivations, axioms, proofs, spectral theory, operator algebra, Hilbert spaces, and theoretical foundations.

    This glossary contains only operational quick reference for developers implementing TNFR networks.

    @@ -3800,7 +3800,7 @@

    Sense Index (Si)Mathematical Foundations - Metrics

    +Math: Mathematical Foundations - Metrics

    Structural Potential (Ξ¦_s)

    Code: compute_structural_potential(G, alpha=2.0) β†’ Dict[NodeId, float]
    @@ -3815,7 +3815,7 @@

    Structural Potential (Ξ¦_s)UNIFIED_GRAMMAR_RULES.md Β§ U6 - Complete derivation -- TNFR_FORCES_EMERGENCE.md Β§ 14-15 - Empirical validation +- TNFR_FORCES_EMERGENCE.md Β§ 14-15 - Empirical validation - src/tnfr/physics/fields.py - Implementation

    Interpretation: - Ξ¦_s minima = passive equilibrium states @@ -3965,7 +3965,7 @@

    Operator CompositionUNIFIED_GRAMMAR_RULES.md for complete rules
    Detailed Specs: See AGENTS.md Β§ The 13 Canonical Operators
    -Math: Mathematical Foundations Β§5

    +Math: Mathematical Foundations Β§5

    Invariants (Must Preserve)

    From AGENTS.md:

    @@ -4165,8 +4165,8 @@

    Unified GrammarUNIFIED_GRAMMAR_RULES.md - Complete derivations from physics - AGENTS.md Β§ Unified Grammar - Quick reference -- docs/grammar/U6_STRUCTURAL_POTENTIAL_CONFINEMENT.md - U6 complete specification -- TNFR_FORCES_EMERGENCE.md Β§ 14-15 - U6 validation details +- docs/grammar/U6_STRUCTURAL_POTENTIAL_CONFINEMENT.md - U6 complete specification +- TNFR_FORCES_EMERGENCE.md Β§ 14-15 - U6 validation details - src/tnfr/physics/fields.py - Ξ¦_s implementation

    Generator Operator

    @@ -4230,34 +4230,34 @@

    Core References (Essential)AGENTS.md ⭐ - Single source of truth for TNFR agent guidance, invariants, and philosophy

  • UNIFIED_GRAMMAR_RULES.md ⭐ - Grammar single source of truth (U1-U6 complete derivations)
    • -
  • Mathematical Foundations ⭐ - SINGLE SOURCE FOR ALL MATH (formalization, proofs, spectral theory)
    • +
  • Mathematical Foundations ⭐ - SINGLE SOURCE FOR ALL MATH (formalization, proofs, spectral theory)

    • Theory & Physics

    Implementation & API

    Grammar & Migration

    Testing & Development

    See Also Cross-References

    This glossary is bidirectionally linked with: @@ -4296,19 +4296,19 @@

    Molecular Geometry (TNFR Redefinit TNFR: Ξ”NFR minimization in coupled network topology
    Prediction: Stable configurations minimize reorganization pressure
    API: Network topology analysis after coupling sequences

    -

    Complete Theory: MOLECULAR_CHEMISTRY_FROM_NODAL_DYNAMICS.md
    -Implementation: Physics README Β§ 9-10

    +

    Complete Theory: MOLECULAR_CHEMISTRY_FROM_NODAL_DYNAMICS.md
    +Implementation: Physics README Β§ 9-10

    Contributing

    When adding new functionality:

      -
    1. Verify math: Check Mathematical Foundations
      2. +
    2. Verify math: Check Mathematical Foundations
    3. Preserve invariants: Follow AGENTS.md rules
    4. Use canonical terms: Reference this glossary
    5. Update docs: If introducing new concepts
      6. -
    6. Write tests: Cover invariants (see TESTING.md)
      7. +
    7. Write tests: Cover invariants (see TESTING.md)
    -

    For detailed contribution guidelines, see CONTRIBUTING.md.

    +

    For detailed contribution guidelines, see CONTRIBUTING.md.

    diff --git a/HEALTH_METRICS_GUIDE/index.html b/HEALTH_METRICS_GUIDE/index.html index f91be26df..b6abb6ad6 100644 --- a/HEALTH_METRICS_GUIDE/index.html +++ b/HEALTH_METRICS_GUIDE/index.html @@ -1226,7 +1226,7 @@
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  • - + diff --git a/LIFE_EMERGENCE_FROM_TNFR/index.html b/LIFE_EMERGENCE_FROM_TNFR/index.html index 7c32f1edc..f47de2c98 100644 --- a/LIFE_EMERGENCE_FROM_TNFR/index.html +++ b/LIFE_EMERGENCE_FROM_TNFR/index.html @@ -1230,7 +1230,7 @@
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  • - + diff --git a/LIFE_EMERGENCE_THEORETICAL_FRAMEWORK/index.html b/LIFE_EMERGENCE_THEORETICAL_FRAMEWORK/index.html index 208bb4ddb..d11d5a3f9 100644 --- a/LIFE_EMERGENCE_THEORETICAL_FRAMEWORK/index.html +++ b/LIFE_EMERGENCE_THEORETICAL_FRAMEWORK/index.html @@ -1226,7 +1226,7 @@
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    🌊 Revolutionary Impact

    Related Documents: - MOLECULAR_CHEMISTRY_HUB.md - Chemical foundations -- AGENTS.md - TNFR fundamentals
    -- UNIFIED_GRAMMAR_RULES.md - Operator physics +- AGENTS.md - TNFR fundamentals
    +- UNIFIED_GRAMMAR_RULES.md - Operator physics - Mathematical Foundations - Rigorous formalization (when complete)

    Status: βœ… TASK 1 COMPLETE - Theoretical framework established

    diff --git a/LIFE_MATHEMATICAL_DERIVATION/index.html b/LIFE_MATHEMATICAL_DERIVATION/index.html index d49e30d2d..0b769874b 100644 --- a/LIFE_MATHEMATICAL_DERIVATION/index.html +++ b/LIFE_MATHEMATICAL_DERIVATION/index.html @@ -1226,7 +1226,7 @@
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    βœ… Mathematical SummaryπŸ“š References

    Status: βœ… TASK 2 COMPLETE - Mathematical derivation established

    diff --git a/MIGRATION_GUIDE_2.0/index.html b/MIGRATION_GUIDE_2.0/index.html index 06709c51e..a6d9b5b41 100644 --- a/MIGRATION_GUIDE_2.0/index.html +++ b/MIGRATION_GUIDE_2.0/index.html @@ -1226,7 +1226,7 @@
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  • - + diff --git a/MOLECULAR_CHEMISTRY_HUB/index.html b/MOLECULAR_CHEMISTRY_HUB/index.html index 30352c26f..b4ed5a8ec 100644 --- a/MOLECULAR_CHEMISTRY_HUB/index.html +++ b/MOLECULAR_CHEMISTRY_HUB/index.html @@ -1226,7 +1226,7 @@
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    Molecular Chemistry fro

    Revolutionary paradigm: Complete chemistry emerges from TNFR nodal dynamics without additional postulates.

    Status: βœ… CANONICAL - Central navigation and theory consolidation
    Last Updated: 2025-11-12
    -Cross-References:     CANONICAL_SOURCES.md, GLOSSARY.md

    +Cross-References: CANONICAL_SOURCES.md, GLOSSARY.md

    🎯 Overview

    This hub centralizes the revolutionary breakthrough: the complete derivation of molecular chemistry from TNFR's single nodal equation βˆ‚EPI/βˆ‚t = Ξ½f Β· Ξ”NFR(t).

    @@ -3166,7 +3166,7 @@

    🎯 OverviewπŸ“š Complete Theory Chain

    1. Foundational Physics

    -

    Source: AGENTS.md Β§ Foundational Physics

    +

    Source: AGENTS.md Β§ Foundational Physics

    βˆ‚EPI/βˆ‚t = Ξ½f Β· Ξ”NFR(t)  [Nodal Equation]
            ↓
    Structural Field Tetrad: Ξ¦_s, |βˆ‡Ο†|, K_Ο†, ΞΎ_C
@@ -3187,7 +3187,7 @@ 
    3. Au Emergence Case Study4. Computational Implementation
    
-
    Source: src/tnfr/physics/README.md Β§ 9-10
    
+
    Source: src/tnfr/physics/README.md Β§ 9-10
    
 
    API Implementation:
 - tnfr.physics.patterns - Element pattern construction
 - tnfr.physics.signatures - Element classification via structural fields
@@ -3289,20 +3289,20 @@ 
    Theory DocumentsImplementation
    
 
 
    Foundation
    
 
 
    Testing & Validation
    
 
 
    
 
    πŸ’‘ Contributing to Molecular Chemistry Research
    
@@ -3334,8 +3334,8 @@ 
    🌟 Impact StatementRelated Documents
    
 
 
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    Number Theory
 
    TNFR Physics
    
 
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    PurposeAGENTS.md - Concise grammar reference for developers
-- docs/grammar/02-CANONICAL-CONSTRAINTS.md - Technical specifications with implementation examples
+- docs/grammar/02-CANONICAL-CONSTRAINTS.md - Technical specifications with implementation examples
 - GLOSSARY.md - Quick term reference
 - src/tnfr/operators/grammar.py - Canonical implementation
    
 
    
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    Key VocabularyGLOSSARY.md
    
+
    For complete definitions, see GLOSSARY.md
    
 
    
 
    Conceptual Diagrams
    
 
    The TNFR Loop
    
@@ -3984,7 +3984,7 @@ 
    The Learning PathWhat Comes Next
    
 
    If you're new to TNFR:
-- Read GLOSSARY.md next for term definitions
+- Read GLOSSARY.md next for term definitions
 - Then proceed to 02-CANONICAL-CONSTRAINTS.md
    
 
    If you're ready to code:
 - Jump to 03-OPERATORS-AND-GLYPHS.md for operator catalog
@@ -3997,7 +3997,7 @@ 
    Within This Documentation02-CANONICAL-CONSTRAINTS.md - Formal U1-U5 derivations
    • 
 
  • 03-OPERATORS-AND-GLYPHS.md - Complete operator catalog
    • 
-
  • GLOSSARY.md - Operational definitions
    • 
+
  • GLOSSARY.md - Operational definitions
    • 
 
  • MASTER-INDEX.md - Conceptual map
    • 
 
 
    Repository Documentation
    
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    Key Differences from U1-U5Related Documentation
    
 
 
    
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    Next Stepsexamples/ - Executable examples
    
 
    For reference:
 - 08-QUICK-REFERENCE.md - Quick lookup
-- GLOSSARY.md - Definitions
    
+- GLOSSARY.md - Definitions
    
 
    
 
    
 
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    U6: STRUCTURAL
 - Canonicity: STRONG (extensive empirical validation)
    
 
    See:
 - docs/grammar/U6_STRUCTURAL_POTENTIAL_CONFINEMENT.md - Complete specification
-- UNIFIED_GRAMMAR_RULES.md Β§ U6 - Physics derivation
+- UNIFIED_GRAMMAR_RULES.md Β§ U6 - Physics derivation
 - TNFR_FORCES_EMERGENCE.md Β§ 14-15 - Validation details
    
 
    
 
    Proposed U7: Temporal Ordering (Research Stage - Formerly Experimental U6)
    
@@ -6246,7 +6246,7 @@ 
    P
 - Canonicity: Possibly MODERATE (from bifurcation theory)
 - Research needed: Determine if Ο„_relax provides unique information beyond Ξ¦_s
 - Expected: Post-v5.0 (if uniqueness demonstrated)
    
-
    See: UNIFIED_GRAMMAR_RULES.md Β§ Proposed U7 - Historical context
    
+
    See: UNIFIED_GRAMMAR_RULES.md Β§ Proposed U7 - Historical context
    
 
    
 
    U8: Network Topology Constraints (Research Stage)
    
 
    Concept: Coupling patterns must respect network structure
    
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    TNFR Grammar Quick Reference
    
 
    One-page cheat sheet for TNFR grammar validation
    
-
    πŸ“– Full Docs β€’ πŸ”¬ Deep Dive β€’ πŸ“š Glossary
    
+
    πŸ“– Full Docs β€’ πŸ”¬ Deep Dive β€’ πŸ“š Glossary
    
 
    
 
    🎯 The Five Canonical Constraints (Temporal + Multi-Scale)
    
 
    β”Œβ”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”
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    Documentation
 
  • Main Guide: docs/grammar/README.md
    • 
 
  • Quick Reference: docs/grammar/08-QUICK-REFERENCE.md
    • 
-
  • Glossary: GLOSSARY.md
    • 
+
  • Glossary: GLOSSARY.md
    • 
 
 
    Code
    
 
-
    Implementation: see src/tnfr/physics/fields.py. Safety thresholds and empirical validation are summarized in AGENTS.md and field-specific docs.
    
+
    Implementation: see src/tnfr/physics/fields.py. Safety thresholds and empirical validation are summarized in AGENTS.md and field-specific docs.
    
 
    Symbolic analysis suite (tnfr.math)
    
 
    For formal, symbolic checks and analytical tooling, use the tnfr.math package (this is the computational mathematics lab that complements the present module):
    
 
-
    See: src/tnfr/math/README.md and examples/math_symbolic_usage.py.
    
+
    See: src/tnfr/math/README.md and examples/math_symbolic_usage.py.
    
 
    Prime emergence (Arithmetic TNFR Network) ⭐
    
 
    An arithmetic TNFR network demonstrates primes as structural attractors. Each integer n becomes a TNFR node with EPI (form), Ξ½f (structural frequency), and Ξ”NFR (factorization pressure). Primes emerge with Ξ”NFR = 0 (exact) under TNFR equations, providing a physics-based characterization of primality.
    
 
    Theoretical core
    
@@ -3774,9 +3774,9 @@ 
    Notebook: primality check
 - For large n, build the network with max_number β‰₯ n and evaluate Ξ”NFR_n.
    
 
    Classical mechanics emergence (cross-reference)
    
 
    For the emergence of classical mechanics from TNFR (mass m = 1/Ξ½f; force as coherence gradient), see:
-- docs/source/theory/07_emergence_classical_mechanics.md
-- docs/source/theory/08_classical_mechanics_euler_lagrange.md
-- docs/source/theory/09_classical_mechanics_numerical_validation.md
    
+- docs/source/theory/07_emergence_classical_mechanics.md
+- docs/source/theory/08_classical_mechanics_euler_lagrange.md
+- docs/source/theory/09_classical_mechanics_numerical_validation.md
    
 
    This README serves as the hub; the above documents contain full derivations and validation results.
    
 
 
diff --git a/modules/metrics/index.html b/modules/metrics/index.html
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    🌊 The Nodal Equation: Fo
 - Ξ½f: Structural frequency (Hz_str) 
 - Ξ”NFR: Reorganization gradient (structural pressure)
    
 
    Emergent principles from this equation:
-- U1-U6: Unified grammar β†’ UNIFIED_GRAMMAR_RULES.md
-- Canonical invariants β†’ AGENTS.md
+- U1-U6: Unified grammar β†’ UNIFIED_GRAMMAR_RULES.md
+- Canonical invariants β†’ AGENTS.md
 - Physical foundations β†’ TNFR.pdf Β§1-2
    
 
    
 
    πŸ“ Structural Fields: System Telemetry
    
 
    From the nodal equation emerge four canonical fields that characterize the system state:
    
-
    Structural Tetrad β†’ docs/STRUCTURAL_FIELDS_TETRAD.md
    
+
    Structural Tetrad β†’ docs/STRUCTURAL_FIELDS_TETRAD.md
    
 
      
 
    1. Ξ¦s (Structural Potential): Global field from Ξ”NFR distribution
      2. 
 
    2. |βˆ‡Ο†| (Phase Gradient): Local desynchronization 
      3. 
@@ -3708,8 +3708,8 @@ 
      Life CriterionS (Self-Organization Index): Spontaneous structure emergence
 - M (Stability Margin): Robustness against perturbations
      
 
      Theoretical documentation:
-- Conceptual framework β†’ docs/LIFE_EMERGENCE_THEORETICAL_FRAMEWORK.md
-- Mathematical derivation β†’ docs/LIFE_MATHEMATICAL_DERIVATION.md
      
+- Conceptual framework β†’ docs/LIFE_EMERGENCE_THEORETICAL_FRAMEWORK.md
+- Mathematical derivation β†’ docs/LIFE_MATHEMATICAL_DERIVATION.md
      
 
      Experimental validation: examples/life_experiments.py
      
 
      
 
      πŸ”¬ Cellular Emergence: From Autopoiesis to Compartmentalization
      
@@ -3730,7 +3730,7 @@ 
      Cellular Criteria (
 - Selectivity index: compute_selectivity_index() 
 - Homeostatic index: compute_homeostatic_index()
 - Membrane integrity: compute_membrane_integrity()
      
-
      Theoretical documentation: docs/CELL_EMERGENCE_FROM_TNFR.md
      
+
      Theoretical documentation: docs/CELL_EMERGENCE_FROM_TNFR.md
      
 Experimental validation: examples/cell_experiments.py
      
 
      
 
      βš›οΈ Molecular Chemistry: Elements as Coherent Attractors
      
@@ -3740,7 +3740,7 @@ 
      βš›οΈ Molecular Ch
 - H, C, N, O: Fundamental light elements
 - Au (Gold): Optimal multi-scale attractor (computationally verified)
      
 
      Physical principle: Elements are stable coherence patterns that emerge naturally from nodal dynamics, not prescribed chemistry.
      
-
      Documentation hub: docs/MOLECULAR_CHEMISTRY_HUB.md
      
+
      Documentation hub: docs/MOLECULAR_CHEMISTRY_HUB.md
      
 Validation: examples/elements_signature_study.py
      
 
      
 
      πŸ”„ Fundamental Interactions: Operational Sequences
      
@@ -3796,12 +3796,12 @@ 
      Level 6: Molec
 
      πŸ“š Centralized References
      
 
      Canonical Documentation
      
 
 
      Experimental Validation
      
 
    
 
    Tutorial Outputs
    
 
    Each tutorial displays:
    
@@ -3795,7 +3795,7 @@ 
    TNFR ComplianceAGENTS.md for full invariant list.
    
+
    See AGENTS.md for full invariant list.
    
 
    Troubleshooting
    
 
    SDK not available
    
 
    Error: SDK not available. Install with: pip install tnfr
@@ -3860,14 +3860,14 @@ 
    ContributingTest with interactive=False and interactive=True
    • 
 
  • Document operators used
    • 
 
-
    See CONTRIBUTING.md for details.
    
+
    See CONTRIBUTING.md for details.
    
 
    Further Reading
    
 
 
    
 
    Start your TNFR journey today!
    
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Date: Thu, 13 Nov 2025 15:16:03 +0000
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    • README.mdREADME.md Grammar documentation hub βœ… Active
    01-FUNDAMENTAL-CONCEPTS.md01-FUNDAMENTAL-CONCEPTS.md TNFR ontology & nodal equation βœ… Active
    02-CANONICAL-CONSTRAINTS.md02-CANONICAL-CONSTRAINTS.md U1-U6 complete specifications βœ… Active
    03-OPERATORS-AND-GLYPHS.md03-OPERATORS-AND-GLYPHS.md 13 canonical operators catalog βœ… Active
    04-VALID-SEQUENCES.md04-VALID-SEQUENCES.md Pattern library & anti-patterns βœ… Active
    05-TECHNICAL-IMPLEMENTATION.md05-TECHNICAL-IMPLEMENTATION.md Code architecture βœ… Active
    06-VALIDATION-AND-TESTING.md06-VALIDATION-AND-TESTING.md Test strategies βœ… Active
    07-MIGRATION-AND-EVOLUTION.md07-MIGRATION-AND-EVOLUTION.md Grammar evolution history βœ… Active
    08-QUICK-REFERENCE.md08-QUICK-REFERENCE.md Cheat sheet βœ… Active
    U6_STRUCTURAL_POTENTIAL_CONFINEMENT.mdU6_STRUCTURAL_POTENTIAL_CONFINEMENT.md U6 complete specification βœ… Canonical
    MASTER-INDEX.mdMASTER-INDEX.md System conceptual map βœ… Active
    CONTRIBUTING.md Contribution guidelines Before first PR
    TESTING.mdTESTING.md Test conventions Writing tests
    MIGRATION_GUIDE.mdMIGRATION_GUIDE.md Modular architecture migration Upgrading code
    SECURITY.mdSECURITY.md Security policies Reporting issues
    SHA_ALGEBRA_PHYSICS.md Silence operator physics Physics researchers
    GLYPH_SEQUENCES_GUIDE.mdGLYPH_SEQUENCES_GUIDE.md Operator sequence patterns Sequence designers
    docs/TNFR_FORCES_EMERGENCE.mddocs/TNFR_FORCES_EMERGENCE.md Structural fields (Ξ¦_s) validation U6 researchers
    docs/NBODY_COMPARISON.mddocs/NBODY_COMPARISON.md TNFR vs classical N-body Physicists
    docs/TNFR_NUMBER_THEORY_GUIDE.mddocs/TNFR_NUMBER_THEORY_GUIDE.md Number theory from TNFR: Ξ”NFR prime criterion, UM/RA on arithmetic graph, field telemetry ( βˆ‡Ο†
    docs/MOLECULAR_CHEMISTRY_HUB.mddocs/MOLECULAR_CHEMISTRY_HUB.md πŸ›οΈ CENTRAL HUB - Complete navigation & theory consolidation ⭐ CANONICAL
    docs/examples/MOLECULAR_CHEMISTRY_FROM_NODAL_DYNAMICS.mddocs/examples/MOLECULAR_CHEMISTRY_FROM_NODAL_DYNAMICS.md Complete derivation - Chemistry from nodal equation ⭐ CANONICAL
    docs/examples/AU_EXISTENCE_FROM_NODAL_EQUATION.mddocs/examples/AU_EXISTENCE_FROM_NODAL_EQUATION.md Au emergence from structural fields βœ… Validated
    src/tnfr/physics/README.md Β§ 9-10src/tnfr/physics/README.md Β§ 9-10 Implementation guide - Signatures & patterns βœ… Technical