Fix documentation build: update broken links and remove missing files from nav

Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>

Author: Copilot

docs/source/advanced/ARCHITECTURE_GUIDE.md

@@ -809,9 +809,9 @@ Before creating a PR with factory changes:
 
 ## References
 
-- [AGENTS.md](../../../AGENTS.md) - TNFR paradigm fundamentals
-- [CONTRIBUTING.md](../../../CONTRIBUTING.md) - General contribution guidelines
-- [ARCHITECTURE.md](../../../ARCHITECTURE.md) - Overall project structure
+- [AGENTS.md](https://github.com/fermga/TNFR-Python-Engine/blob/main/AGENTS.md) - TNFR paradigm fundamentals
+- [CONTRIBUTING.md](https://github.com/fermga/TNFR-Python-Engine/blob/main/CONTRIBUTING.md) - General contribution guidelines
+- [ARCHITECTURE.md](https://github.com/fermga/TNFR-Python-Engine/blob/main/ARCHITECTURE.md) - Overall project structure
 - [Performance Optimization](PERFORMANCE_OPTIMIZATION.md) - Caching and optimization patterns
 - [Testing Strategies](TESTING_STRATEGIES.md) - Test patterns and coverage requirements
 - [Foundations](../foundations.md) - Mathematical foundations

docs/source/advanced/DEVELOPMENT_WORKFLOW.md

@@ -751,7 +751,7 @@ make verify-refs-verbose
    - This guide
    - [ARCHITECTURE_GUIDE.md](ARCHITECTURE_GUIDE.md)
    - [TESTING_STRATEGIES.md](TESTING_STRATEGIES.md)
-   - [CONTRIBUTING.md](../../../CONTRIBUTING.md)
+   - [CONTRIBUTING.md](https://github.com/fermga/TNFR-Python-Engine/blob/main/CONTRIBUTING.md)
 
 2. **Search GitHub Issues**:
    - Known issues and solutions
@@ -833,8 +833,8 @@ mypy --help                        # Mypy options
 - [Architecture Guide](ARCHITECTURE_GUIDE.md) - Factory patterns and dependencies
 - [Testing Strategies](TESTING_STRATEGIES.md) - Testing best practices
 - [Performance Optimization](PERFORMANCE_OPTIMIZATION.md) - Optimization techniques
-- [CONTRIBUTING.md](../../../CONTRIBUTING.md) - Contribution guidelines
-- [README.md](../../../README.md) - Project overview
+- [CONTRIBUTING.md](https://github.com/fermga/TNFR-Python-Engine/blob/main/CONTRIBUTING.md) - Contribution guidelines
+- [README.md](https://github.com/fermga/TNFR-Python-Engine/blob/main/README.md) - Project overview
 
 ---
 

docs/source/advanced/TESTING_STRATEGIES.md

@@ -923,8 +923,8 @@ pytest tests/ --memprof
 - [Architecture Guide](ARCHITECTURE_GUIDE.md) - Factory patterns and dependency management
 - [Performance Optimization](PERFORMANCE_OPTIMIZATION.md) - Optimization strategies
 - [Development Workflow](DEVELOPMENT_WORKFLOW.md) - Contributing guidelines
-- [CONTRIBUTING.md](../../../CONTRIBUTING.md) - General contribution guide
-- [TESTING.md](../../../TESTING.md) - Test strategy overview
+- [CONTRIBUTING.md](https://github.com/fermga/TNFR-Python-Engine/blob/main/CONTRIBUTING.md) - General contribution guide
+- [TESTING.md](https://github.com/fermga/TNFR-Python-Engine/blob/main/TESTING.md) - Test strategy overview
 
 ---
 

docs/source/theory/README.md

@@ -110,8 +110,8 @@ Hands-on exploration and visualization of TNFR concepts:
 
 ### Related Documentation
 - [TNFR Fundamental Concepts](../getting-started/TNFR_CONCEPTS.md) — Intuitive introduction
-- [GLOSSARY](../../../GLOSSARY.md) — Terminology reference
-- [AGENTS.md](../../../AGENTS.md) — Canonical invariants for AI agents
+- [GLOSSARY](https://github.com/fermga/TNFR-Python-Engine/blob/main/GLOSSARY.md) — Terminology reference
+- [AGENTS.md](https://github.com/fermga/TNFR-Python-Engine/blob/main/AGENTS.md) — Canonical invariants for AI agents
 
 ## 📋 Document Status
 

docs/source/user-guide/METRICS_INTERPRETATION.md

@@ -1,6 +1,6 @@
 # Metrics Interpretation Guide
 
-[Home](../index.rst) › [User Guide](../user-guide/) › Metrics Interpretation
+[Home](../home.md) › Metrics Interpretation
 
 This guide explains how to interpret and use TNFR's key metrics: Total Coherence (C(t)), Sense Index (Si), structural frequency (νf), phase (φ), and reorganization gradient (ΔNFR).
 

docs/source/user-guide/OPERATORS_GUIDE.md

@@ -1,6 +1,6 @@
 # Operators Guide: The 13 Structural Operators
 
-[Home](../index.rst) › [User Guide](../user-guide/) › Operators Guide
+[Home](../home.md) › Operators Guide
 
 This guide provides a comprehensive reference for TNFR's 13 canonical structural operators. These operators are the **only valid way** to modify networks in TNFR, ensuring all changes are traceable, coherent, and reproducible.
 
@@ -606,7 +606,7 @@ Safe_Exploration := Dissonance Operator* Coherence
 Multi_Scale := Recursivity(Sequence)
 ```
 
-See [Glyph Sequences Guide](../../../GLYPH_SEQUENCES_GUIDE.md) for comprehensive patterns.
+See [Glyph Sequences Guide](https://github.com/fermga/TNFR-Python-Engine/blob/main/GLYPH_SEQUENCES_GUIDE.md) for comprehensive patterns.
 
 ## Monitoring Operator Effects
 
@@ -718,7 +718,7 @@ def adaptive_operator(G, node):
 ## See Also
 
 - **[API Reference](../api/operators.md)** - Complete operator API
-- **[Glyph Sequences Guide](../../../GLYPH_SEQUENCES_GUIDE.md)** - Canonical patterns
+- **[Glyph Sequences Guide](https://github.com/fermga/TNFR-Python-Engine/blob/main/GLYPH_SEQUENCES_GUIDE.md)** - Canonical patterns
 - **[Metrics Interpretation](METRICS_INTERPRETATION.md)** - Understanding effects
 - **[Troubleshooting](TROUBLESHOOTING.md)** - Solving common issues
 - **[Examples](../examples/README.md)** - Practical operator usage

docs/source/user-guide/TROUBLESHOOTING.md

@@ -1,6 +1,6 @@
 # Troubleshooting Guide
 
-[Home](../index.rst) › [User Guide](../user-guide/) › Troubleshooting
+[Home](../home.md) › Troubleshooting
 
 This guide helps you diagnose and solve common problems when working with TNFR networks.
 

mkdocs.yml

@@ -31,25 +31,16 @@ nav:
       - Performance Optimization: advanced/PERFORMANCE_OPTIMIZATION.md
       - Testing Strategies: advanced/TESTING_STRATEGIES.md
       - Development Workflow: advanced/DEVELOPMENT_WORKFLOW.md
-      - Theory Deep Dive: advanced/THEORY_DEEP_DIVE.md
       - Mathematical Foundations: foundations.md
   - Mathematical Foundations:
-      - Overview: theory/00_overview.ipynb
       - Primers:
           - Structural frequency primer: theory/01_structural_frequency_primer.ipynb
           - Phase synchrony lattices: theory/02_phase_synchrony_lattices.ipynb
           - ΔNFR gradient fields: theory/03_delta_nfr_gradient_fields.ipynb
           - Coherence metrics walkthrough: theory/04_coherence_metrics_walkthrough.ipynb
+          - NFR validator & metrics: theory/04_nfr_validator_and_metrics.ipynb
           - Sense index calibration: theory/05_sense_index_calibration.ipynb
           - Recursivity cascades: theory/06_recursivity_cascades.ipynb
-      - Emergence of Physics:
-          - Classical Mechanics: theory/07_emergence_classical_mechanics.md
-      - Operators & Validators:
-          - Hilbert space ℋ_NFR: theory/01_hilbert_space_h_nfr.ipynb
-          - Coherence operator Ĉ: theory/02_coherence_operator_hatC.ipynb
-          - Frequency operator Ĵ: theory/03_frequency_operator_hatJ.ipynb
-          - NFR validator & metrics: theory/04_nfr_validator_and_metrics.ipynb
-          - Unitary dynamics & ΔNFR: theory/05_unitary_dynamics_and_delta_nfr.ipynb
   - Security:
       - Monitoring: security/monitoring.md
       - Dependency Auditing: security/dependency-auditing.md