Fix broken documentation links - replace .md with correct HTML paths

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

Author: Copilot

404.html

@@ -1219,7 +1219,7 @@
 
 
     <li class="md-nav__item">
-      <a href="/TNFR-Python-Engine/grammar/GLOSSARY.md" class="md-nav__link">
+      <a href="/TNFR-Python-Engine/GLOSSARY/" class="md-nav__link">
 
 
 
@@ -1472,7 +1472,7 @@
 
 
     <li class="md-nav__item">
-      <a href="/TNFR-Python-Engine/grammar/DEPRECATION-INDEX.md" class="md-nav__link">
+      <a href="/TNFR-Python-Engine/grammar/" class="md-nav__link">
 
 
 

AGENTS/index.html

@@ -1230,7 +1230,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/GLOSSARY.md" class="md-nav__link">
+      <a href="../GLOSSARY/" class="md-nav__link">
 
 
 
@@ -1483,7 +1483,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/DEPRECATION-INDEX.md" class="md-nav__link">
+      <a href="../grammar/" class="md-nav__link">
 
 
 
@@ -4136,7 +4136,7 @@ <h2 id="core-mission">🎯 Core Mission<a class="headerlink" href="#core-mission
 <p><strong>Repository</strong>: https://github.com/fermga/TNFR-Python-Engine</p>
 <h3 id="quick-links">Quick Links<a class="headerlink" href="#quick-links" title="Permanent link">&para;</a></h3>
 <ul>
-<li>Canonical Math Hub: <a href="src/tnfr/mathematics/README.md">src/tnfr/mathematics/README.md</a></li>
+<li>Canonical Math Hub: <a href="https://github.com/fermga/TNFR-Python-Engine/tree/main/src/tnfr/mathematics/README">src/tnfr/mathematics/README.md</a></li>
 <li>Theory: <a href="TNFR.pdf">TNFR.pdf</a> · <a href="../UNIFIED_GRAMMAR_RULES/">UNIFIED_GRAMMAR_RULES.md</a></li>
 <li>Operators Grammar: <a href="src/tnfr/operators/grammar.py">src/tnfr/operators/grammar.py</a></li>
 <li>Structural Fields: <a href="src/tnfr/physics/fields.py">src/tnfr/physics/fields.py</a></li>
@@ -4377,7 +4377,7 @@ <h3 id="u6-structural-potential-confinement">U6: STRUCTURAL POTENTIAL CONFINEMEN
 <li><strong>Usage</strong>: Telemetry-based safety check (read-only, not sequence constraint)</li>
 <li><strong>Typical</strong>: Valid sequences maintain Δ Φ_s ≈ 0.6 (30% of threshold)</li>
 <li><strong>Canonicity</strong>: STRONG (2,400+ experiments across 5 topologies, universal)</li>
-<li><strong>See</strong>: <a href="docs/grammar/U6_STRUCTURAL_POTENTIAL_CONFINEMENT.md">docs/grammar/U6_STRUCTURAL_POTENTIAL_CONFINEMENT.md</a> for complete specification</li>
+<li><strong>See</strong>: <a href="grammar/U6_STRUCTURAL_POTENTIAL_CONFINEMENT/">docs/grammar/U6_STRUCTURAL_POTENTIAL_CONFINEMENT.md</a> for complete specification</li>
 </ul>
 <p><strong>See</strong>: <a href="../UNIFIED_GRAMMAR_RULES/">UNIFIED_GRAMMAR_RULES.md</a> for complete derivations</p>
 <hr />
@@ -4865,7 +4865,7 @@ <h4 id="phase-curvature-k_-canonical-newly-promoted-nov-2025"><strong>Phase Curv
 - Import from <a href="src/tnfr/physics/fields.py">src/tnfr/physics/fields.py</a>
 - Compute via <code>compute_phase_curvature(G)</code> [CANONICAL]
 - Optional multiscale check: <code>k_phi_multiscale_safety(G, alpha_hint=2.76)</code></p>
-<p><strong>Documentation</strong>: See <a href="benchmarks/K_PHI_RESEARCH_SUMMARY.md">benchmarks/K_PHI_RESEARCH_SUMMARY.md</a> and
+<p><strong>Documentation</strong>: See <a href="benchmarks/K_PHI_RESEARCH_SUMMARY/">benchmarks/K_PHI_RESEARCH_SUMMARY.md</a> and
 <code>benchmarks/enhanced_fragmentation_test.py</code> for empirical validation.</p>
 <hr />
 <h4 id="coherence-length-_c-canonical-newly-promoted-nov-2025"><strong>Coherence Length (ξ_C)</strong> - CANONICAL ⭐ <strong>NEWLY PROMOTED (Nov 2025)</strong><a class="headerlink" href="#coherence-length-_c-canonical-newly-promoted-nov-2025" title="Permanent link">&para;</a></h4>
@@ -4910,7 +4910,7 @@ <h4 id="coherence-length-_c-canonical-newly-promoted-nov-2025"><strong>Coherence
 not captured by Φ_s, |∇φ|, or K_φ. Enables detection of genuine phase 
 transitions through divergence near critical points. Topology-dependent 
 critical exponents suggest rich universality class structure in TNFR networks.</p>
-<p><strong>Documentation</strong>: See <a href="docs/XI_C_CANONICAL_PROMOTION.md">docs/XI_C_CANONICAL_PROMOTION.md</a> for complete 
+<p><strong>Documentation</strong>: See <a href="XI_C_CANONICAL_PROMOTION/">docs/XI_C_CANONICAL_PROMOTION.md</a> for complete 
 experimental validation, <a href="docs/XI_C_BREAKTHROUGH_REPORT.txt">docs/XI_C_BREAKTHROUGH_REPORT.txt</a> for detailed 
 analysis, and <a href="benchmarks/results/xi_c_critical_behavior_analysis.png">benchmarks/results/xi_c_critical_behavior_analysis.png</a> for 
 visualization of critical behavior across topologies.</p>

API_CONTRACTS/index.html

@@ -1226,7 +1226,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/GLOSSARY.md" class="md-nav__link">
+      <a href="../GLOSSARY/" class="md-nav__link">
 
 
 
@@ -1479,7 +1479,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/DEPRECATION-INDEX.md" class="md-nav__link">
+      <a href="../grammar/" class="md-nav__link">
 
 
 

ARCHITECTURE/index.html

@@ -1230,7 +1230,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/GLOSSARY.md" class="md-nav__link">
+      <a href="../GLOSSARY/" class="md-nav__link">
 
 
 
@@ -1483,7 +1483,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/DEPRECATION-INDEX.md" class="md-nav__link">
+      <a href="../grammar/" class="md-nav__link">
 
 
 
@@ -3824,7 +3824,7 @@ <h3 id="unified-canonical-constraints-u1-u6">Unified Canonical Constraints (U1-U
 <p>For complete physics derivations, canonical definitions, and implementation details, see:
 - <strong><a href="../UNIFIED_GRAMMAR_RULES/">UNIFIED_GRAMMAR_RULES.md</a></strong> - Complete mathematical derivations
 - <strong><a href="../AGENTS/#-unified-grammar-u1-u6">AGENTS.md § Unified Grammar</a></strong> - Concise reference
-- <strong><a href="docs/grammar/02-CANONICAL-CONSTRAINTS.md">docs/grammar/02-CANONICAL-CONSTRAINTS.md</a></strong> - Technical specification</p>
+- <strong><a href="grammar/02-CANONICAL-CONSTRAINTS/">docs/grammar/02-CANONICAL-CONSTRAINTS.md</a></strong> - Technical specification</p>
 <p><strong>Quick Summary</strong>:
 - <strong>U1</strong>: STRUCTURAL INITIATION &amp; CLOSURE - Start with generators, end with closures
 - <strong>U2</strong>: CONVERGENCE &amp; BOUNDEDNESS - Destabilizers require stabilizers
@@ -3839,7 +3839,7 @@ <h3 id="migration-from-old-systems">Migration from Old Systems<a class="headerli
 <li><strong>RC1-RC4 System</strong> (in <code>canonical_grammar.py</code>) - Deprecated</li>
 </ul>
 <p><strong>New Unified System</strong> (U1-U4 in <code>grammar.py</code>) - Active</p>
-<p>See <a href="docs/grammar/07-MIGRATION-AND-EVOLUTION.md">Grammar Migration Guide</a> for migration instructions.</p>
+<p>See <a href="grammar/07-MIGRATION-AND-EVOLUTION/">Grammar Migration Guide</a> for migration instructions.</p>
 <h2 id="layered-responsibilities">Layered responsibilities<a class="headerlink" href="#layered-responsibilities" title="Permanent link">&para;</a></h2>
 <table>
 <thead>

CANONICAL_OZ_SEQUENCES/index.html

@@ -1226,7 +1226,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/GLOSSARY.md" class="md-nav__link">
+      <a href="../GLOSSARY/" class="md-nav__link">
 
 
 
@@ -1479,7 +1479,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/DEPRECATION-INDEX.md" class="md-nav__link">
+      <a href="../grammar/" class="md-nav__link">
 
 
 

CANONICAL_SOURCES/index.html

@@ -1230,7 +1230,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/GLOSSARY.md" class="md-nav__link">
+      <a href="../GLOSSARY/" class="md-nav__link">
 
 
 
@@ -1483,7 +1483,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/DEPRECATION-INDEX.md" class="md-nav__link">
+      <a href="../grammar/" class="md-nav__link">
 
 
 
@@ -3509,15 +3509,15 @@ <h3 id="tier-1-ultimate-sources-physics-philosophy">Tier 1: Ultimate Sources (Ph
 <h3 id="tier-2-specialized-documentation-single-responsibility">Tier 2: Specialized Documentation (Single Responsibility)<a class="headerlink" href="#tier-2-specialized-documentation-single-responsibility" title="Permanent link">&para;</a></h3>
 <p>These documents cover specific aspects in depth. They MAY provide context but MUST reference Tier 1 for canonical definitions.</p>
 <ol>
-<li><strong><a href="docs/grammar/02-CANONICAL-CONSTRAINTS.md">docs/grammar/02-CANONICAL-CONSTRAINTS.md</a></strong> - U1-U6 technical specification</li>
+<li><strong><a href="grammar/02-CANONICAL-CONSTRAINTS/">docs/grammar/02-CANONICAL-CONSTRAINTS.md</a></strong> - U1-U6 technical specification</li>
 <li>Detailed constraint specifications</li>
 <li>Implementation examples</li>
 <li>Test requirements</li>
 <li>
 <p><strong>Must reference</strong>: UNIFIED_GRAMMAR_RULES.md for derivations</p>
 </li>
 <li>
-<p><strong><a href="docs/grammar/U6_STRUCTURAL_POTENTIAL_CONFINEMENT.md">docs/grammar/U6_STRUCTURAL_POTENTIAL_CONFINEMENT.md</a></strong> - U6 complete specification</p>
+<p><strong><a href="grammar/U6_STRUCTURAL_POTENTIAL_CONFINEMENT/">docs/grammar/U6_STRUCTURAL_POTENTIAL_CONFINEMENT.md</a></strong> - U6 complete specification</p>
 </li>
 <li>U6 physics, validation, implementation</li>
 <li>
@@ -3533,15 +3533,15 @@ <h3 id="tier-2-specialized-documentation-single-responsibility">Tier 2: Speciali
 <p><strong>Must reference</strong>: AGENTS.md for invariants, operators, grammar</p>
 </li>
 <li>
-<p><strong><a href="TESTING.md">TESTING.md</a></strong> - Test strategy</p>
+<p><strong><a href="TESTING/">TESTING.md</a></strong> - Test strategy</p>
 </li>
 <li>Testing requirements</li>
 <li>Invariant test examples</li>
 <li>
 <p><strong>Must reference</strong>: AGENTS.md for invariant definitions</p>
 </li>
 <li>
-<p><strong><a href="CONTRIBUTING.md">CONTRIBUTING.md</a></strong> - Development workflow</p>
+<p><strong><a href="https://github.com/fermga/TNFR-Python-Engine/blob/main/CONTRIBUTING/">CONTRIBUTING.md</a></strong> - Development workflow</p>
 </li>
 <li>Contribution guidelines</li>
 <li>Commit templates</li>
@@ -3551,15 +3551,15 @@ <h3 id="tier-2-specialized-documentation-single-responsibility">Tier 2: Speciali
 <h3 id="tier-2b-molecular-chemistry-module-breakthrough">Tier 2b: Molecular Chemistry Module ⭐ <strong>BREAKTHROUGH</strong><a class="headerlink" href="#tier-2b-molecular-chemistry-module-breakthrough" title="Permanent link">&para;</a></h3>
 <p>Revolutionary extension: Complete chemistry emerges from TNFR nodal dynamics.</p>
 <ol>
-<li><strong><a href="docs/MOLECULAR_CHEMISTRY_HUB.md">docs/MOLECULAR_CHEMISTRY_HUB.md</a></strong> - <strong>CENTRAL CHEMISTRY HUB</strong></li>
+<li><strong><a href="MOLECULAR_CHEMISTRY_HUB/">docs/MOLECULAR_CHEMISTRY_HUB.md</a></strong> - <strong>CENTRAL CHEMISTRY HUB</strong></li>
 <li>Single source navigation for molecular chemistry breakthrough</li>
 <li>Theory consolidation and learning paths</li>
 <li>Complete cross-reference matrix for chemistry derivation</li>
 <li>
 <p><strong>Must reference</strong>: AGENTS.md for nodal equation foundations</p>
 </li>
 <li>
-<p><strong><a href="docs/examples/MOLECULAR_CHEMISTRY_FROM_NODAL_DYNAMICS.md">docs/examples/MOLECULAR_CHEMISTRY_FROM_NODAL_DYNAMICS.md</a></strong> - <strong>CANONICAL CHEMISTRY THEORY</strong></p>
+<p><strong><a href="examples/MOLECULAR_CHEMISTRY_FROM_NODAL_DYNAMICS/">docs/examples/MOLECULAR_CHEMISTRY_FROM_NODAL_DYNAMICS.md</a></strong> - <strong>CANONICAL CHEMISTRY THEORY</strong></p>
 <ul>
 <li>Complete derivation: nodal equation → molecular chemistry  </li>
 <li>Chemical bonds as phase synchronization (U3)</li>
@@ -3569,14 +3569,14 @@ <h3 id="tier-2b-molecular-chemistry-module-breakthrough">Tier 2b: Molecular Chem
 </ul>
 </li>
 <li>
-<p><strong><a href="docs/examples/AU_EXISTENCE_FROM_NODAL_EQUATION.md">docs/examples/AU_EXISTENCE_FROM_NODAL_EQUATION.md</a></strong> - Au emergence theory</p>
+<p><strong><a href="examples/AU_EXISTENCE_FROM_NODAL_EQUATION/">docs/examples/AU_EXISTENCE_FROM_NODAL_EQUATION.md</a></strong> - Au emergence theory</p>
 <ul>
 <li>Physics-grounded derivation: fields → signatures → Au-like patterns</li>
 <li><strong>Must reference</strong>: AGENTS.md for structural fields, nodal equation</li>
 </ul>
 </li>
 <li>
-<p><strong><a href="src/tnfr/physics/README.md">src/tnfr/physics/README.md</a></strong> § 9-10 - Implementation guide</p>
+<p><strong><a href="https://github.com/fermga/TNFR-Python-Engine/tree/main/src/tnfr/physics/README">src/tnfr/physics/README.md</a></strong> § 9-10 - Implementation guide</p>
 <ul>
 <li>Element signatures API (<code>tnfr.physics.signatures</code>)</li>
 <li>Element pattern builders (<code>tnfr.physics.patterns</code>)</li>
@@ -3588,7 +3588,7 @@ <h3 id="tier-3-supporting-documentation-references-only">Tier 3: Supporting Docu
 <p>These documents provide guidance, tutorials, examples. They MUST NOT define canonical concepts - only reference and use them.</p>
 <ol>
 <li>
-<p><strong><a href="README.md">README.md</a></strong> - Entry point</p>
+<p><strong><a href="README/">README.md</a></strong> - Entry point</p>
 <ul>
 <li>Project overview</li>
 <li>Installation</li>
@@ -3607,7 +3607,7 @@ <h3 id="tier-3-supporting-documentation-references-only">Tier 3: Supporting Docu
 </ul>
 </li>
 <li>
-<p><strong><a href="docs/grammar/README.md">docs/grammar/README.md</a></strong> - Grammar navigation</p>
+<p><strong><a href="grammar/README/">docs/grammar/README.md</a></strong> - Grammar navigation</p>
 <ul>
 <li>Grammar documentation index</li>
 <li>Learning sequence</li>

CELL_EMERGENCE_FROM_TNFR/index.html

@@ -1230,7 +1230,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/GLOSSARY.md" class="md-nav__link">
+      <a href="../GLOSSARY/" class="md-nav__link">
 
 
 
@@ -1483,7 +1483,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/DEPRECATION-INDEX.md" class="md-nav__link">
+      <a href="../grammar/" class="md-nav__link">
 
 
 

CROSS_REFERENCE_MATRIX/index.html

@@ -1226,7 +1226,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/GLOSSARY.md" class="md-nav__link">
+      <a href="../GLOSSARY/" class="md-nav__link">
 
 
 
@@ -1479,7 +1479,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/DEPRECATION-INDEX.md" class="md-nav__link">
+      <a href="../grammar/" class="md-nav__link">
 
 
 
@@ -3561,11 +3561,11 @@ <h2 id="for-developers">🎓 For Developers<a class="headerlink" href="#for-deve
 <hr />
 <h2 id="related-documents">📖 Related Documents<a class="headerlink" href="#related-documents" title="Permanent link">&para;</a></h2>
 <ul>
-<li><strong><a href="../CANONICAL_SOURCES.md">CANONICAL_SOURCES.md</a></strong> - Documentation hierarchy</li>
+<li><strong><a href="../CANONICAL_SOURCES/">CANONICAL_SOURCES.md</a></strong> - Documentation hierarchy</li>
 <li><strong><a href="../DOCUMENTATION_HIERARCHY/">DOCUMENTATION_HIERARCHY.md</a></strong> - Visual diagrams</li>
-<li><strong><a href="../DOCUMENTATION_INDEX.md">DOCUMENTATION_INDEX.md</a></strong> - Complete navigation</li>
-<li><strong><a href="../AGENTS.md">AGENTS.md</a></strong> - Primary theory source</li>
-<li><strong><a href="../UNIFIED_GRAMMAR_RULES.md">UNIFIED_GRAMMAR_RULES.md</a></strong> - Mathematical derivations</li>
+<li><strong><a href="../DOCUMENTATION_INDEX/">DOCUMENTATION_INDEX.md</a></strong> - Complete navigation</li>
+<li><strong><a href="../AGENTS/">AGENTS.md</a></strong> - Primary theory source</li>
+<li><strong><a href="../UNIFIED_GRAMMAR_RULES/">UNIFIED_GRAMMAR_RULES.md</a></strong> - Mathematical derivations</li>
 </ul>
 <hr />
 <h2 id="summary">✨ Summary<a class="headerlink" href="#summary" title="Permanent link">&para;</a></h2>

DOCUMENTATION_HIERARCHY/index.html

@@ -1226,7 +1226,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/GLOSSARY.md" class="md-nav__link">
+      <a href="../GLOSSARY/" class="md-nav__link">
 
 
 
@@ -1479,7 +1479,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../grammar/DEPRECATION-INDEX.md" class="md-nav__link">
+      <a href="../grammar/" class="md-nav__link">
 
 
 
@@ -3156,7 +3156,7 @@
 
 <h1 id="documentation-hierarchy-visual-reference">Documentation Hierarchy - Visual Reference<a class="headerlink" href="#documentation-hierarchy-visual-reference" title="Permanent link">&para;</a></h1>
 <p><strong>Mermaid diagrams showing TNFR documentation structure</strong></p>
-<p>See <a href="../CANONICAL_SOURCES.md">CANONICAL_SOURCES.md</a> for complete hierarchy specification.</p>
+<p>See <a href="../CANONICAL_SOURCES/">CANONICAL_SOURCES.md</a> for complete hierarchy specification.</p>
 <hr />
 <h2 id="canonical-documentation-hierarchy">Canonical Documentation Hierarchy<a class="headerlink" href="#canonical-documentation-hierarchy" title="Permanent link">&para;</a></h2>
 <div class="highlight"><pre><span></span><code>graph TB
@@ -3322,9 +3322,9 @@ <h2 id="usage">Usage<a class="headerlink" href="#usage" title="Permanent link">&
 <p><strong>Rule</strong>: If adding &gt;100 words about a concept, check if it's already canonical. If yes, reference instead of replicate.</p>
 <hr />
 <p><strong>Related</strong>:
-- <a href="../CANONICAL_SOURCES.md">CANONICAL_SOURCES.md</a> - Complete hierarchy specification
+- <a href="../CANONICAL_SOURCES/">CANONICAL_SOURCES.md</a> - Complete hierarchy specification
 - <a href="../DOCUMENTATION_INDEX/">DOCUMENTATION_INDEX.md</a> - Full documentation map
-- <a href="../AGENTS.md">AGENTS.md</a> - Primary canonical source</p>
+- <a href="../AGENTS/">AGENTS.md</a> - Primary canonical source</p>