feat: integrate canonical nodal diagnostics

Intent: retain verified structural dynamics and remove plan-only scaffolding.

Operators involved: Coherence, Coupling, Resonance, Recursivity.

Affected invariants: #1 nodal equation integrity; #2 phase-coherent coupling; #3 multi-scale fractality; #4 grammar compliance; #5 structural metrology; #6 reproducible dynamics.

Key changes: integrate transport, tetrad, U6, morphism, winding, cache, provenance, and exact circulant diffusion safeguards; remove dated execution artifacts and rejected experimental paths.

Expected risks/dissonances: finite-window and auxiliary-model scopes remain explicit; Recursivity temporal mixing remains network-scale only.

Metrics: full suite 3631 passed, 1 skipped; 900 internal Markdown references valid.

Author: TNFR AI Agent

benchmarks/emergent_arithmetic_pulse.py

@@ -25,7 +25,7 @@
     (p-1)/2 -- the pulse's spectral_multiplicity field reads (p-1)/2 exactly.
   - M3 COMPOSITES ENRICH THE CHORD MULTIPLICATIVELY: the tone-count is
     multiplicative (15 -> 9 = 3x3, 45 -> 12 = 4x3), encoding the factorization
-    TYPE (the ontological-ladder rank, NT theory 9.8).
+    TYPE (the ontological-ladder rank, NT theory 9.12).
   - M4 A PRIME IS MAXIMALLY DEGENERATE: just gcd(k,p-1)+1 tones no matter how
     large p is -- mean multiplicity ~ (p-1)/d grows, the chord stays minimal.
 

benchmarks/emergent_fractal_simplex_dimension.py

@@ -165,20 +165,20 @@ def spectral_dimension(eigvals: np.ndarray) -> float:
     return -2.0 * float(np.median(slope[k // 4:k - k // 4]))
 
 
-def _canonical_anchor_ok(G) -> bool:
-    """Anchor: hand-built L_sym spectrum == canonical engine spectrum."""
+def _canonical_anchor_ok(G) -> bool | None:
+    """Anchor: hand-built spectrum equals the canonical engine spectrum."""
     try:
         from tnfr.physics.structural_diffusion import structural_eigenmodes
     except Exception:
-        return True  # engine spectrum unavailable; L_sym stands alone
+        return None
     try:
         out = structural_eigenmodes(G)
         ev = np.asarray(out[0] if isinstance(out, tuple) else out, float)
         mine = np.sort(l_sym_eigvals(G))
         ev = np.sort(ev[: len(mine)])
         return bool(np.allclose(ev, mine, atol=1e-8))
     except Exception:
-        return True
+        return None
 
 
 def main() -> None:
@@ -197,7 +197,8 @@ def main() -> None:
     G3, _ = sierpinski_simplex(3, 3)
     anchor = _canonical_anchor_ok(G3)
     print(f"  node-count recurrence N(m,k)=m*N(m,k-1)-C(m,2): {m1_ok}")
-    print(f"  L_sym spectrum == canonical structural_eigenmodes: {anchor}")
+    anchor_label = "UNAVAILABLE" if anchor is None else str(anchor)
+    print(f"  L_sym spectrum == canonical structural_eigenmodes: {anchor_label}")
     assert m1_ok, "self-similar construction node counts are wrong"
 
     # M2 -- DEFINITE similarity dimension, SET BY THE LOCAL GRADE.

benchmarks/emergent_musical_nfr.py

@@ -50,7 +50,7 @@
     python benchmarks/emergent_musical_nfr.py
 
 Theoretical anchor: EMERGENT_ONTOLOGY.md section 5.5 (the pulse); theory/
-TNFR_NUMBER_THEORY.md (9.12 the arithmetic pulse, 9.7 the wall);
+TNFR_NUMBER_THEORY.md (9.13 the arithmetic pulse, 9.7 the wall);
 src/tnfr/physics/structural_diffusion.py (compute_emergent_pulse);
 benchmarks/emergent_rhythm.py + inverse_spectrum_to_symmetry.py.
 Status: RESEARCH.

benchmarks/external_phase_gate_validation.py

@@ -36,14 +36,8 @@
 
 REPO_ROOT = Path(__file__).resolve().parents[1]
 SRC_DIR = REPO_ROOT / "src"
-sys.path.insert(0, str(SRC_DIR))
-
-loaded_tnfr = sys.modules.get("tnfr")
-loaded_path = str(getattr(loaded_tnfr, "__file__", "")) if loaded_tnfr else ""
-if loaded_tnfr is not None and not loaded_path.startswith(str(SRC_DIR)):
-    for name in list(sys.modules):
-        if name == "tnfr" or name.startswith("tnfr."):
-            del sys.modules[name]
+if str(SRC_DIR) not in sys.path:
+    sys.path.insert(0, str(SRC_DIR))
 
 import networkx as nx  # noqa: E402
 

examples/08_emergent_geometry/155_ontological_position_of_numbers.py

@@ -41,7 +41,7 @@
   A(m)=prod(e+ceil(e/2)+1) at small exponents -- rho(p)=3 (cyclotomy k=2),
   rho(p^2)=4, rho(p^3)=6 -- and is multiplicative there. So primality (rho=3)
   and the factorization TYPE (Omega, tau) are read off the spectrum -- the
-  arithmetic emerges (TNFR_NUMBER_THEORY.md §9.5-9.8).
+    arithmetic emerges (TNFR_NUMBER_THEORY.md §9.5-9.12).
 - Layer 4: rho gives the factorization TYPE, never the prime IDENTITIES (15 and
   35 share rho=9); the unannotated scalar rank also aliases at high prime powers
   (the §9.7 / ex 154 scalar wall) -- the same e-pi / Fix(S_n)^perp wall as the

examples/08_emergent_geometry/156_emergence_directness_law.py

@@ -224,7 +224,7 @@ def experiment_5_the_law(results):
     print()
     print("  one law: topological(occupant)=Fix-invariant=DIRECT; spectral(stage)")
     print("  =Fix^perp-trapped=PARTIAL(the wall); process=consumes-input=CIRCULAR.")
-    print("  Unifies the position ladder (155/§9.8), particle classification (§7.1),")
+    print("  Compares the position ladder (155/§9.12), particle classification (§7.1),")
     print("  the Riemann/number wall (§9.5-9.7, §10.5) and the §0 axis under ONE")
     print("  principle: representation theory of the coupling's symmetry group.")
     print()

examples/10_applications/90_phase_gate_monitor_demo.py

@@ -14,16 +14,10 @@
 import sys
 from pathlib import Path
 
-ROOT = Path(__file__).resolve().parents[1]
+ROOT = Path(__file__).resolve().parents[2]
 SRC = ROOT / "src"
-sys.path.insert(0, str(SRC))
-
-loaded_tnfr = sys.modules.get("tnfr")
-loaded_path = str(getattr(loaded_tnfr, "__file__", "")) if loaded_tnfr else ""
-if loaded_tnfr is not None and not loaded_path.startswith(str(SRC)):
-    for name in list(sys.modules):
-        if name == "tnfr" or name.startswith("tnfr."):
-            del sys.modules[name]
+if str(SRC) not in sys.path:
+    sys.path.insert(0, str(SRC))
 
 import networkx as nx  # noqa: E402
 

examples/10_applications/91_breast_cancer_phase_gate_demo.py

@@ -29,16 +29,10 @@
 from pathlib import Path
 from typing import Any, Mapping
 
-ROOT = Path(__file__).resolve().parents[1]
+ROOT = Path(__file__).resolve().parents[2]
 SRC = ROOT / "src"
-sys.path.insert(0, str(SRC))
-
-loaded_tnfr = sys.modules.get("tnfr")
-loaded_path = str(getattr(loaded_tnfr, "__file__", "")) if loaded_tnfr else ""
-if loaded_tnfr is not None and not loaded_path.startswith(str(SRC)):
-    for name in list(sys.modules):
-        if name == "tnfr" or name.startswith("tnfr."):
-            del sys.modules[name]
+if str(SRC) not in sys.path:
+    sys.path.insert(0, str(SRC))
 
 import networkx as nx  # noqa: E402
 from sklearn.datasets import load_breast_cancer  # noqa: E402

examples/10_applications/92_wine_quality_phase_gate_demo.py

@@ -26,16 +26,10 @@
 from typing import Any, Mapping
 from urllib.request import urlopen
 
-ROOT = Path(__file__).resolve().parents[1]
+ROOT = Path(__file__).resolve().parents[2]
 SRC = ROOT / "src"
-sys.path.insert(0, str(SRC))
-
-loaded_tnfr = sys.modules.get("tnfr")
-loaded_path = str(getattr(loaded_tnfr, "__file__", "")) if loaded_tnfr else ""
-if loaded_tnfr is not None and not loaded_path.startswith(str(SRC)):
-    for name in list(sys.modules):
-        if name == "tnfr" or name.startswith("tnfr."):
-            del sys.modules[name]
+if str(SRC) not in sys.path:
+    sys.path.insert(0, str(SRC))
 
 import networkx as nx  # noqa: E402
 from sklearn.neighbors import NearestNeighbors  # noqa: E402

examples/10_applications/93_structural_interface_demo.py

@@ -45,16 +45,10 @@
     except Exception:  # pragma: no cover - best-effort console setup
         pass
 
-ROOT = Path(__file__).resolve().parents[1]
+ROOT = Path(__file__).resolve().parents[2]
 SRC = ROOT / "src"
-sys.path.insert(0, str(SRC))
-
-loaded_tnfr = sys.modules.get("tnfr")
-loaded_path = str(getattr(loaded_tnfr, "__file__", "")) if loaded_tnfr else ""
-if loaded_tnfr is not None and not loaded_path.startswith(str(SRC)):
-    for name in list(sys.modules):
-        if name == "tnfr" or name.startswith("tnfr."):
-            del sys.modules[name]
+if str(SRC) not in sys.path:
+    sys.path.insert(0, str(SRC))
 
 import numpy as np  # noqa: E402