chore: bump version to 0.0.3.3

TNFR AI Agent · TNFR AI Agent · commit 1de147d8d2cb · 2026-03-07T12:12:48.000+01:00
Version bump across 20 files (pyproject.toml, _version.py, CITATION.cff,
.zenodo.json, AGENTS.md, CHANGELOG.md, and 14 documentation files).
Historical references to 0.0.3.2 preserved in CHANGELOG, factorization-lab,
and simple.py.
diff --git a/.github/agents/my-agent.md b/.github/agents/my-agent.md
@@ -2,7 +2,7 @@
 ## Theoretical Framework for Coherent Pattern Analysis
 
 **Status**: Primary theoretical reference document  
-**Version**: 0.0.3.2 (March 2026)  
+**Version**: 0.0.3.3 (March 2026)  
 **Authority**: This repository contains the current implementation of TNFR theory  
 **Repository**: https://github.com/fermga/TNFR-Python-Engine  
 **PyPI Package**: https://pypi.org/project/tnfr/  
@@ -1418,7 +1418,7 @@ TNFR models coherent dynamic patterns on graph-coupled networks. Development pra
 
 ---
 
-**Version**: 0.0.3.2  \n**Last Updated**: 2026-03-06  \n**Status**: CANONICAL - Primary reference for TNFR agent guidance  \n**PyPI Release**: STABLE - Available via `pip install tnfr`  \n**Production Ready**: Complete Tetrad Fields + Unified Grammar U1-U6 + Simplified SDK + Grammar-Aware Dynamics + Structural Conservation Theorem + Integrity Monitor  
+**Version**: 0.0.3.3  \n**Last Updated**: 2026-03-07  \n**Status**: CANONICAL - Primary reference for TNFR agent guidance  \n**PyPI Release**: STABLE - Available via `pip install tnfr`  \n**Production Ready**: Complete Tetrad Fields + Unified Grammar U1-U6 + Simplified SDK + Grammar-Aware Dynamics + Structural Conservation Theorem + Integrity Monitor  
 
 ---
 
diff --git a/.zenodo.json b/.zenodo.json
@@ -1,8 +1,8 @@
 {
   "title": "TNFR-Python-Engine: Resonant Fractal Nature Theory Implementation",
   "description": "Canonical computational implementation of TNFR - a paradigm shift from modeling 'things' to modeling coherent patterns that persist through resonance. This Python package provides the complete TNFR physics engine including the 13 structural operators, unified grammar validation (U1-U6), and the four canonical structural fields (Φ_s, |∇φ|, K_φ, ξ_C). Features include: nodal equation dynamics (∂EPI/∂t = νf·ΔNFR), structural potential confinement, phase synchronization, and multi-scale coherence analysis.",
-  "version": "0.0.3.2",
-  "publication_date": "2026-03-06",
+  "version": "0.0.3.3",
+  "publication_date": "2026-03-07",
   "doi": "10.5281/zenodo.17602860",
   "creators": [
     {
diff --git a/AGENTS.md b/AGENTS.md
@@ -2,7 +2,7 @@
 ## Theoretical Framework for Coherent Pattern Analysis
 
 **Status**: Primary theoretical reference document  
-**Version**: 0.0.3.2 (March 2026)  
+**Version**: 0.0.3.3 (March 2026)  
 **Authority**: This repository contains the current implementation of TNFR theory  
 **Repository**: https://github.com/fermga/TNFR-Python-Engine  
 **PyPI Package**: https://pypi.org/project/tnfr/  
@@ -1638,7 +1638,7 @@ TNFR models coherent dynamic patterns. Development practices should reflect this
 
 ---
 
-**Version**: 0.0.3.2  
+**Version**: 0.0.3.3  
 **Last Updated**: 2026-03-07  
 **Status**: CANONICAL - Primary reference for TNFR agent guidance  
 **PyPI Release**: STABLE - Available via `pip install tnfr`  
diff --git a/ARCHITECTURE.md b/ARCHITECTURE.md
@@ -1,6 +1,6 @@
 # TNFR Python Engine - Architecture Guide
 
-**Version**: 0.0.3.2  
+**Version**: 0.0.3.3  
 **Status**: Production-ready framework with mathematical foundations  
 **Foundation**: Universal Tetrahedral Correspondence (φ↔Φ_s, γ↔|∇φ|, π↔K_φ, e↔ξ_C)
 
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,19 @@
 
 All notable changes to this project will be documented in this file.
 
+## [0.0.3.3] - 2026-03-07
+
+### Documentation Audit (Sessions 1-4)
+
+- **Comprehensive tone audit**: Removed speculative/grandiose language across 25+ files
+- **TNFR_RIEMANN_RESEARCH_NOTES.md**: Reduced from 2679 to 1499 lines (removed unfounded claims)
+- **AGENTS.md**: Fixed 'inevitability' → 'derivation strength', updated conservation test count (62 → 88), verified all 40+ cross-reference links
+- **Synced .github/agents/my-agent.md** with AGENTS.md corrections
+- **Updated test counts** to 1,655 across 8 files
+- **Removed orphaned file**: src/train_gmx_optimizer.py
+- **Fixed contradictions** between AGENTS.md and theory/ documents
+- **Validated**: 1653 passed, 2 skipped
+
 ## [0.0.3.2] - 2026-03-06
 
 ### Documentation & Consistency Fixes
diff --git a/CITATION.cff b/CITATION.cff
@@ -2,8 +2,8 @@ cff-version: 1.2.0
 title: "TNFR-Python-Engine: Resonant Fractal Nature Theory Implementation"
 message: "If you use this software, please cite it as below."
 type: software
-version: "0.0.3.2"
-date-released: "2026-03-06"
+version: "0.0.3.3"
+date-released: "2026-03-07"
 authors:
   - given-names: "F. F. Martinez Gamo"
     family-names: ""
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,6 +1,6 @@
 # Contributing to TNFR
 
-**Version**: 0.0.3.2  
+**Version**: 0.0.3.3  
 **Status**: Complete theoretical framework with Universal Tetrahedral Correspondence  
 **Authority**: Canonical constants derived from TNFR theory  
 **Quality**: Production-ready with 1,655 tests (1,646 passing, 9 skipped)  
diff --git a/LICENSE.md b/LICENSE.md
@@ -49,7 +49,7 @@ If you use this software in your research, please cite:
   author = {Martinez Gamo, F. F.},
   title = {TNFR-Python-Engine: Resonant Fractal Nature Theory Implementation},
   year = {2025},
-  version = {0.0.3.2},
+  version = {0.0.3.3},
   doi = {10.5281/zenodo.17602860},
   url = {https://github.com/fermga/TNFR-Python-Engine}
 }
diff --git a/README.md b/README.md
@@ -161,7 +161,7 @@ make smoke-tests                   # smoke tests (Unix)
   author = {Martinez Gamo, F. F.},
   title = {TNFR-Python-Engine: Resonant Fractal Nature Theory Implementation},
   year = {2025},
-  version = {0.0.3.2},
+  version = {0.0.3.3},
   doi = {10.5281/zenodo.17602860},
   url = {https://github.com/fermga/TNFR-Python-Engine}
 }
diff --git a/TESTING.md b/TESTING.md
@@ -566,4 +566,4 @@ pytest -W error
 ---
 
 **Last Updated**: November 2025  
-**Version**: 0.0.3.2
+**Version**: 0.0.3.3
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "tnfr"
-version = "0.0.3.2"
+version = "0.0.3.3"
 description = "Resonant Fractal Nature Theory (TNFR) - Computational engine for modeling coherent patterns through resonance dynamics"
 readme = "README.md"
 authors = ["F. F. Martinez Gamo"]
@@ -9,7 +9,7 @@ packages = [{include = "tnfr", from = "src"}]
 
 [project]
 name = "tnfr"
-version = "0.0.3.2"
+version = "0.0.3.3"
 description = "Resonant Fractal Nature Theory (TNFR) - Computational engine for modeling coherent patterns through resonance dynamics"
 readme = "README.md"
 requires-python = ">=3.10"
diff --git a/src/tnfr/_version.py b/src/tnfr/_version.py
@@ -1,3 +1,3 @@
 """Version information for TNFR package."""
 
-__version__ = "0.0.3.2"
+__version__ = "0.0.3.3"
diff --git a/theory/APPLIED_STRUCTURAL_ANALYSIS.md b/theory/APPLIED_STRUCTURAL_ANALYSIS.md
@@ -1,7 +1,7 @@
 # Applied Structural Analysis
 
 **Status**: Technical reference
-**Version**: 0.0.3.2
+**Version**: 0.0.3.3
 **Date**: March 2026
 
 ---
diff --git a/theory/FUNDAMENTAL_THEORY.md b/theory/FUNDAMENTAL_THEORY.md
@@ -1,7 +1,7 @@
 # TNFR Fundamental Theory
 
 **Status**: Canonical reference
-**Version**: 0.0.3.2
+**Version**: 0.0.3.3
 **Date**: March 2026
 
 ---
diff --git a/theory/GLOSSARY.md b/theory/GLOSSARY.md
@@ -792,6 +792,6 @@ When adding new functionality:
 3. Follow [CONTRIBUTING.md](CONTRIBUTING.md) for detailed guidelines  
 4. Test with [TESTING.md](TESTING.md) requirements
 
-**Version**: 0.0.3.2 (March 2026)  
+**Version**: 0.0.3.3 (March 2026)  
 **Status**: Complete operational reference for current TNFR implementation  
 **Language**: English only (canonical documentation policy)
diff --git a/theory/PHYSICAL_REGIME_CORRESPONDENCES.md b/theory/PHYSICAL_REGIME_CORRESPONDENCES.md
@@ -1,7 +1,7 @@
 # Physical Regime Correspondences
 
 **Status**: Technical reference
-**Version**: 0.0.3.2
+**Version**: 0.0.3.3
 **Date**: March 2026
 
 ---
diff --git a/theory/README.md b/theory/README.md
@@ -156,4 +156,4 @@ AL, EN, IL, OZ, UM, RA, SHA, VAL, NUL, THOL, ZHIR, NAV, REMESH
 
 ---
 
-**Version**: 0.0.3.2 | **Documents**: 16 (6 canonical + 4 consolidated + 6 extended) | **Examples**: 40 + 2 utility | **Authority**: [../AGENTS.md](../AGENTS.md)
+**Version**: 0.0.3.3 | **Documents**: 16 (6 canonical + 4 consolidated + 6 extended) | **Examples**: 40 + 2 utility | **Authority**: [../AGENTS.md](../AGENTS.md)
diff --git a/theory/STRUCTURAL_CONSERVATION_THEOREM.md b/theory/STRUCTURAL_CONSERVATION_THEOREM.md
@@ -4,7 +4,7 @@
 
 **Status**: CANONICAL — Derived from first principles  
 **Date**: March 2026  
-**Version**: 0.0.3.2  
+**Version**: 0.0.3.3  
 **Prerequisite**: [AGENTS.md](../AGENTS.md) §Foundational Physics, [UNIFIED_GRAMMAR_RULES.md](UNIFIED_GRAMMAR_RULES.md) §U2, §U6
 
 ---
diff --git a/theory/STRUCTURAL_OPERATORS.md b/theory/STRUCTURAL_OPERATORS.md
@@ -4,7 +4,7 @@
 
 **Status**: CANONICAL — All operators derived from the nodal equation  
 **Date**: March 2026  
-**Version**: 0.0.3.2  
+**Version**: 0.0.3.3  
 **Prerequisite**: [FUNDAMENTAL_THEORY.md](FUNDAMENTAL_THEORY.md) §2 (Nodal Equation), [UNIFIED_GRAMMAR_RULES.md](UNIFIED_GRAMMAR_RULES.md) (Grammar U1–U6)
 
 ---
diff --git a/theory/TNFR_NUMBER_THEORY.md b/theory/TNFR_NUMBER_THEORY.md
@@ -1,7 +1,7 @@
 # TNFR Number Theory: Arithmetic Emergence from Structural Dynamics
 
 **Status**: Canonical theoretical reference
-**Version**: 0.0.3.2
+**Version**: 0.0.3.3
 **Date**: March 2026
 
 ---
@@ -607,4 +607,4 @@ Structural triad: $\mathrm{EPI}(30) \approx 3.43$, $\nu_f(30) \approx 0.95$, $C_
 
 ---
 
-**Version**: 0.0.3.2 | **Status**: Canonical | **Authority**: [AGENTS.md](../AGENTS.md)
+**Version**: 0.0.3.3 | **Status**: Canonical | **Authority**: [AGENTS.md](../AGENTS.md)

Original file line number	Diff line number	Diff line change
`@@ -1,8 +1,8 @@`
`1`	`1`	`{`
`2`	`2`	`"title": "TNFR-Python-Engine: Resonant Fractal Nature Theory Implementation",`
`3`	`3`	"description": "Canonical computational implementation of TNFR - a paradigm shift from modeling 'things' to modeling coherent patterns that persist through resonance. This Python package provides the complete TNFR physics engine including the 13 structural operators, unified grammar validation (U1-U6), and the four canonical structural fields (Φ_s, \|∇φ\|, K_φ, ξ_C). Features include: nodal equation dynamics (∂EPI/∂t = νf·ΔNFR), structural potential confinement, phase synchronization, and multi-scale coherence analysis.",
`4`		`- "version": "0.0.3.2",`
`5`		`- "publication_date": "2026-03-06",`
	`4`	`+ "version": "0.0.3.3",`
	`5`	`+ "publication_date": "2026-03-07",`
`6`	`6`	`"doi": "10.5281/zenodo.17602860",`
`7`	`7`	`"creators": [`
`8`	`8`	`{`
Original file line number	Diff line number	Diff line change
`@@ -49,7 +49,7 @@ If you use this software in your research, please cite:`
`49`	`49`	`author = {Martinez Gamo, F. F.},`
`50`	`50`	`title = {TNFR-Python-Engine: Resonant Fractal Nature Theory Implementation},`
`51`	`51`	`year = {2025},`
`52`		`- version = {0.0.3.2},`
	`52`	`+ version = {0.0.3.3},`
`53`	`53`	`doi = {10.5281/zenodo.17602860},`
`54`	`54`	`url = {https://github.com/fermga/TNFR-Python-Engine}`
`55`	`55`	`}`
Original file line number	Diff line number	Diff line change
`@@ -161,7 +161,7 @@ make smoke-tests # smoke tests (Unix)`
`161`	`161`	`author = {Martinez Gamo, F. F.},`
`162`	`162`	`title = {TNFR-Python-Engine: Resonant Fractal Nature Theory Implementation},`
`163`	`163`	`year = {2025},`
`164`		`- version = {0.0.3.2},`
	`164`	`+ version = {0.0.3.3},`
`165`	`165`	`doi = {10.5281/zenodo.17602860},`
`166`	`166`	`url = {https://github.com/fermga/TNFR-Python-Engine}`
`167`	`167`	`}`