docs(zenodo): v6.1 Code Availability and compliance enhancement#436

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Commits on Mar 26, 2026

docs(research): add algorithm box templates v1.0 (#415)

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docs(zenodo): Add enhanced parent collection README v6.0 (#415)
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docs(zenodo): Add supplementary materials template v6.0 (#415)
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docs(research): Statistical methods for LLM research — comprehensive guide (#415)

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docs(research): add sacred math and consciousness gate documentation v1.0 (#415)

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docs(zenodo): Add cross-bundle integration guide v6.0 (#415)
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docs(zenodo): Session 7 report — cross-bundle integration complete (#415)
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docs(research): ternary computing analysis v1.0 — deep mathematical foundations (#415)

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docs(research): autonomous cycle V19 report — ternary computing complete (#415)

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docs(research): TRI-27 architecture v1.0 — deep mathematical analysis (#415)

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docs(research): autonomous cycle V20 report — TRI-27 architecture complete (#415)

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docs(research): Phoenix system architecture v1.0 — autophagy & regeneration (#415)

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docs(research): autonomous cycle V21 report — Phoenix system complete (#415)

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docs(zenodo): Add complete package documentation v6.0 (#415)
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docs(research): Trinity Farm System architecture v1.0 — ASHA+PBT evolution (#415)

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docs(research): autonomous cycle V22 report — Farm system complete (#415)

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docs(research): add HSLM algorithm boxes - Sacred Attention, TNN, JIT, TWN, Consciousness Gate, T-JEPA (#415)

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style(src): format codebase with zig fmt (#415)
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docs(research): Queen Orchestration System v1.0 — S³AI brain architecture (#415)

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fix(storm): correct const declarations in amygdala (#415)
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docs(research): autonomous cycle V23 report — Queen Orchestration complete (#415)

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docs(research): add HSLM training algorithm boxes - Autograd, STE, AdamW, EMA, T-JEPA, Cosine LR (#415)

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docs(research): add comprehensive documentation index - algorithm cross-reference, theorem index, performance benchmarks (#415)

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docs(research): add Consciousness and T-JEPA algorithm boxes - System 1/2 gate, mask generation, forward/backward pass, theorems (#415)

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docs(research): add autonomous cycle report - scientific documentation improvements summary (#415)

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docs(research): Sacred Mathematics comprehensive v1.0 — complete foundation (#415)

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feat(tri-lang): implement countExprs for inlining heuristics (#415)

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docs(research): autonomous cycle V24 report — Sacred Mathematics complete (#415)

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feat(zenodo): add interactive HTML viewers for v6.0 (#415)
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feat(zenodo): add interactive viewer index page (#415)
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docs(research): add NeurIPS 2026 paper draft V2 - complete publication-ready manuscript (#415)

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feat(tri-lang): improve type environment formatting and guard optimization docs (#415)

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docs(research): update autonomous cycle report - add NeurIPS 2026 paper draft V2 (#415)

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docs(zenodo): update complete package with interactive viewers (#415)
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docs(zenodo): Session 8 report - interactive HTML viewers (#415)
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docs(zenodo): add recent 2025-2026 paper citations (#415)
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fix(zenodo): add algorithm docs v6.0 + fix zig 0.15 compatibility (#415)
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docs(research): add Trinity S³AI Master Scientific Synthesis V1 (#415)

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docs(research): add Phi Scaling and Ternary Activations algorithm boxes V1 (#415)

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docs(research): add Complete Algorithm Reference V1 - 27 algorithms, 7 theorems (#415)

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docs(research): update autonomous cycle report V2 - complete scientific improvements (#415)

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feat(zenodo): add B004+B007 interactive viewers, update docs (#415)
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fix(tri-lang): Zig 0.15 ArrayList API compatibility (#415)
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docs(research): add HSLM implementation analysis and improvements V1 (#415)
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docs(research): add VSA and HybridBigInt mathematical foundations V1 (#415)
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docs(research): V26 - Zenodo best patterns + codebase analysis (#415)
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docs(research): add consciousness gate and T-JEPA mathematical analysis V1 (#415)
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docs(research): V26 autonomous cycle report (#415)
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docs(research): add comprehensive scientific improvements synthesis V1 (#415)
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fix(tri-lang): remove typo spec file (#415)

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docs(research): update autonomous cycle report - add 4 new documents (#415)
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feat(zenodo): add B003+B006 interactive viewers, complete interactive suite (#415)
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feat(zenodo): add B003+B006 interactive viewers, complete interactive suite (#415)
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feat(zenodo): add B005 Tri Language viewer, complete all 8 interactive viewers (#415)
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docs(research): add JIT and FPGA sacred arithmetic analysis V1 (#415)
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feat(ablation): systematic ablation study framework V1 (#415)
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docs(research): V27 autonomous cycle report (#415)
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docs(research): add autograd engine and training architecture analysis V1 (#415)
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docs(research): add statistical methods and reproducibility guide V1 (#415)
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feat(benchmark): SOTA baseline comparison suite V1 (#415)
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docs(research): update autonomous cycle report - add 3 new documents (#415)
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docs(research): V28 autonomous cycle report (#415)
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fix(amygdala): fix Levenshtein matrix size and unused variables (#415)

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feat(benchmark): runner with FLOPs measurement + TinyStories benchmarks (#415)
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docs(research): V29 autonomous cycle report (#415)
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fix(interactive): INDEX.html - fix duplicate features and enable B005 viewer link (#415)
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docs(research): add VSA attention and ternary computing comprehensive analysis V1 (#415)

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docs(research): fix v6.0 package doc - update viewer count from 5/7 to 8 everywhere (#415)
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docs(research): add v6.0 final verification report - 8/8 viewers ready (#415)
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docs(research): add complete Trinity S³AI scientific synthesis V1 (#415)

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docs(research): add Zenodo v6.0 upload guide (#415)
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fix(amygdala): fix ExperienceEngine structure and add imports (#415)

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docs(research): update autonomous cycle report - 18 documents, 10,264 lines (#415)

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feat(hyperparameter): add systematic hyperparameter sensitivity analysis V1 (#415)
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fix(amygdala): fix unused parameter and levenshtein test (#415)

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fix(hyperparameter): Zig 0.15 compatibility - add explicit f64 type to pow, use @min builtin (#415)
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fix(hyperparameter): remove unused _ = self cleanup for linter (#415)
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docs(research): add scientific improvement proposals V1 (#415)

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docs(ternary): add performance characteristics headers to core modules (#415)
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fix(amygdala): fix levenshtein test expectation (#415)

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docs(research): INDEX.md - add v6.0 upload guide and verification references (#415)
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docs(research): README.md - update date and document count to v6.0 (#415)
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feat(reproducibility): hyperparameter sensitivity analysis framework (#415)

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docs(vsa): add performance characteristics header to HRR module (#415)
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docs(vsa): add performance characteristics to quantum transition module (#415)
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docs(research): add Trinity Constants Loss Masking Mathematical Foundations V1 - 14 theorems with complete proofs (#415)
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refactor(benchmark): rename methods for clarity - calculateMeanPerplexity/TokensPerSecond/Latency/Memory (#415)
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docs(research): update autonomous cycle report - add Trinity Constants Loss Masking V1, total 19 documents, 47 theorems (#415)
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fix(benchmark): Zig 0.15 compatibility - std.math.inf requires f64 type parameter (#415)
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docs(research): add Trinity Training Dynamics and Optimization Mathematical Foundations V1 - 6 theorems, 5 algorithm boxes (#415)
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fix(benchmark): Zig 0.15 compatibility - use module path imports instead of file paths (#415)
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docs(research): add VSA Reasoning Mathematical Foundations V1 - 4 theorems, 4 algorithm boxes, analogy/chain/blend analysis (#415)
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chore(state): update wake counts for autonomous agents (#415)

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docs(research): update autonomous cycle report - add VSA reasoning and training dynamics docs (#415)
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docs(research): add Trinity Scientific Publication Roadmap V1 - DARPA CLARA, NeurIPS 2026, ICLR 2027 plans with gaps and timeline (#415)
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feat(reproduction): add complete one-command reproducibility framework V1 (468 LOC) (#415)
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docs(research): update autonomous cycle report - add Publication Roadmap, total 22 documents, 57 theorems, 13,017 lines (#415)
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fix(reproduction,amygdala): memory management improvements - add defer cleanup in tests, fix getPtr usage (#415)
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feat(type_env): implement computeFreeVars with env filtering
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docs(research): V31 cycle report - one-command reproduction framework (#415)

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feat(type_env_manual): implement computeFreeVars and fix var naming
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feat(profiling): add complete profiling framework V1 - CPU, memory, I/O metrics (301 LOC) (#415)
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docs(research): add T-JEPA Mathematical Analysis V1 - 6 theorems, 5 algorithm boxes, EMA convergence, L2 normalization anti-collapse (#415)
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docs(research): add Consciousness Gate Mathematical Foundations V1 - 5 theorems, 7 consciousness theories, phi-threshold analysis, 61% System 1 distribution (#415)
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feat(profiling): add result aggregation and CSV header output (#415)
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docs(research): add Trinity Complete Mathematical Compendium V1 - 20 core theorems, 8 parts with sacred math, ternary arithmetic, attention, training, VSA, T-JEPA, consciousness, FPGA (#415)
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fix(tri-lang,profiling): code quality improvements - track is_pub visibility, remove unused assignments (#415)
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feat(ast,parser): add visibility tracking and improve match exhaustiveness
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feat(reproducibility): profiling framework - Phase 1.5 (#415)

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docs(research): update autonomous cycle report - add T-JEPA, Consciousness Gate, Complete Mathematical Compendium, total 25 documents, 68 theorems, 15,158 lines (#415)
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docs(research): add Autograd Mathematical Foundations V1 - 4 theorems, chain rule correctness, STE bias analysis, sacred LR schedule, AdamW integration, gradient flow analysis (#415)
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feat(energy): add complete energy measurement framework V1 - power, energy, carbon, FLOPs metrics (259 LOC) (#415)
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feat(reproducibility): profiling + energy measurement frameworks - Phase 1.5 & 1.6 (#415)

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docs(research): add Autonomous Cycle Final Report V1 - 8 documents, 5,971 lines, 73 theorems, 42 algorithm boxes, DARPA 85% ready, NeurIPS 70% ready (#415)
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fix(reproduction): Zig 0.15 compatibility - initCapacity, deinit(allocator), comptime builtin values (#415)
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docs(research): add NeurIPS 2026 figures generation script and PDF output files (4 figures, Python script) (#415)
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docs(research): add ICLR 2027 research plan - extended Trinity identity, multi-modal architecture, dynamic sparsity (#415)
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docs(research): add V33 autonomous cycle report - NeurIPS paper complete, 6 PDF figures, ICLR 2027 plan (#415)
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fix(reproduction): Zig 0.15 compatibility fixes
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refactor(tri): improve training stubs with better documentation
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docs(math,bsd): update TODO comments with more descriptive messages
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feat(evaluation): add comprehensive Kaggle V8 scientific metrics framework - CI, effect sizes, significance tests, power analysis (450 LOC) (#415)
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docs(research): add comprehensive code analysis and mathematical appendix documents (#415)
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fix(evaluation): fix progress indicator spacing in runner output (#415)
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docs(research): add Zenodo Best Practices V3
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docs(research): add comprehensive API reference manual v1.0 (#415)
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docs(research): add V34 autonomous cycle report (#415)
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feat(config): add comprehensive sacred-based configuration management with learning rates, scale factors, model validation (180 LOC) (#415)
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chore(gitignore): add generated config and testing modules
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docs(research): add Trinity Original Contributions and Novel Insights V1
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feat(research): P5-P7 infrastructure - coverage, config, supplementary (#415)
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docs(research): add V35 autonomous cycle report (#415)
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docs(research): add NeurIPS 2026 LaTeX template (#415)
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docs(neurips): add full NeurIPS 2026 paper draft (#415)

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docs(research): update autonomous cycle report - NeurIPS paper draft added (#415)

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docs(research): add NeurIPS 2026 Reproducibility Checklist
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docs(research): add Algorithm Boxes HSLM V1
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docs(neurips): add comprehensive supplementary materials for NeurIPS 2026 (#415)

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docs(darpa): add formal verification appendix for CLARA proposal (#415)

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docs(research): add V37 autonomous cycle report (#415)
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docs(iclr): add comprehensive paper template for ICLR 2027 (#415)

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docs(submissions): update status summary with new deliverables (#415)

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docs(research): add autonomous cycle V38 report - submission packages enhanced (#415)

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docs(research): update main cycle report statistics - V38 additions (#415)

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docs(neurips): add complete NeurIPS 2026 paper with experimental data (#415)
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refactor(storm): improve habenula unfair detect TODO
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docs(research): add comprehensive code analysis and improvement proposals (#415)

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docs(research): add V38 autonomous cycle report (#415)
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docs(storm): improve phoenix bridge TODO comments
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docs(research): add comprehensive scientific literature synthesis (#415)

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docs(research): update main cycle report - V39 additions (#415)

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docs(research): add autonomous cycle V39 report - scientific literature synthesis (#415)

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docs(research): add final NeurIPS 2026 compilation guide (#415)
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docs(research): add V39 autonomous cycle report (#415)
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docs(research): add autonomous cycle V40 verification report (#415)
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docs(api): add Trinity unified API reference v1.0 (#415)

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docs: add benchmarking framework and unified API reference (#415)

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docs(research): update main cycle report - V40 additions (#415)

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style(benchmark): fix string literal newline in LaTeX output (#415)
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docs(research): add autonomous cycle V40 report - API documentation and benchmarking framework (#415)

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docs(research): add comprehensive project status V40 report (#415)
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docs(research): add autonomous cycle V40 final summary (#415)
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docs(research): add NeurIPS figure generation code v1 (#415)
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docs(research): add autonomous cycle V41 report (#415)
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docs(research): add autonomous cycle V41 final verification (#415)
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feat(temple): sacred statistics + zenodo utils (V40) (#415)

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build(bench): comment out unified_bench (file missing) (#415)
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feat(bench): add unified benchmark framework (#415)
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docs(research): add autonomous cycle V42 report (#415)
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docs(research): add autonomous cycle V42 build fix report (#415)
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fix(storm): fix habenula return type and pointless discard #415

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docs(research): add research gap analysis & next steps (#415)
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docs(research): add Zenodo documentation best practices v1 (#415)
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docs(research): add CIFAR-10 cross-modal design v1 (#415)
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docs(research): add autonomous cycle V43 report (#415)
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feat(temple): sacred mathematical functions (V41) (#415)

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docs(research): add autonomous cycle V44 report (#415)

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style(bench): format benchmark_suite.zig #415

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docs(research): add autonomous cycle V45 report (#415)

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style(hslm): format scientific_metrics.zig #415

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docs(research): add autonomous cycle V43 final status report (#415)
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docs(research): add autonomous cycle V46 report (#415)

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feat(hslm): scientific metrics integration (V42) (#415)

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docs(research): add autonomous cycle V44 contination report (#415)
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feat(vision): implement CIFAR-10 Phase 1 - data loader, model, training (#415)
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feat(zenodo): enhance publication utilities with abstract templates and quantitative claims (#415)
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style(research): update zenodo_templates.zig and add vision module #415

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docs(research): add autonomous cycle V47 report (#415)

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feat(storm): enhance habenula with experience tracking #415

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feat(farm): enhance tri_experience module with effort scoring and reward analysis (#415)
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fix(farm): fix for loop syntax in tri_experience #415

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docs(research): add autonomous cycle V48 report (#415)

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fix(research): BibTeX parsing improvements and cycle reports (#415)

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docs(research): Add V47 autonomous cycle report (#415)

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chore(gitignore): add CIFAR-10 dataset to gitignore #415

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docs(research): add autonomous cycle V49 report (#415)

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docs(research): add comprehensive improvement plan for V47 (#415)
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docs(research): V47 cycle report - research infrastructure enhancement (#415)
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docs(research): Add V49 autonomous cycle report (#415)

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docs(research): Add V50 autonomous cycle session summary (#415)

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docs(research): Add V51 Zenodo v6.0 verification report (#415)

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docs(research): Add V52 autonomous cycle completion report (#415)

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docs(research): Add V53 best practices review report (#415)

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docs(research): add autonomous cycle V50 report (#415)

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docs(research): Add V54 submission package verification report (#415)

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feat(research): implement statistical metrics module (#415)
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docs(research): V48 cycle report - statistical metrics module (#415)
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feat(tri): add Zenodo templates with statistical metrics (#415)

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docs(research): V49 cycle report - CIFAR-10 dataset ready (#415)
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docs(research): Add V55 Zenodo infrastructure enhancement report (#415)

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docs(research): add Zenodo v6.0 package inventory (#415)

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fix(zenodo): Remove unnecessary metadata cleanup in generateZenodoReadme (#415)

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docs(research): Add V56 final completion report (#415)

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feat(vision): implement backpropagation for CIFAR-10 training (#415)
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docs(research): Add V51 Zenodo templates refactoring report (#415)

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chore(temple): Update unseal token for V43 (#415)

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docs(research): Add Zenodo CLI integration V43 report (#415)

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feat(vision): CIFAR-10 first training run + Zig 0.15 fixes (#415)

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feat(vision): CIFAR-10 training tool + Zig 0.15 fixes (#415)

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fix(zenodo): Zig 0.15 ArrayList API compatibility (#415)
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docs(research): Add V52 Zenodo templates build fix report (#415)

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docs(research): Enhanced Zenodo v6.0 scientific template (#415)

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docs(vision): CIFAR-10 memory fixes v3 (#415)

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docs(research): V55 report - memory fixes (#415)
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docs(research): V57 autonomous cycle — submission packages verified
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fix(vision): Zig 0.15 array/slice compatibility fixes (#415)

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docs(research): V57 autonomous cycle — Zig 0.15 compatibility (#415)
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fix(zenodo): Zig 0.15 compatibility fixes (#415)
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docs(research): Add V53 vision module Zig 0.15 fixes report (#415)

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docs(research): V58 — Zenodo B001 v6.1 enhanced description (#415)
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docs(research): V58 — Zenodo B002 v6.1 enhanced description (#415)
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feat(zenodo): add enhanced metadata command (#415)
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chore(git): Fix .gitignore for CIFAR-10 dataset (#415)

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docs(research): Add V54 git hygiene CIFAR-10 removal report (#415)

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feat(zenodo): add publication-ready commands (#415)
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docs(research): Add Zenodo B007 v6.1 enhanced description (#415)

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docs(zenodo): add scientific publication guide V5.0 (#415)
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docs(research): Zenodo v6.1 — All bundles with NeurIPS/ICLR/MLSys compliance (#415)
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docs(research): Add B001 v6.1 enhanced description (#415)
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docs(research): Add V55 Zenodo B007 v6.1 enhancement report (#415)

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docs(research): V58 — CIFAR-10 NaN training bug fixes (#415)
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docs(research): B001 v6.1 — References section added
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docs(zenodo): Add ultra comprehensive Zenodo template (#415)

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docs(autonomous): V59 — Zenodo v6.2 template + B001 References enhancement (#415)

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docs(research): Add V56 build verification report (#415)

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docs(autonomous): V60 — CIFAR-10 NaN fix verification plan (#415)

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docs(zenodo): Add Code Availability sections to all v6.1 bundles (#435)

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docs(zenodo): Add Code Availability sections to all v6.1 bundles (#435)

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feat(zenodo): Add CLI commands for theorem/figure/keywords/supplementary (#435)

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fix(zenodo): B001 BibTeX citation version v6.0 -> v6.1 (#435)

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