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Research-Stack/0-Core-Formalism/otom
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Brandon Schneider b58c1201ac Remove legacy Python prototypes superseded by Lean formalization 
Deleted 58 Python files (~31K lines) that were experimental prototypes
and bootstrapping scripts now superseded by the Lean source of truth:

0-Core-Formalism/core/ (2 files):
  - field_solver_emulator.py
  - formalize_mass_number.py

0-Core-Formalism/lean/LeanGPT/ (17 files):
  - All LLM bootstrapping scripts (algorithm_bootstrap, automated_conviction_loop,
    classify_algorithms, external_model_bridge, genetic_hypothesis_generator,
    group_algorithms_by_domain, hutter_prize_full_test, hutter_prize_test,
    hypothesis_generator, mathematical_law_conviction, otom_pipeline,
    performance_profiler, refine_algorithms_by_domain, skeptical_agent_concern_fix,
    skeptical_agent_swarm, wgsl_hypothesis_runner)

0-Core-Formalism/lean/Semantics/ (1 file):
  - expand_domains.py

0-Core-Formalism/otom/ (4 files):
  - scripts/validate_routing.py
  - tools/ene/ene_artifact_salvage_extractor.py
  - tools/genetics/emit_selection_receipt.py
  - tools/genetics/selection_metrics.py

2-Search-Space/ (14 files):
  - FAMM/solve_famm_sorry.py
  - GhostPivot/gist_pivot_poc.py
  - PIST/hybrid_tsm_pist_torus.py, pist_sweep.py
  - SVQF/microgrid_voxel_emulation.py
  - manifold/ (9 files: api/server, collapse_editor, particle_interaction,
    projection_engine, relativity_adapter, self_typing_engine, soliton_search,
    substrate_bridge)
  - search/generate_lut.py, ingest_pd.py, sweep_manifold.py

3-Mathematical-Models/ (20 files):
  - dna_benchmark/compressors/ (5 files)
  - pist_biological_polymorphic_shifter_v3*.py (5 files)
  - fiber_optic_vibrational_tensor/fiber_optic_tensor_network.py
  - manifold_compression/src/ (2 files)
  - fix_kwargs_meta.py, fix_metadata.py, fix_remaining.py, fix_sbox.py
  - genetics/Allelica/Allelica.py

These prototypes expressed formal concepts in Python that are now
formalized in Lean (747+ Lean modules). Per AGENTS.md, Lean is the
source of truth for formal claims.

Generated with [Devin](https://cli.devin.ai/docs)

Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
2026-05-19 15:34:17 +00:00
..
.github/workflows initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00
data Add selection metrics synthetic fixture 2026-05-05 13:22:32 -05:00
docs Consolidate research stack updates 2026-05-05 21:09:48 -05:00
formal/lean/SidonAudit initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00
hardware/verilog/core initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00
prototypes/webgpu-lean-ontology initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00
specs initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00
tools/lean/Semantics Remove legacy Python prototypes superseded by Lean formalization 2026-05-19 15:34:17 +00:00
CITATION.cff initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00
CONCEPTS.md initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00
README.md initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00

README.md

OTOM — Ordered Transformation & Orchestration Model

OTOM is the canonical GitHub seed repository for the Research Stack: a Lean-first system for information theory, compression, graph/torsion routing, neural/manifold semantics, infrastructure shims, and hardware extraction targets.

Grounding axioms

  1. Lean is the source of truth. Python, Rust, Verilog, GraphML, Mermaid, and UI surfaces are extraction targets or projections.
  2. Publishing pipeline: Substrate / ENE ↔ Surface / Notion ↔ Intent / Linear ⟹ Metatype.
  3. Settlement lifecycle: SEED → FORMING → STABLE → CRYSTALLIZED → COMPRESSED.

Authority rule

Lean / Graph.lean      = canonical structure and proof authority
GraphML               = transport format
Mermaid               = static projection
Ace Knowledge Graph   = interactive projection only
Notion                = semantic registry / spec source
Linear                = task graph
Airtable              = operational mirror if connected later
Consensus             = literature context, not proof
GitHub                = code/provenance surface once seeded

Nothing updates canonical memory directly. Every item must become an artifact first:

artifact → fingerprint → route → outcome → memory

Placement tuple

All promoted artifacts use:

Project → Domain → Type → Settlement State

See docs/plumbing/PROJECT_DOMAIN_TYPE_MAP.md.

Current bootstrap docs

Canonical Lean entry

tools/lean/Semantics/Semantics/Constitution.lean

Repository status

This repo is being seeded from connected-source audit results. Treat current modules as FORMING until lake build and proof obligations are wired into CI.