Research-Stack/5-Applications
Brandon Schneider 6679908f7b fix(arch): enforce Lean-first hierarchy across project — remove all secondary-Lean language
Project-wide sweep to find and fix every place Lean was treated as secondary,
optional, or subordinate to Python/Rust. The invariant: Lean is the source of
truth. Python and Rust are extraction targets only; they contain no logic, no
invariant checks, no decisions.

Changes:

1-Distributed-Systems/ene/src/lib.rs
  - CRITICAL: Remove 'Rust is the canonical implementation language for
    operational components' — replace with correct extraction-target framing

1-Distributed-Systems/agents/claw/README.md
  - Remove 'canonical implementation lives in rust/' and 'source of truth is
    ultraworkers/claw-code' blanket claims — scope to CLI binary only;
    add Research Stack domain-logic note (Lean is source of truth per AGENTS.md)
  - 'canonical Rust workspace' → 'Rust workspace (I/O extraction target)'

1-Distributed-Systems/agents/claw/src/Tool.py
  - 'Python-first porting summary' → 'Lean-to-Python extraction summary'

1-Distributed-Systems/agents/claw/src/projectOnboardingState.py
  - python_first: bool = True → lean_first: bool = True (Lean always leads)

6-Documentation/docs/specs/ENE_MEMORY_ATLAS_SPEC.md
  - CRITICAL: 'Python first (reference) ... Lean-formal next' → correct order:
    Lean specification first, Python extraction shim, Verilog hardware extraction

6-Documentation/docs/recovered/geocognition_equation_types_map.mmd
  - 'Lean owns logic; Rust owns boundary' → 'Lean owns all logic and decisions;
    Rust is boundary shim only'

6-Documentation/docs/semantics/HYPER_DIMENSIONAL_PHYSICS_INTRO.md
  - 'Python implementation ... Lean formalization' → 'Lean specification (source
    of truth) ... Python extraction shim'

6-Documentation/docs/geometry/GEOMETRY_TAXONOMY_FOR_NLOCAL_ADAPTATION.md
  - 'reference specification for the Python implementation' → 'source of truth;
    Python is an extraction shim against this spec'

6-Documentation/docs/protocols/TM_MCP_SPECIFICATION.md
  - 'Python reference implementation' → 'Python extraction shim' (×2)

5-Applications/scripts/snn/README.md
  - 'deterministic Python reference' → 'Python extraction shim / golden-vector
    harness'; add TODO(lean-port) note; RTL must match 'Python shim (pending
    Lean golden vector)' not 'Python reference'

6-Documentation/docs/METAPROBE_APPROACH.md
  - 'DeltaGCLCompression.lean — Lean implementation / scripts/delta_gcl_encoder.py
    — Python reference implementation' → Lean is source of truth / Python is
    extraction shim

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

Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
2026-05-26 22:40:03 -05:00
..
AppFlowy-Cloud Add EC2 recovery backup: NixOS config, AppFlowy compose/env template, credential server bootstrap, recovery guide 2026-05-18 10:44:23 -05:00
audio-dsp Track remaining source and documentation inventory 2026-05-11 22:18:31 -05:00
audit initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00
cff Track remaining source and documentation inventory 2026-05-11 22:18:31 -05:00
compression-core Track remaining source and documentation inventory 2026-05-11 22:18:31 -05:00
hutter_prize initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00
linear-native-tauri Bump the linear-tauri-cargo-minor-patch group 2026-05-20 23:03:27 -05:00
nodupe Patch NoDupe qs vulnerability 2026-05-25 20:52:25 -05:00
notion-native-tauri Bump the notion-tauri-cargo-minor-patch group 2026-05-20 23:03:27 -05:00
parquet_compressor Bump dashmap 2026-05-20 23:03:27 -05:00
pist-scripts initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00
plugins/substack-connector Track remaining source and documentation inventory 2026-05-11 22:18:31 -05:00
scripts fix(arch): enforce Lean-first hierarchy across project — remove all secondary-Lean language 2026-05-26 22:40:03 -05:00
teleport-kanban Bump the cargo group across 3 directories with 1 update 2026-05-20 23:02:48 -05:00
tests initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00
text-to-cad docs(agents): project-wide AGENTS.md audit — cross-refs, baseline, contracts 2026-05-26 22:34:46 -05:00
tools-scripts archive: remove experimental tools-scripts, scripts, and shim probes 2026-05-25 18:14:31 -05:00
finance_manager.py chore: preserve working tree before secure wipe 2026-05-13 17:36:02 -05:00
README.md initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00
requirements_swarm_api.txt initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00
visualizer_service.py initial: sovereign research stack (consolidated, weightless, and lfs-optimized) 2026-05-04 18:11:36 -05:00

5-Applications

Purpose: End-to-end pipelines, integration tests, automation scripts, benchmarks, audit.

Depends on: 0 through 4

Contents (Target)

Source Destination
5-Applications/scripts/ 5-Applications/scripts/
5-Applications/tests/ 5-Applications/tests/
5-Applications/out/ 5-Applications/out/
5-Applications/audit/ 5-Applications/audit/

Scripts

  • build_manifold_graphml.py
  • export_manifold_to_obsidian.py
  • hot_swap_daemon.py
  • hot_swap_manager.py

Pipeline

  1. Generate provably hard question (Builder: ADD clock)
  2. Route via OmnidirectionalInterface (Lean)
  3. Execute via DomainModelIntegration (Lean → Python shim)
  4. Store in Google Drive topological storage (Warden: SUBTRACT clock)
  5. Hardware triumvirate integration (Judge: PAUSE clock)