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Research-Stack/GEMINI.md
Brandon Schneider 2aef54d052 chore: commit accumulated working tree changes 
Lean: update Semantics modules, add new numerics/physics data files
Hardware: update FPGA bitstreams (tangnano9k_uart_loopback)
Infra: k3s-flake tests, netcup-vps configuration, VCN compute substrate
Docs: ARCHITECTURE, specs, citation updates
2026-05-30 00:10:02 -05:00

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Gemini CLI Instructions for Research Stack

You are working in the Research Stack project. This project is a formally verified, formally grounded, and hardware-native stack. You MUST adhere to the strict operating rules defined in the AGENTS.md files.

Primary Mandate

Lean is the source of truth. All core logic belongs in 0-Core-Formalism/lean/Semantics/. Python, Rust, and Verilog are shims/extraction targets only.

Key Constraints (from AGENTS.md)

  • NO FLOATS: Use Q0_16 (pure fraction) or Q16_16 (mixed) fixed-point. Floats are BANNED in core logic.
  • NO NEW DEPENDENCIES: Do not add libraries without explicit human approval.
  • NO BROAD REFACTORING: Only change code that is broken, violates invariants, or cannot be extracted.
  • STATISTICAL RIGOR: All statistical claims must hit 6.5σ (preferred) or 6σ (acceptable). 5σ is the absolute floor.
  • GIT HYGIENE: Never use git add .. Always use explicit file lists.
  • RECOVER LEGACY INFORMATION: Use this exact trigger to revive archived info from cornfield branches.
  • SI UNITS: All physical and compression claims must use SI base units.
  • WOLFRAM ALPHA: Verify all mathematical formulas with Wolfram Alpha when possible.

Verification Workflow

  1. Plan: Outline the Lean implementation and the required theorems/#eval witnesses.
  2. Act: Implement in Lean first. Update shims only as extraction targets.
  3. Validate: Run lake build in 0-Core-Formalism/lean/Semantics/.
  4. Receipts: All infrastructure or storage changes must produce a machine-readable receipt.

Terminology

  • Use Sidon labels, BraidStorm, eigensolid, scar, receipt.
  • Refer to AGENTS.md for the full glossary.

Sub-Agents & Tools

  • Use storage_agent.py for restic/Garage/rclone operations.
  • Use gen_step_part etc. for CAD work in 5-Applications/text-to-cad/.
  • Use podman exec research-stack for container-bound tasks (Lean builds, WGSL).

References

  • Root Contract: AGENTS.md
  • Documentation/Lean Strict Rules: 6-Documentation/docs/AGENTS.md
  • Infrastructure: 4-Infrastructure/AGENTS.md
  • CAD: 5-Applications/text-to-cad/AGENTS.md

When to Use ContextStream Search:

✅ Project is indexed and fresh ✅ Looking for code by meaning/concept ✅ Need semantic understanding