Research-Stack/REBASE_RULES.md

REBASE RULES — Research Stack Agent / Rules Manifest

Purpose: This file is a rebase seed. When starting a fresh project map, copy only the files and rules listed here. Do not migrate runtime state, stale audits, or completed assignment boards.

Principle: Port the contracts and the rituals, not the state.

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1. Core Operating Contracts (MUST PORT)

These files are the source of truth for every agent, skill, and editor hook. They are actively maintained and cross-referenced throughout the stack.

File	Scope
AGENTS.md (root)	Master operating contract: post-interaction workflow, programming-choice flow, Q16_16 doctrine, Git hygiene, Do-Not-Sweep rules, glossary, claim boundaries.
0-Core-Formalism/lean/Semantics/AGENTS.md	Lean/Semantics local contract: blessed Compiler surface, build baselines, quarantine boundaries, proof-tactic lessons, current solidification anchors.
4-Infrastructure/AGENTS.md	Infrastructure and shim contract: storage stack, hardware-witness boundaries, ENE schema, compute dispatch pattern.
6-Documentation/docs/AGENTS.md	Strict LLM operating rules: anti-drift evidence standards, bind primitive, naming conventions, sigma levels, SI units, deletion criteria, PQC policy.
5-Applications/text-to-cad/AGENTS.md	CAD harness contract: generated CAD/URDF source-of-truth, viewer handoff, repo policies.
scripts/qc-flag/AGENTS.md	Lean QC protocol: 7-check inspection protocol.
shared-data/artifacts/lean_expert_agent/AGENTS.md	Lean expert agent /inspect protocol and output format.
.github/RRC_OPERATING_CONTRACT.md	Rainbow Raccoon Compiler gate definition: ACCEPT / HOLD / QUARANTINE.

Non-negotiable rules extracted from the contracts

1. Lean is the source of truth. Python, Rust, and Verilog are extraction targets only.
2. Programming choice flow — before writing new logic, check this decision tree in order:
   • Admissibility / routing / alignment / gating decision? → Lean only.
   • Emitting a top-level receipt or JSON bundle? → Semantics.AVMIsa.Emit only.
   • Classifying rows / computing alignment scores? → Lean (Semantics.RRC.*).
   • Supplying raw input features (equation text, IDs, weak_axes)? → Python shim OK, no admissibility logic, regenerable from source.
   • Float arithmetic in a compute path? → STOP. Use Q16_16.ofNat, Q16_16.ofRatio, or Q16_16.ofRawInt.
   • Advancing promotion status in shim space? → STOP. not_promoted until a Lean gate passes.
   • Pure I/O (read/write JSON, subprocess, format output)? → Python shim OK. Receipt output routes through AVMIsa.Emit.
3. No Float in compute paths. ofFloat is permitted only at JSON/sensor boundaries and must be immediately bracketed.
4. Post-interaction workflow (mandatory after any code/receipt/architecture change):
   • Update the nearest scoped AGENTS.md for every touched subtree.
   • Run lake build Compiler (and full lake build if Lean files touched).
   • Commit with an explicit file list; never git add ..
   • Run git status --branch --short --untracked-files=all.
5. Do Not Sweep: never run git add ., git checkout -- ., or git clean -fdx.
6. Secrets are runtime-only: use environment variables (OLLAMA_API_KEY, DEEPSEEK_API_KEY, etc.); never commit literal keys.
7. Legacy recovery is explicit: use RECOVER LEGACY INFORMATION: <path/commit/concept> only. Current cornfield ref: backup/distilled-with-vcd-history-2026-05-11.

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2. Editor / Agent Configs (MUST PORT)

These files inject the contracts into editor/agent runtimes.

File	Purpose
.cursorrules	Cursor: ContextStream init()/context()/search() rules.
.devin/config.json	Devin: programming-choice reminder hook.
.devin/hooks.json	Devin: ContextStream hooks.
.devin/hooks/programming-choice-reminder.sh	Injects programming-choice flow + post-interaction checklist before every user message.
.claude/settings.json	Claude Code: ContextStream hooks.
.cursor/hooks.json	Cursor: ContextStream hooks.
.roo/mcp.json	Roo: MCP server definitions.
.mcp.json (root)	Minimal MCP config: filesystem, git, fetch, contextstream, lean, remote-lean-proof, sympy, wolfram, aws, github, headroom.
.contextstream/config.json	ContextStream workspace/project IDs.
.kilo/rules/contextstream.md	Kilo Code manual ContextStream rules (no hooks available).
.roo/rules/contextstream.md	Roo Code ContextStream rules.
.windsurf/rules/contextstream.md	Windsurf ContextStream rules.

ContextStream-first workflow (enforced or self-enforced in every editor)

• First message: init(folder_path=...) → context(user_message=...).
• Subsequent messages: context(user_message=...) FIRST.
• Before any file search: search(mode="auto") BEFORE Glob/Grep/Read/Explore/Task/EnterPlanMode.
• After edits: project(action="index") in editors without auto-indexing.
• Save transcripts: save_exchange=true in editors without auto-saving.

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3. Skills (MUST PORT)

Skill	Path	Purpose
lean-proof	.devin/skills/lean-proof/SKILL.md	Mandatory for all Lean work: proof quality, Q16_16 contract, #eval witnesses, promotion gate.
contextstream-workflow	.github/skills/contextstream-workflow/SKILL.md	Persistent memory: plans, tasks, decisions, lessons.
research-stack-workflow	.github/skills/research-stack-workflow/SKILL.md	Token-efficient proof workflow; local inference first on neon.
headroom	.opencode/skills/headroom/SKILL.md	Context compression and cross-agent memory.
cad	5-Applications/text-to-cad/skills/cad/SKILL.md	Script-driven STEP/STL/DXF/GLB generation.
urdf	5-Applications/text-to-cad/skills/urdf/SKILL.md	URDF generation and validation.
rrc-compile	.claude/skills/rrc-compile/SKILL.md	RRC pipeline orchestrator.
rrc-scale-analysis	.claude/skills/rrc-scale-analysis/SKILL.md	RRC pre-flight Q16_16 scale-band analysis.

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4. MCP Servers (MUST PORT)

From .mcp.json / .roo/mcp.json:

Server	Role
contextstream	Persistent memory / context / search
filesystem	Read/write proof artifacts and receipts
git	History, blame, diff
fetch	HTTP docs and RFCs
lean	Lean 4 / Mathlib typecheck bridge
remote-lean-proof	Hermes / OpenCode / Codex proof backend
sympy	Symbolic arithmetic verification
wolfram-alpha	Formula verification (needs WOLFRAM_APP_ID)
aws	AWS API access
github	PRs, issues, CI
headroom	Token / context compression

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5. Conditional Items (PORT ONLY IF DOMAIN REMAINS ACTIVE)

File	Condition
.windsurf/lifeguard.yaml	Keep only if genetics / GCCL / Mass Number abstraction work continues. Contains safety doctrine for biological-equivalence claims, reverse-collapse, bounded recursion, and claim-state hygiene.
.opencode/agents/*.md	Keep only if the target sorry/theorem is still open in the new rebase. These are task-specific subagent prompts.
.claude/workflows/ground-disproved-theorems.js	Keep only if Claude Code still uses this workflow.

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6. DROP — Do Not Port

Item	Reason
.consolidation-manifests/	Historical SHA256 manifests from 2026-05-04. Not load-bearing.
.headroom/*.db	Runtime memory databases; regenerate on first use.
.agents/plugins/marketplace.json	References a dormant ./plugins/substack-connector. Not load-bearing.
.github/copilot-instructions.md	Core rules are valid, but the "Current Project State" block is stale (2026-05-28). Port rules separately, not this file as authority.
.windsurf/SORRY_AUDIT.md	Stale audit (2026-05-28). Root AGENTS.md now reports 0 sorries in the active Compiler surface. Archive only.
.windsurf/ASSIGNMENTS.md	Dated 2026-04-19; all assignments marked COMPLETE and references old paths. Historical residue.
Staging manifests (stack_solidification_staging_manifest_2026-05-09.md, etc.)	Historical archives; referenced but not authoritative.
Cornfield / legacy branches	Do not merge or base work on them. Use only via explicit recovery trigger.

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7. Minimal Rebase Checklist

Use this when standing up the new project map.

• Copy all files in Section 1 (Core Operating Contracts).
• Copy all files in Section 2 (Editor / Agent Configs).
• Copy all files in Section 3 (Skills).
• Copy/adapt .mcp.json and .roo/mcp.json with current server paths.
• Update .contextstream/config.json with new workspace/project IDs if they change.
• Review Section 5 conditional items and keep only active-domain rules.
• Verify Section 6 dropped items are not carried over.
• Run lake build Compiler and confirm job count matches the new baseline.
• Update build baseline and commit hash in 0-Core-Formalism/lean/Semantics/AGENTS.md.

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8. Design Note for the New Map

When designing the new project layout, preserve these boundary rules:

• Lean owns decisions; Python owns I/O.
• Semantics.AVMIsa.Emit is the sole top-level receipt boundary.
• shared-data/ is ignored by default. Promote only durable receipts with git add -f -- <path>.
• Research artifacts go outside the git tree (e.g. /home/researcher/research/ in the container model).
• Every new compression path needs two Lean theorems: eigensolid_convergence and receipt_invertible.

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9. Cornfield Recovery Manifest (SilverSight Port)

What is the cornfield? Concepts developed during Research Stack sessions that were archived, quarantined, or left as probes — not in the active Lean Compiler surface, but recoverable. The canonical record lives in extraction/cornfield_concepts.json. The databases are authoritative.

Database state (2026-06-21):

• arxiv.math_objects WHERE id LIKE 'cf_%': 19 rows
• ene.packages WHERE package_type = 'cornfield_concept': 19 packages
• ene.relations (cornfield edges): 23 relates_to edges
• Gremlin concepts graph, cohort=cornfield: 19 vertices, 38 edges

To add a new cornfield concept: append to extraction/cornfield_concepts.json, run uv run scripts/load_cornfield.py.

9a. Port — Carry to SilverSight

ID	Concept	Action	Priority
cf_phi_universal	Φ = Σ wᵢ/ln(Nᵢ) — universal field equation	promote_to_foundation	P0 CRITICAL
cf_codebase_memory	FAMM 7-domain bank + thermal + scar + dual-map	port_as_stub	HIGH — skeleton for SilverSight memory model
cf_codebase_fsdu	ΔS = S_ahead − S_behind scar differential gate	port_as_stub	HIGH — discrete form of NKHodgeFAMM scar
cf_codebase_receipt	Receipt-gated memory access	port_as_stub	HIGH — completes AVMIsa.Emit → Hermes chain
cf_hachimoji_shell	N=2^m base alphabet, k=⌊n^(1/m)⌋ shell	promote_to_active	HIGH — physics grounding for SpectralSignature
cf_w_axis_omega	Ordinal/cost/bridge pressures for AngrySphinx	formalize_in_lean	HIGH — FORMALIZATION_DRAFT, missing from synthesis
cf_ms3c_nested_gear	4-weight balanced shear scoring {0.25×4}	extend_s3c_shell	MEDIUM — softer gate than binary Q0_2 threshold
cf_gap_space_padic	p-adic ultrametric generalizes Sidon gap	extract_padic_gap	MEDIUM — unifies CrossDomainOneOverN family
cf_padic_calculus	p-adic integration, Haar measure	extend_cross_domain_1_over_n	MEDIUM
cf_eit_invariant	PHI = non-Euclidean correction to Landauer	link_phi_to_landauer	MEDIUM — one import away
cf_coherence_kernel	R_O = 1/7 invariant	formalize_as_constant	MEDIUM — 1/7 in two independent contexts
cf_info_thermo	Landauer + PHI_NE correction	merge_into_landauer	MEDIUM
cf_landauer_genetic_clock	E_gen = G·ε·E_r; T_clock formula	merge_into_landauer	MEDIUM — bridges Hachimoji to HutterPrize
cf_genus3_topology	β₂(Σ₃)=1 → NKHodgeFAMM fails	link_to_nk_hodge	MEDIUM — explicit counterexample class
cf_adiabatic_limit	g_ε=g_B/ε²+g_F, ε→0 collapse	link_to_nk_hodge	MEDIUM — formal justification for Q0_2 threshold
cf_morphic_dsp	Morphic scalar field + neural network bridge	extract_missing_formulations	LOW — active module exists, probe has more
cf_rrf_ranking	rrf_score = Σ 1/(k+rᵢ), k=60	add_to_graph_rank	LOW — already used in shim layer
cf_semantic_basin_overflow	100×bandwidth × 50M×compression = 5×10⁹	link_to_phantom	LOW — context for phantom coupling scale

9b. Drop — Do Not Port

ID	Reason
cf_snap_citations	INFRA GAP, not a concept — ingest cit-HepPh/HepTh to arxiv.citations before port (2 COPY commands from neon-64gb:/home/allaun/snap_data/)

9c. Cornfield Query Patterns

-- All cornfield concepts by priority
SELECT pkg, archetype, provenance->>'lean_status'
FROM ene.packages WHERE package_type='cornfield_concept'
ORDER BY archetype;

-- Cornfield → active module connections (via Gremlin)
-- g.V().has('cohort','cornfield').out('depends_on').values('id')

-- Concepts needing Lean formalization
SELECT id, name FROM arxiv.math_objects
WHERE id LIKE 'cf_%' AND lean_status IN ('ARCHIVED','UNDOCUMENTED','FORMALIZATION_DRAFT');

9d. Invariant for the new map

Every new cornfield concept recovered into SilverSight must satisfy:

• Either imports an existing active Lean module (inherits its proof constraints), OR
• Has a silversight_action of formalize_in_lean with a named stub theorem in the build baseline.

No floating concepts. If it's not reachable from Semantics.AVMIsa.Emit via imports or depends_on, it is not on the map.

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Generated from active Research Stack agent rules and contracts. Principle: port contracts and rituals, not state. Cornfield manifest last updated: 2026-06-21 — 19 concepts.