Update repository agent operating contracts

0-Core-Formalism/lean/Semantics/AGENTS.md

@@ -33,6 +33,30 @@ lake build
 
 - `Semantics.BeaverMaskFreshness` is a finite admission gate for Beaver-mask
   freshness negative controls.
+- `Semantics.HCMMR.Kernels.EntropyCollapseDetector` is the finite arithmetic
+  receipt for the corrected entropy-collapse detector. It intentionally keeps
+  logarithmic/Hurst quantities as scaled receipt constants and proves the
+  dense-rank crossing count, D2 numerator, and Kendall tail values with
+  executable Lean checks.
 - Stack status receipts live under `shared-data/data/stack_solidification/`.
-- The current staged slice is documented in
+- The canonical arithmetic note is
-  `../../../6-Documentation/docs/stack_solidification_staging_manifest_2026-05-09.md`.
+  `../../../6-Documentation/docs/distilled/ArithmeticSpec_Corrected_2026-05-11.md`.
+  Treat `sigma_q` on `n=8` as a deterministic window feature, not as a robust
+  Hurst estimator.
+- The K=21 prime-gap rerun receipt is
+  `../../../shared-data/data/stack_solidification/prime_gap_k21_rerun_receipt_2026-05-11.md`.
+  Its conclusion is deliberately bounded: rare surviving windows are candidate
+  motifs, not a general prime-gap collapse theorem.
+- Historical staged slices are documented in
+  `../../../6-Documentation/docs/stack_solidification_staging_manifest_2026-05-09.md`
+  and
+  `../../../6-Documentation/docs/stack_solidification_staging_manifest_2026-05-10.md`.
+
+## Local Quarantine Boundaries
+
+- The root `.gitignore` excludes known local formal scratch/WIP such as
+  `2-Search-Space/FAMM/FAMM_FSDU.lean` and `4-Infrastructure/hardware/test.lean`.
+  Do not revive ignored Lean files into the clean build surface without first
+  making them compile under a narrow target.
+- Generated `*_tb.v` and `*_test_vectors.json` files are build artifacts unless
+  a task explicitly promotes one as a hardware receipt.

4-Infrastructure/AGENTS.md

@@ -13,6 +13,13 @@ Scope: `4-Infrastructure/`
 - Treat `/usr/bin/sem` as GNU Parallel on this machine unless proven otherwise;
   use the isolated `sem` binary documented in stack solidification receipts when
   needed.
+- Remote model/API probes must be secret-clean. Read provider credentials from
+  environment variables only (`OLLAMA_API_KEY`, `DEEPSEEK_API_KEY`, etc.); never
+  embed literal keys in scripts, receipts, prompts, or docs.
+- LLM/model outputs are reviewer receipts, not validation. If a model review is
+  promoted, store the answer and a machine-readable receipt with prompt/answer
+  hashes under `shared-data/artifacts/`, and state which files formed the
+  context.
 
 ## Preferred Checks
 
@@ -21,6 +28,10 @@ python3 -m py_compile 4-Infrastructure/shim/<script>.py
 python3 -m json.tool <receipt>.json >/dev/null
 ```
 
+For API-facing or receipt-writing scripts, also run a touched-file secret scan
+before staging. Treat the repository credential hook as a backstop, not the
+first detector.
+
 For Tang Nano 9K work, keep the boundaries explicit:
 
 - bitstream present

5-Applications/text-to-cad/AGENTS.md

@@ -24,27 +24,44 @@ Project-specific context may live under `models/`. Keep project-local notes comp
 
 ## Python Environment
 
-Prefer the repo-local CAD runtime when it exists:
+The root workspace pins Python 3.11.15 in `.python-version` and exposes the CAD
+setup through root `package.json` scripts. From the repository root, prefer:
+
+```bash
+npm run install-python
+npm run setup-cad-env
+npm run verify-cad
+```
+
+These commands mirror the checked-in VS Code tasks in `.vscode/tasks.json`.
+
+Inside this harness, prefer the repo-local CAD runtime when it exists:
 
 ```bash
 ./.venv/bin/python
 ```
 
 This environment has the CAD dependencies required by the skill tools, including
-`build123d` and `OCP`. If `.venv` is missing or cannot import those modules,
+`build123d` and `OCP`. If `.venv` is missing or cannot import those modules and
-create/install it from the repo root before running CAD tools:
+the root scripts are unavailable, create/install it from this harness root:
 
 ```bash
 python3.11 -m venv .venv
 ./.venv/bin/pip install -r requirements-cad.txt
 ```
 
+Do not commit `.venv`, Python caches, or local package caches. They are runtime
+state, not CAD source.
+
 ## Source Of Truth
 
 - Generated CAD and URDF outputs are derived artifacts.
 - Package-local render, topology, component, and review-image artifacts are derived artifacts.
 - Do not hand-edit generated artifacts unless explicitly instructed. Edit the owning source file or imported source file first, then regenerate explicit targets with the relevant skill tool.
 - If regenerated output differs from checked-in generated files, the regenerated output is authoritative.
+- Root `.python-version`, root `package.json` scripts, and root VS Code tasks
+  are workspace setup surfaces. Update them when the preferred CAD rebuild
+  command changes.
 
 ## Prompt Artifacts
 

6-Documentation/docs/AGENTS.md

@@ -1,7 +1,7 @@
 # AGENTS.md — Strict LLM Operating Rules
 
 **Repository:** Sovereign Stack / Research Stack
-**Version:** 2.1 — Anti-Drift Evidence Standards (2026-04-29)
+**Version:** 2.2 — Anti-Drift Evidence Standards (2026-05-12)
 **Paradigm:** Functional Collapse — All models reduce to a single `bind` primitive.
 **Ground Truth:** Lean 4 (`0-Core-Formalism/lean/Semantics/`).
 **Goal:** Zero-guesswork, proven-correct, hardware-native code.
@@ -259,6 +259,34 @@ else:
 - Achieved: 6 sigma (error < ±5 samples)
 - If error > ±10 samples: alert user, do not commit
 
+### 5.3 Entropy-Collapse Detector Arithmetic
+
+The canonical detector arithmetic is
+`distilled/ArithmeticSpec_Corrected_2026-05-11.md`, mirrored by
+`0-Core-Formalism/lean/Semantics/Semantics/HCMMR/Kernels/EntropyCollapseDetector.lean`.
+
+Hard boundaries:
+
+- Dense ranking is mandatory. Equal values get equal rank; tied pairs do not
+  create braid crossings.
+- For W=8, the corrected example has `crossings = 12`, not 18.
+- `K=7` is not selective under the random-permutation null:
+  `P(count > 7) = 38129/40320 = 94.57%`.
+- `K=21` is a heuristic random-permutation calibration:
+  strict `count > 21` gives `1230/40320 = 3.05%`; inclusive `count >= 21`
+  gives `2191/40320 = 5.43%`.
+- `sigma_q` on an `n=8` window is a deterministic window feature, not a robust
+  long-series Hurst estimate.
+- 1D Renyi D2 is bounded in `[0,1]`; `D_c = 1.2` is a definition mismatch for
+  this estimator. `D_c = 0.7` is heuristic.
+- Prime gaps do not satisfy the random-permutation null. Ties, non-uniform gap
+  marginals, overlapping windows, local dependence, and multiple testing must
+  be stated before making any prime-gap signal claim.
+
+The current bounded conclusion is: the original prime-gap result was mostly an
+artifact of non-selective `K=7`; strict `K=21` leaves rare candidate motifs, not
+evidence of a general prime-gap collapse phenomenon.
+
 ---
 
 ## 6. File and Edit Discipline
@@ -678,6 +706,11 @@ theorem energyConserved (initial final : PhysicalState) :
 - Elegance is not effect size
 - Coherence is not compression gain
 
+LLM reviews may be stored as reviewer receipts only when they include prompt
+hash, answer hash, model, timestamp, and the exact context files. They can guide
+follow-up work, but they do not override Lean checks, arithmetic receipts,
+hardware receipts, or empirical baselines.
+
 **Valid evidence requires:**
 - Reproducible benchmarks with corpus provenance
 - SI units for physically projectable claims

AGENTS.md

@@ -10,6 +10,11 @@ This file is the first stop for coding agents working in this repository.
 - Prefer repo-native tools and receipt generators over ad hoc summaries.
 - Treat Lean as the source of truth for formal or hardware-adjacent claims.
 - Keep claims bounded: a receipt proves only the gate it actually checks.
+- Secrets are runtime-only. Use environment variables such as `OLLAMA_API_KEY`
+  or `DEEPSEEK_API_KEY`; never paste, print, or commit literal provider keys.
+- For repo-stabilization tasks, finish with a clean `git status --branch --short
+  --untracked-files=all` and an empty `git clean -nd` dry run before claiming
+  the tree is stable.
 
 ## Core Surfaces
 
@@ -18,7 +23,11 @@ This file is the first stop for coding agents working in this repository.
 - Hardware bring-up: `4-Infrastructure/hardware/`
 - Documentation and wiki surfaces: `6-Documentation/`
 - Stack receipts: `shared-data/data/stack_solidification/`
-- Current scoped staging map: `6-Documentation/docs/stack_solidification_staging_manifest_2026-05-09.md`
+- Promoted review receipts: `shared-data/artifacts/deepseek_review/`
+- CAD harness: `5-Applications/text-to-cad/`
+- Historical scoped staging maps:
+  `6-Documentation/docs/stack_solidification_staging_manifest_2026-05-09.md`
+  and `6-Documentation/docs/stack_solidification_staging_manifest_2026-05-10.md`
 
 ## Verification Expectations
 
@@ -26,6 +35,12 @@ This file is the first stop for coding agents working in this repository.
 - For Python shims, run `python3 -m py_compile` on touched files.
 - For JSON receipts, run `python3 -m json.tool` or a repo-native receipt parser.
 - For hardware claims, distinguish software witness, bitstream presence, SRAM load, flash persistence, UART beacon, and live hardware receipt.
+- Before committing, run `git diff --cached --check` and a staged secret scan
+  for touched source/receipt files. The repository credential hook is a final
+  gate, not a substitute for local review.
+- For root CAD setup changes, JSON-parse `package.json`, `.vscode/settings.json`,
+  and `.vscode/tasks.json`, then use the pinned Python/CAD commands documented
+  in `5-Applications/text-to-cad/AGENTS.md`.
 
 ## Do Not Sweep
 
@@ -40,6 +55,30 @@ git clean -fdx
 
 Use explicit file lists from the relevant staging manifest.
 
+`shared-data/` is ignored by default because most of it is generated or
+offloaded. Promote only specific, durable receipts with `git add -f -- <path>`,
+and keep empty/failed model outputs out of Git unless they are themselves the
+evidence under review.
+
+## Git Remote Hygiene
+
+- The active branch may not have an upstream. Inspect with
+  `git rev-parse --abbrev-ref --symbolic-full-name @{u}` before assuming push
+  state.
+- For GitHub sync, prefer the `github` remote and verify the remote head after
+  push:
+
+```bash
+git fetch github <branch>
+git rev-list --left-right --count FETCH_HEAD...HEAD
+git push -u github <branch>
+git ls-remote --heads github <branch>
+```
+
+- Dependabot banners printed by GitHub after push may be stale relative to the
+  live alert API. Treat the push result and remote-head hash separately from
+  dependency-alert remediation.
+
 ## Legacy Recovery Trigger
 
 The phrase **`RECOVER LEGACY INFORMATION`** is the explicit retrieval trigger