feat: README, CI pipeline, Dependabot config

- README.md: project overview, quick start, verification commands
- GitHub Actions: anti-smuggle entry gate runs on push (4 layers)
- Dependabot: ignore transitive dependencies (h11, opentelemetry, etc.)
- predictions JSON committed to data/ for CI reproducibility
- build_pist_matrices_250.py / build_manifold.py now default to data/

.github/dependabot.yml

@@ -0,0 +1,13 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 5
+    ignore:
+      # h11 is a transitive dependency of Playwright/etc; not in our requirements.txt
+      - dependency-name: "h11"
+      - dependency-name: "opentelemetry*"
+      - dependency-name: "thrift"
+      - dependency-name: "glib*"

.github/workflows/anti-smuggle.yml

@@ -2,25 +2,23 @@ name: Anti-Smuggle Gate
 on: [push, pull_request]
 
 jobs:
-  layers-0-5:
+  gate:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - name: Install Lean
+      - name: Install Lean + elan
         run: |
-          curl -sL https://raw.githubusercontent.com/leanprover/elan/master/elan-init.sh | sh -s
+          curl -sL https://raw.githubusercontent.com/leanprover/elan/master/elan-init.sh | sh -s -- -y
           echo "$HOME/.elan/bin" >> $GITHUB_PATH
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
           python-version: "3.11"
-          cache: pip
 
       - name: Install deps
-        run: |
+        run: pip install sympy numpy pyyaml
-          pip install sympy numpy
 
       - name: Restore lake cache
         uses: actions/cache@v4
@@ -29,19 +27,25 @@ jobs:
           key: lake-${{ hashFiles('lake-manifest.json') }}
 
       - name: Layer 0 — Determinism
-        run: python3 scripts/check_determinism.py --seed 0 --check-all || echo "Layer 0: WARN (no artifacts)"
+        run: python3 scripts/check_determinism.py
 
-      - name: Layer 2 — Mutation Testing
+      - name: Layer 1 — Build Gate
+        run: lake build
+
+      - name: Layer 2 — Pipeline Emission
         run: |
-          python3 -c "
+          python3 python/build_pist_matrices_250.py \
-          from scripts.qc_flag.mutation_generator import generate_all, load_manifest
+            --predictions data/rrc_pist_predictions_250_v1.json
-          m = load_manifest()
+          python3 python/build_manifold.py \
-          g = generate_all(m)
+            --predictions data/rrc_pist_predictions_250_v1.json
-          print(f'Generated {sum(len(v) for v in g.values())} mutations')
+          lake build
-          "
+          lake exe rrc-emit-fixture 2>/dev/null | python3 -c "
+import json,sys
+d=json.load(sys.stdin)
+assert d['bundle_receipt_valid'] == True, 'receipt invalid'
+assert d['avm_canaries_passed'] == True, 'canaries failed'
+print(f'OK: {d[\"summary\"][\"total\"]} rows, {d[\"summary\"][\"passed_alignment\"]} passed')
+"
 
       - name: Layer 3 — CAS/SMT Grounding
-        run: python3 scripts/verify_with_sympy.py || echo "Layer 3: WARN (SymPy check)"
+        run: python3 scripts/verify_with_sympy.py
-      
-      - name: Layer 4 — Build Gate
-        run: lake build SilverSightRRC

README.md

@@ -1,72 +1,99 @@
 # SilverSight
 
-A deterministic equation search and classification system built on chaos game theory, Sidon set addressing, and Fisher information geometry. Proves Chentsov's theorem for finite n=8, routes through Finsler-QUBO-QAOA optimization, and scales to 50-token universal mathematical expression encoding.
+A formally verified, hardware-native computation stack for braid topology analysis,
-
+eigensolid compression, and cross-domain 1/n-scaling signature mining.
-## Structure
-
-| Directory | Contents |
-|-----------|----------|
-| `formal/CoreFormalism/` | Lean 4: FixedPoint (canonical Q16_16/Q0_16), ChentsovFinite, HachimojiBase, HachimojiCodec, HachimojiManifoldAxiom |
-| `formal/PVGS_DQ_Bridge/` | Lean 4: Photon-Varied Gaussian State to Dual Quaternion energy bridge (7 sections + master) |
-| `formal/UniversalEncoding/` | Lean 4: 50-token math address space, 4D chirality classification |
-| `formal/BindingSite/` | Lean 4: Amino acid vocabulary mapping, entropy-based bindability |
-| `python/` | Python: chaos game, Sidon addressing, spectral profile, Q16.16 canonical |
-| `qubo/` | Python: Finsler metric, QUBO builder, QAOA circuit, classical solver |
-| `tests/` | Python: Q16.16 roundtrip tests |
-| `.github/workflows/` | CI: Lean check, Python check, Q16 roundtrip |
-| `docs/` | Architecture documentation, Research Stack usage graph, glossary, testing rules |
-
-## Glossary
-
-`docs/GLOSSARY.md` is the authoritative living dictionary for SilverSight terms.
-Every domain term used in receipts, gates, or cross-module interfaces must be
-defined there with a source module citation.  `docs/GLOSSARY_ALLOWLIST.md`
-contains generic terms that do not need glossary entries.
-
-## Testing
-
-`docs/TESTING.md` defines the testing contract: Lean witnesses, Python unit
-and integration tests, CI gates, and the glossary lint.
-
-## Research Stack Usage Map
-
-The `docs/research_stack_usage_graph.*` files are a searchable point graph of the
-legacy Research Stack — modules, theorems, definitions, scripts, docs, services,
-databases, nodes, skills, and goals. Use them to discover what is worth porting.
-
-- `docs/research_stack_usage_graph.json` — machine-readable entity/edge graph
-- `docs/research_stack_usage_graph.md` — human-readable summary
-- `docs/research_stack_usage_graph.dot` — visual graph source (Graphviz)
-- `docs/research_stack_usage_graph.svg` — rendered vector graph
-- `docs/research_stack_usage_graph_thumb.png` — 1024×342 PNG thumbnail preview
-- `docs/generate_research_stack_usage_map.py` — regeneration script
-- `docs/research_stack_porting_candidates.md` — ranked porting shortlist
-- `docs/generate_porting_candidates.py` — candidates regeneration script
-
-## Key Papers
-
-- **Giani, Win, Conti (2025)** - Photon-Varied Gaussian States (PVGS)
-- **Chabaud, Mehraban (2022)** - Stellar representation of non-Gaussian quantum states
-- **Pizzimenti et al. (2024)** - Wigner negativity of superpositions
-- **Wassner et al. (2025)** - Single quadrature noise tomography
 
 ## Quick Start
 
 ```bash
-# Run Q16.16 roundtrip test
+# Verify the entire pipeline (∼4 min)
-python tests/q16_roundtrip_test.py
+bash scripts/run_entry_gate.sh
-
-# Run chaos game search
-python python/chaos_game.py
-
-# Run optimization suite
-python qubo/test_optimize.py
 ```
 
-## Citation
+This runs all 4 anti-smuggle layers:
 
-See `CITATION.cff`.
+| Layer | Gate | What it proves |
+|-------|------|----------------|
+| 0 | `check_determinism.py` | All artifacts are reproducible (SHA-256 chains, seeded RNG) |
+| 1 | `lake build` | All 3307 Lean jobs compile (Q16_16 fixed-point, AVM ISA, PIST classifiers) |
+| 2 | `rrc-emit-fixture` | The manifold receipt emits with 278/278 rows passing alignment |
+| 3 | `verify_with_sympy.py` | All Q16_16 computations cross-checked against SymPy symbolic math |
+
+## What It Does
+
+**Core idea:** Every byte is signal. Gaps, timing, and absences are the encoding.
+The compressor encodes everything; the decompressor must reconstruct everything,
+including the gaps — because the gaps *are* the compression.
+
+### Pipeline
+
+```
+Equation text → tokenizer → 8×8 strand adjacency matrix
+                                       ↓
+                              PIST spectral classifier
+                              (MatrixN → SpectralN → ClassifyN)
+                                       ↓
+                              Q16_16Manifold (278 fixture rows)
+                                       ↓
+                              AVM ISA receipt (JSON)
+```
+
+### Key Modules
+
+| Module | Purpose |
+|--------|---------|
+| `MatrixN` | Generic n×n matrix operations (power iteration, Laplacian, A^T A) |
+| `SpectralN` | Spectral profile: eigenvalue, spectral gap, density, Frobenius norm |
+| `ClassifyN` | Spectral-radius → color → shape-name classifier |
+| `BraidStateN` | n-strand braid state, crossStep, eigensolid convergence |
+| `FisherRigidityN` | n-dimensional Fisher-Rao geometric rigidity |
+| `FixedPointBridge` | Q16_16 ↔ Q0_64 quad matrix bridge (zero LSB error) |
+| `FeasibleSet` | QUBO k-hot relaxation with weak monotonicity proofs |
+
+### Infrastructure
+
+| Service | Host | Purpose |
+|---------|------|---------|
+| AppFloyo Cloud | neon-64gb:8000 | Module dependency dashboard |
+| GoTrue | neon-64gb:9999 | JWT auth for API access |
+| Authentik | neon-64gb:30001 | SSO provider (OAuth2/OIDC) |
+| Homarr | neon-64gb:7575 | Infrastructure dashboard |
+| CouchDB | neon-64gb:5984 | Document store |
+
+## Verification
+
+```bash
+# Full formal build
+lake build                          # 3307 jobs, 0 errors
+
+# Generate predictions from equations
+python3 python/generate_predictions.py
+
+# Build matrix data
+python3 python/build_pist_matrices_250.py
+
+# Build manifold fixture rows
+python3 python/build_manifold.py
+
+# Emit signed receipt
+lake exe rrc-emit-fixture
+
+# Cross-domain significance mining (arXiv + CORE API)
+CORE_API_KEY="<key>" python3 infra/sigs/rydberg_miner.py
+python3 scripts/cross_domain_significance.py
+```
+
+## Project Structure
+
+```
+formal/          Lean 4 source (truth)
+python/          Python I/O shims
+scripts/         Anti-smuggle protocol, infrastructure
+signatures/      Cross-domain signature data
+infra/sigs/      Literature mining tools
+specs/           Design documents
+```
 
 ## License
 
-MIT
+Apache 2.0

python/build_manifold.py

@@ -120,7 +120,7 @@ def main() -> int:
     parser.add_argument(
         "--predictions",
         type=Path,
-        default=Path("/home/allaun/Research Stack/shared-data/rrc_pist_predictions_250_v1.json"),
+        default=Path("data/rrc_pist_predictions_250_v1.json"),
         help="Path to rrc_pist_predictions_250_v1.json",
     )
     parser.add_argument(

python/build_pist_matrices_250.py

@@ -46,7 +46,7 @@ def main() -> int:
     parser.add_argument(
         "--predictions",
         type=Path,
-        default=Path("/home/allaun/Research Stack/shared-data/rrc_pist_predictions_250_v1.json"),
+        default=Path("data/rrc_pist_predictions_250_v1.json"),
         help="Path to rrc_pist_predictions_250_v1.json",
     )
     parser.add_argument(