Track DeepSeek review receipts and CAD setup tasks

.python-version

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+3.11.15

.vscode/settings.json

@@ -1,5 +1,6 @@
 {
     "cmake.sourceDirectory": "/home/allaun/Documents/Research Stack/2-Search-Space/simulations/heat-2D",
+    "python.defaultInterpreterPath": "/home/allaun/.local/share/uv/python/cpython-3.11-linux-x86_64-gnu/bin/python3.11",
     "files.watcherExclude": {
         "**/.git/objects/**": true,
         "**/.git/subtree-cache/**": true,

.vscode/tasks.json

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+{
+  "version": "2.0.0",
+  "tasks": [
+    {
+      "label": "Install Python 3.11.15",
+      "type": "shell",
+      "command": "uv",
+      "args": [
+        "python",
+        "install",
+        "3.11.15"
+      ],
+      "options": {
+        "cwd": "${workspaceFolder}"
+      },
+      "problemMatcher": [],
+      "presentation": {
+        "echo": true,
+        "reveal": "always",
+        "focus": false,
+        "panel": "shared",
+        "showReuseMessage": true,
+        "clear": false
+      }
+    },
+    {
+      "label": "Setup CAD Environment",
+      "type": "shell",
+      "command": "bash",
+      "args": [
+        "-c",
+        "cd 5-Applications/text-to-cad && python3.11 -m venv .venv && ./.venv/bin/pip install -r requirements-cad.txt"
+      ],
+      "options": {
+        "cwd": "${workspaceFolder}"
+      },
+      "problemMatcher": [],
+      "presentation": {
+        "echo": true,
+        "reveal": "always",
+        "focus": false,
+        "panel": "shared"
+      }
+    },
+    {
+      "label": "Verify CAD Dependencies",
+      "type": "shell",
+      "command": "./.venv/bin/python",
+      "args": [
+        "-c",
+        "import build123d; import OCP; print('CAD dependencies OK')"
+      ],
+      "options": {
+        "cwd": "${workspaceFolder}/5-Applications/text-to-cad"
+      },
+      "problemMatcher": [],
+      "presentation": {
+        "echo": true,
+        "reveal": "always",
+        "focus": false,
+        "panel": "shared"
+      }
+    }
+  ]
+}

package.json

@@ -2,6 +2,11 @@
   "name": "research-stack",
   "private": true,
   "description": "Local Research Stack tooling dependencies.",
+  "scripts": {
+    "install-python": "uv python install 3.11.15",
+    "setup-cad-env": "cd 5-Applications/text-to-cad && python3.11 -m venv .venv && ./.venv/bin/pip install -r requirements-cad.txt",
+    "verify-cad": "cd 5-Applications/text-to-cad && ./.venv/bin/python -c \"import build123d; import OCP; print('CAD dependencies OK')\""
+  },
   "dependencies": {
     "better-sqlite3": "^12.4.1"
   }

shared-data/artifacts/deepseek_review/prime_gap_entropy_collapse_deepseek_deepseek-v3.2_20260512T033551Z.md

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+**1. YES/NO VERDICT TABLE**
+
+| Question | Verdict | Notes |
+|----------|---------|-------|
+| Q1: Internal consistency of canonical arithmetic? | YES | All computed values match the spec and Lean receipt. |
+| Q2: Is K=7 invalid as a selective threshold? | YES | FPR ≈94.57% under random-permutation null. |
+| Q3: Is K=21 defensible for ~5% FPR? | YES (with caveats) | Strict `>21`: 3.05% FPR. Inclusive `>=21`: 5.43% FPR (slightly above 5%). |
+| Q4: Does prime-gap signal survive corrected threshold? | YES (severely attenuated) | Strict `>21`: 38 fires (0.0038% of windows). Inclusive `>=21`: 190 fires (0.019%). Original `>7`: 86,565 fires (8.66%). |
+| Q5: Is the provided conclusion appropriately worded? | YES | Correctly states original was artifact, surviving fires are rare candidate motifs, not general phenomenon. |
+| Q6: Is the fusion rule correct for intended semantics? | YES | `braid(t→t+1)` AND `sigma_q(t+1)` AND `D_q(t+1)` correctly targets turbulent transition into collapsed arrival window. |
+
+---
+
+**2. ARITHMETIC RECHECK**
+
+- **Crossing count**: `dense_rank(A)=[0,2,1,0,2,1,0,1]`, `dense_rank(B)=[2,1,0,2,1,0,1,2]`. 12 crossings verified.
+- **D₂**: `sum p² = 22/64 = 0.34375`. `D₂ = -log(0.34375)/log(8) ≈ 0.5135`.
+- **σ_q (Hurst)**: MSD(1)=64/7≈9.143, MSD(2)=8, MSD(4)=10. OLS slope=0.0646, `σ_q=0.0323`.
+- **Kendall SD**: Variance = `8×7×21/72 = 16.3333`, SD = `√16.3333 = 4.04145`.
+- **Exact tail probabilities** (W=8, 40320 permutations):
+  - `P(count>7) = 38129/40320 ≈ 0.9457`
+  - `P(count>21) = 1230/40320 ≈ 0.0305`
+  - `P(count>=21) = 2191/40320 ≈ 0.0543`
+- **All values match** the canonical spec and Lean receipt.
+
+---
+
+**3. STATISTICAL INTERPRETATION**
+
+- **K=7 threshold**: HEURISTIC and non-selective (94.57% FPR under random permutations). Using it as a braid component in a triple condition does not control false positives.
+- **K=21 threshold**: HEURISTIC calibration to ~5% FPR under random-permutation null. Strict `>21` yields 3.05% FPR; inclusive `>=21` yields 5.43% FPR.
+- **σ_q and D₂ thresholds**: `σ_c=0.4` and `D_c=0.7` are HEURISTIC. `σ_q=0.0323` is a DETERMINISTIC WINDOW FEATURE (n=8 is too short for reliable Hurst estimation).
+- **Prime-gap data**: The random-permutation null is not appropriate for prime gaps (ties, non-uniform marginal distribution, local dependence). Therefore, the FPRs above are not reliable for prime gaps.
+
+---
+
+**4. PRIME-GAP SIGNAL VERDICT**
+
+- **Original signal (`cross>7`)**: 86,565 fires in 999,991 windows (8.66%). This high rate is expected given the 94.57% FPR of the braid component alone.
+- **Corrected strict (`cross>21`)**: 38 fires (0.0038%). **Survives but extremely rare**.
+- **Corrected inclusive (`cross>=21`)**: 190 fires (0.019%). **Survives but rare**.
+- **Interpretation**: The original claim of common firing on prime gaps was an artifact of the non-selective K=7. The corrected thresholds reduce fires by factors of ~2,300 (strict) and ~450 (inclusive). Surviving windows are candidate structured motifs (e.g., alternating patterns) but do not support a general entropy-collapse phenomenon.
+
+---
+
+**5. FUSION-RULE VERDICT**
+
+- **Rule**: `braid(t→t+1) AND sigma_q(window t+1) AND D_q(window t+1)`
+- **Intended semantics**: Detect turbulent transition (braid) into a window that is already collapsed (low σ_q and D₂). Using `window t` for σ_q/D₂ would detect collapse in the departure window, which could fire early.
+- **Verdict**: The rule correctly implements the intended semantics.
+
+---
+
+**6. FAILURE MODES**
+
+1. **Tied ranks**: Dense ranking excludes ties, but the permutation null assumes distinct values. Prime gaps have ties (e.g., many gaps of 2). This invalidates the permutation FPR.
+2. **Overlapping sliding windows**: Windows overlap by 7 points, violating independence assumptions. Multiple testing corrections are non-trivial.
+3. **Prime-gap marginal distribution**: Gaps are not uniformly distributed (e.g., even gaps except 1, high frequency of 2). The random-permutation null is inappropriate.
+4. **Local dependence**: Prime gaps exhibit local patterns (e.g., twin primes, gap chains). The braid crossing statistic assumes independent permutations.
+5. **Using permutation-tail FPR on non-permutation data**: The 5% FPR threshold is derived under a random-permutation null, which does not hold for prime gaps. Actual FPR unknown.
+6. **Multiple testing**: Testing ~1 million overlapping windows without correction inflates family-wise error rate.
+
+---
+
+**7. NEXT VALIDATION TESTS**
+
+1. **Permutation test on prime gaps**:
+   - **Method**: For each window pair, shuffle the 8 gap values within each window independently (preserving marginal distribution but breaking local structure). Compute the number of fires under the corrected threshold.
+   - **Expected**: If the observed fires (38 strict, 190 inclusive) are within the 95% percentile of the permutation distribution, the signal is consistent with chance.
+2. **Block bootstrap test**:
+   - **Method**: Resample blocks of prime gaps (block length >8) to preserve local dependence. Compute firing rates.
+   - **Expected**: If the observed firing rate is not significantly higher than bootstrap rates, the signal may be due to dependence.
+3. **Non-overlapping windows**:
+   - **Method**: Use non-overlapping windows (t=0,8,16,...) to reduce dependence.
+   - **Expected**: If fires remain rare, strengthens signal; if they disappear, suggests overlapping-window artifact.
+4. **Synthetic data with same marginal distribution**:
+   - **Method**: Generate i.i.d. sequences from the empirical gap distribution (first 1M primes). Compute firing rate.
+   - **Expected**: If observed fires exceed synthetic fires, suggests structure beyond marginal distribution.
+5. **Adjust for multiple testing**:
+   - **Method**: Apply Bonferroni or Šidák correction to the per-window threshold (e.g., `alpha = 0.05 / 999,991`).
+   - **Expected**: The corrected threshold becomes more stringent (K>21). If fires persist, they are more significant.
+
+---
+
+**8. CANONICAL SPEC PATCHES**
+
+Add these explicit warnings and clarifications to the canonical spec:
+
+1. **Thresholds are heuristic**:
+   "K=21, σ_c=0.4, D_c=0.7 are calibrated to a white-noise random-permutation null. They do not guarantee a 5% FPR for non-permutation data (e.g., prime gaps)."
+
+2. **Window features are not estimators**:
+   "σ_q (Hurst) and D₂ computed on n=8 are DETERMINISTIC WINDOW FEATURES, not statistically reliable long-series estimators. Do not report confidence intervals or p-values."
+
+3. **Prime-gap null mismatch**:
+   "Prime gaps violate the random-permutation null due to ties, non-uniform marginal distribution, and local dependence. Permutation-based FPRs are not applicable."
+
+4. **Multiple testing**:
+   "Sliding windows overlap, violating independence. Family-wise error rate is uncontrolled. Any claimed signal must survive multiple-testing correction."
+
+5. **Fusion rule clarification**:
+   "The fusion rule uses `sigma_q(window t+1)` and `D_q(window t+1)` to detect collapse in the arrival window, not

shared-data/artifacts/deepseek_review/prime_gap_entropy_collapse_deepseek_deepseek-v3.2_20260512T033551Z.receipt.json

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shared-data/artifacts/deepseek_review/prime_gap_entropy_collapse_deepseek_deepseek-v4-flash_continuation_20260512T033849Z.md

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+the current window. The arrival window is the one immediately following the candidate transition, so the fusion rule is inherently predictive, not contemporaneous."
+
+6. **No ground truth for prime gaps**:
+   "There is no known 'true' critical transition in prime gaps. All detected events are unvalidated. The method can only flag candidate windows for further study, not confirm a phase change."
+
+7. **Parameter sensitivity**:
+   "Results depend on window size (n=8), step size (1), and feature thresholds. Small changes in n or thresholds can eliminate or create signals. Report sensitivity analysis."
+
+8. **Edge effects**:
+   "The first and last n-1 windows have incomplete neighbors for the fusion rule. Exclude them or treat separately."
+
+9. **Reproducibility**:
+   "All code, data, and random seeds must be published. The permutation null requires exact replication of the shuffling procedure."
+
+10. **Interpretation caveat**:
+    "Even if a window passes all criteria, it may be a false positive due to the heuristic thresholds and null mismatch. Do not claim statistical significance without a valid null model."

shared-data/artifacts/deepseek_review/prime_gap_entropy_collapse_deepseek_deepseek-v4-flash_continuation_20260512T033849Z.receipt.json

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