fix: verify expansion artifacts before the paper release republishes them

.github/dependabot.yml

@@ -3,8 +3,7 @@ updates:
   - package-ecosystem: pip
     directory: /
     schedule:
-      interval: weekly
-      day: monday
+      interval: monthly
       time: "09:00"
       timezone: America/Los_Angeles
     open-pull-requests-limit: 5

CLAUDE.md

@@ -18,7 +18,11 @@ the development lock with `pip install -r requirements/dev.lock`, then run
 - Lint: `.venv/bin/ruff check .` (CI enforces this; must stay clean). Auto-fix: `ruff check . --fix`.
 - Dependency changes: edit `pyproject.toml`, then run
   `scripts/update_dependency_locks.sh`; commit `poetry.lock` and every changed
-  export under `requirements/`.
+  export under `requirements/`. Because `pyproject.toml` and `poetry.lock` are
+  release-critical fingerprinted inputs, a dependency change also requires
+  regenerating both artifact releases from the new clean source commit
+  (expansion wrapper first, then the paper wrapper); Dependabot lock-only PRs
+  therefore cannot pass CI and are handled through this coordinated flow.
 - Operational scripts import `quantcortex.*`, so run them with the root on the
   path: `PYTHONPATH=. .venv/bin/python scripts/<name>.py`
   (validate_performance, generate_report, survivorship_demo, verify_brokers,

docs/img/performance_manifest.json

@@ -1,11 +1,11 @@
 {
   "schema_version": 4,
-  "generated_at": "2026-07-02T05:47:22Z",
+  "generated_at": "2026-07-02T06:57:57Z",
   "generator": {
     "path": "scripts/generate_report.py",
     "script_sha256": "b536aa7fc5e4fe7df6c7ff28c0992629a489869eaec46486db7aff1cb946099b",
     "git": {
-      "source_commit": "dddead6351d956223e2c7aecf959dd2d93388be9",
+      "source_commit": "34096ad11c1ae33531186a86961a9e2e883d60a9",
       "worktree_clean_at_start": true
     },
     "source_tree": {

paper/build_manifest.json

@@ -1,18 +1,18 @@
 {
   "anonymous_pdf": {
     "path": "quantcortex_audit_anonymous.pdf",
-    "sha256": "7a7e5283b098957602eea34e38dde3ffe5b2968a622f4789e0ad8bdbe0c3bbb6"
+    "sha256": "74bd8f67606e4bad177b81c49f3818fd2682abceef3b39cb279bb497d5b8d062"
   },
   "pdf": {
     "path": "quantcortex_audit_neurips2026.pdf",
-    "sha256": "cf50fea34c2020061d86815c586106de87f26c9e29af46336524b899d1365cc2"
+    "sha256": "c2a16206747a6f9205396cb040d7cd01d0f5306319570286a218d9072388e7af"
   },
   "schema_version": 1,
-  "source_commit": "dddead6351d956223e2c7aecf959dd2d93388be9",
-  "source_date_epoch": 1782970812,
+  "source_commit": "34096ad11c1ae33531186a86961a9e2e883d60a9",
+  "source_date_epoch": 1782975290,
   "source_manifest": {
     "path": "quantcortex_audit_neurips2026.sources.sha256",
-    "sha256": "39e28d3967612a086eaab5d81bbb69023dbb939900c119f42d28cab3ec48a631"
+    "sha256": "e550f507515e06a0ee005ec23b828d0ed346230841a99c718063589249c3d443"
   },
   "tectonic_bundle": {
     "name": "default_bundle_v33.tar",

paper/expansion/results/manifest.json

@@ -163,9 +163,9 @@
       }
     ]
   },
-  "generated_at": "2026-07-02T05:40:12Z",
+  "generated_at": "2026-07-02T06:54:51Z",
   "git": {
-    "source_commit": "dddead6351d956223e2c7aecf959dd2d93388be9",
+    "source_commit": "34096ad11c1ae33531186a86961a9e2e883d60a9",
     "tracked_worktree_clean_at_start": true
   },
   "protocol": {
@@ -290,9 +290,9 @@
       "quantcortex/timing/vix_scaler.py": "a3667424e5573fb289e63c26c69da6a68d6c943742359f0466d29b25c56e3686",
       "schemas/canonical_target_tape.schema.json": "4f1c0bf6d5360305d2982adea78de3f61c4bc1ebae9207cb2ba2bd4379b43d44",
       "scripts/fetch_expansion_data.py": "678b5c7fcc1b89e333fc5298b1fdaeb8994de713bc7b2b5ed461e1ec1eb94403",
-      "scripts/release_expansion_artifacts.sh": "c66de150012bc2ad4ea06f65e2f8993a564c003c717e3b220cf6c2f665d363e0",
+      "scripts/release_expansion_artifacts.sh": "727e7b9c023df48550481f38887624e5c6154217e279af2d4e77da11b93c7400",
       "scripts/run_expansion_experiments.py": "df9932dc67a1e1151faebc5dfd742f0aa622dfcf8093ce5ef9c55d9be4fbaf59"
     },
-    "sha256": "3aeaab12c2c63f8022700be3a45978b4ca4f429703fde4566877eb4f2c830f0f"
+    "sha256": "3cea145651a58cdbb70509df5f53c56ff22d6ddf07c3bbe282280940d918777f"
   }
 }

paper/quantcortex_audit_anonymous.sha256

@@ -1 +1 @@
-7a7e5283b098957602eea34e38dde3ffe5b2968a622f4789e0ad8bdbe0c3bbb6  quantcortex_audit_anonymous.pdf
+74bd8f67606e4bad177b81c49f3818fd2682abceef3b39cb279bb497d5b8d062  quantcortex_audit_anonymous.pdf

paper/quantcortex_audit_neurips2026.sha256

@@ -1 +1 @@
-cf50fea34c2020061d86815c586106de87f26c9e29af46336524b899d1365cc2  quantcortex_audit_neurips2026.pdf
+c2a16206747a6f9205396cb040d7cd01d0f5306319570286a218d9072388e7af  quantcortex_audit_neurips2026.pdf

paper/quantcortex_audit_neurips2026.sources.sha256

@@ -4,11 +4,11 @@ c2b36aafee0ad2e3ac631e05a5fc1b20e1acce10dd0b4758667f0a809cafff51  checklist.tex
 62609e68cbc90516cf19a46d52f80bf07ab0a4751880e4c078cc9be4ba842a5c  references.bib
 0c1ad36961fcd9198dcc2558cf2793e1df39973bde8264fd701f5e7970672757  neurips_2026.sty
 06f4407daed7bcd594e00bbf2751e7bd32c5d00eae530b2a6b2f66625b864162  preregistration.md
-32e1a703329d6767d4184a940009c158a723738ba53c7de0ecc57bfac861da9b  results/generated_values.tex
-105d350319bac9a92bfb746d10da7414ad7de43140b69f6987ec5b54eca4c713  results/manifest.json
+4cee7de114227526d83abaae47a0c647451a864056955e91d099f846dfc4dfc4  results/generated_values.tex
+046e5cc9146f4344c144b9fa947e8b18d6f8c2b7a2bce26c5cc96f03c4d5576c  results/manifest.json
 e49e41a12a19fa5404a573ba5e21eb8a2888e616985f8c610d9652866923315c  expansion/protocol.json
 2dbaa11bfdd9a1936b45114f61bd96c53e3d57eefe103a75c488352486c0e2f9  expansion/results/generated_values.tex
-1db304ba19a96ac6890c3b6bec2bb7dc13793bf1298af990712b03ce617c4066  expansion/results/manifest.json
+8c9cfa381e4382bd7fe45af82e9f9d6a1a4c0503fd35db824053381e5c8d16a8  expansion/results/manifest.json
 18608aa1250c4554b2e27b507211f764fdf1ec1fb8e4b9f09e080601505e2e3a  figures/accounting_summary.pdf
 6765f7d1f827577ba648af7545d006ef7f005f0091194605c6130100215ac18c  figures/audit_protocol.pdf
 19df4c9eabe88add863ed4be4e9315aa0084b833be9deb4d5bb7633e769ced07  figures/bootstrap_robustness.pdf

paper/results/generated_values.tex

@@ -4,7 +4,7 @@
 \newcommand{\PaperRequiredWarmupSessions}{274}
 \newcommand{\PaperBootstrapReplications}{5,000}
 \newcommand{\PaperInputDigest}{efb384a62157e56a0cd8065abf45c1ed07d90ec26c681e5d54d74fe4cb9c55e1}
-\newcommand{\PaperSourceTreeDigest}{5bf7019e1a5f23262701fa5d8e02780c9f274a9b12821a4323818fd282efd295}
+\newcommand{\PaperSourceTreeDigest}{1c05d00cea1d0e9acc5118c3e9302fc50111a327ed15c48e25019a40cecec5b8}
 \newcommand{\PaperNetCAGR}{1.40\%}
 \newcommand{\PaperGrossCAGR}{3.17\%}
 \newcommand{\PaperCashCAGR}{2.50\%}

paper/results/manifest.json

@@ -20,7 +20,7 @@
     "results/cost_sensitivity.csv": "25b9969cf8ecdabd19e7761ad2973252c9f5b9f994b6dc147595a2a112c24d88",
     "results/engine_comparison.csv": "ea0322dcd2aa4a1eb3b5996045c3a4b2ed25a85684a578ee788b013b99b643cd",
     "results/evaluation_contract.json": "77ee05ce64622ef9ba1bfbd7dae85c4f6fd44f07db0b21feaf6b3e0e418673e7",
-    "results/generated_values.tex": "32e1a703329d6767d4184a940009c158a723738ba53c7de0ecc57bfac861da9b",
+    "results/generated_values.tex": "4cee7de114227526d83abaae47a0c647451a864056955e91d099f846dfc4dfc4",
     "results/protocol_switches.csv": "20d5a0dc37e07a20c1f2772c8e9940ff6464ef1da98692edd5fdb06531bc2393",
     "results/return_decomposition.csv": "53a84aa9b91c92f0037e48dc09154807cbf003ccf0038f39da8406108bf709cc",
     "results/sharpe_uncertainty.csv": "aead873ced9b25c76c6944aa6e3ba0901ade65c784fa5cb8cc10ad1c6c01f136",
@@ -240,14 +240,14 @@
     "path": "results/evaluation_contract.json",
     "schema_version": 1
   },
-  "generated_at": "2026-07-02T05:47:22Z",
+  "generated_at": "2026-07-02T06:57:57Z",
   "generator": {
     "dependency_lock": {
       "path": "poetry.lock",
       "sha256": "d4e2e756f8ba3ca67ca0e7592c56d1e3c42303fd8b5af06dd52f25658d9e6ceb"
     },
     "git": {
-      "source_commit": "dddead6351d956223e2c7aecf959dd2d93388be9",
+      "source_commit": "34096ad11c1ae33531186a86961a9e2e883d60a9",
       "worktree_clean_at_start": true
     },
     "packages": {
@@ -261,7 +261,7 @@
     "path": "scripts/run_paper_experiments.py",
     "platform": "macOS-26.4-arm64-arm-64bit-Mach-O",
     "python": "3.14.4",
-    "script_sha256": "922bf3c414e0eadca5c13ee831528347dd83a0cd174efbdf15a987b511845de5",
+    "script_sha256": "25010ce7302d1113e48fb7095dabf1e0bb5b283ba9270455cdbf55382718530e",
     "source_tree": {
       "file_count": 112,
       "files": {
@@ -375,10 +375,10 @@
         "quantcortex/timing/vix_scaler.py": "a3667424e5573fb289e63c26c69da6a68d6c943742359f0466d29b25c56e3686",
         "schemas/canonical_target_tape.schema.json": "4f1c0bf6d5360305d2982adea78de3f61c4bc1ebae9207cb2ba2bd4379b43d44",
         "schemas/evaluation_contract.schema.json": "970f24f587e669925306625d12c5a84dffd03ff5b222a59905849b2fa222784f",
-        "scripts/release_paper_artifacts.sh": "410b1f444ce242b94fa9ba7bcf5868fcc74ad664f2c24f9503d4f3a230e8b38c",
-        "scripts/run_paper_experiments.py": "922bf3c414e0eadca5c13ee831528347dd83a0cd174efbdf15a987b511845de5"
+        "scripts/release_paper_artifacts.sh": "fbf68e79be2479e089e638d88923de3aa675dacbfc1e180ffe75b2a05eaecf39",
+        "scripts/run_paper_experiments.py": "25010ce7302d1113e48fb7095dabf1e0bb5b283ba9270455cdbf55382718530e"
       },
-      "sha256": "5bf7019e1a5f23262701fa5d8e02780c9f274a9b12821a4323818fd282efd295"
+      "sha256": "1c05d00cea1d0e9acc5118c3e9302fc50111a327ed15c48e25019a40cecec5b8"
     },
     "threadpools": [
       {

scripts/release_expansion_artifacts.sh

@@ -9,10 +9,12 @@ if [[ ! -x "${python_bin}" ]]; then
   printf '%s\n' "Python environment not found: ${python_bin}" >&2
   exit 1
 fi
-# Generation runs from a detached worktree at the source commit, so only
-# uncommitted changes to release-critical source can corrupt a release.
-# Scoping the cleanliness check to those paths keeps the wrapper rerunnable
-# while regenerated artifacts sit uncommitted in the working tree.
+# Generation runs from a detached worktree at the source commit, so
+# uncommitted changes outside release-critical source cannot alter what is
+# generated here. Scoping the cleanliness check to those paths keeps the
+# wrapper rerunnable while regenerated artifacts sit uncommitted in the
+# working tree; the paper wrapper independently verifies those artifacts
+# against this release's manifest before republishing them.
 release_source_paths=(
   quantcortex
   schemas/canonical_target_tape.schema.json

scripts/release_paper_artifacts.sh

@@ -10,11 +10,13 @@ if [[ ! -x "${python_bin}" ]]; then
   exit 1
 fi
 
-# Generation runs from a detached worktree at the source commit, so only
-# uncommitted changes to release-critical source can corrupt a release.
-# Scoping the cleanliness check to those paths lets the paper release run
-# after the expansion wrapper has deposited regenerated artifacts in the
-# working tree, which the documented dual-release flow requires.
+# Generation runs from a detached worktree at the source commit, so
+# uncommitted changes outside release-critical source cannot alter what is
+# generated. Scoping the cleanliness check to those paths lets the paper
+# release run after the expansion wrapper has deposited regenerated artifacts
+# in the working tree, which the documented dual-release flow requires. The
+# expansion artifacts that this release republishes are separately verified
+# against the expansion manifest below before they are copied.
 release_source_paths=(
   quantcortex
   schemas
@@ -250,6 +252,16 @@ if [[ "${expansion_source_commit}" != "${source_commit}" ]]; then
     "expansion source: ${expansion_source_commit}" >&2
   exit 1
 fi
+# The copied expansion artifacts are republished inside the built PDFs, so
+# verify every file against the expansion manifest before copying. A tampered
+# or unexpected expansion output must fail the release, not flow into print.
+PYTHONPATH="${repo_root}" "${python_bin}" - "${repo_root}/paper/expansion" <<'PY'
+import sys
+
+from scripts.run_paper_experiments import verify_expansion_artifacts
+
+verify_expansion_artifacts(sys.argv[1])
+PY
 rm -rf "${source_worktree}/paper/expansion/results" \
        "${source_worktree}/paper/expansion/figures"
 cp -R "${repo_root}/paper/expansion/results" \

scripts/run_paper_experiments.py

@@ -203,6 +203,61 @@ def _json_sha256(value: object) -> str:
     return hashlib.sha256(encoded).hexdigest()
 
 
+def verify_expansion_artifacts(expansion_root: Path) -> None:
+    """Fail closed unless the expansion artifact tree matches its manifest.
+
+    The paper release republishes ``paper/expansion/results`` and
+    ``paper/expansion/figures`` inside the built PDFs, so every file it copies
+    must be exactly the file the expansion manifest recorded. Rejects absolute
+    or parent-traversing manifest paths, symlinks, missing files, digest
+    mismatches, and files present on disk that the manifest does not list
+    (``results/manifest.json`` itself is the only exception, because it cannot
+    record its own hash).
+    """
+    expansion_root = Path(expansion_root)
+    manifest_path = expansion_root / "results" / "manifest.json"
+    if manifest_path.is_symlink() or not manifest_path.is_file():
+        raise SystemExit(f"expansion manifest missing: {manifest_path}")
+    manifest = json.loads(manifest_path.read_text(encoding="utf-8"))
+    artifacts = manifest.get("artifacts")
+    if not isinstance(artifacts, dict) or not artifacts:
+        raise SystemExit("expansion manifest lists no artifacts")
+
+    resolved_root = expansion_root.resolve()
+    for relative, expected in artifacts.items():
+        candidate = Path(relative)
+        if candidate.is_absolute() or ".." in candidate.parts:
+            raise SystemExit(f"unsafe expansion artifact path: {relative}")
+        artifact = expansion_root / candidate
+        if artifact.is_symlink():
+            raise SystemExit(f"expansion artifact is a symlink: {relative}")
+        if not artifact.is_file():
+            raise SystemExit(f"expansion artifact missing: {relative}")
+        if not artifact.resolve().is_relative_to(resolved_root):
+            raise SystemExit(f"unsafe expansion artifact path: {relative}")
+        if _sha256(artifact) != expected:
+            raise SystemExit(f"expansion artifact digest mismatch: {relative}")
+
+    allowed = {Path(relative) for relative in artifacts}
+    allowed.add(Path("results/manifest.json"))
+    for subdirectory in ("results", "figures"):
+        directory = expansion_root / subdirectory
+        if not directory.is_dir():
+            raise SystemExit(f"expansion directory missing: {subdirectory}")
+        for found in sorted(directory.rglob("*")):
+            if found.is_symlink():
+                raise SystemExit(
+                    "unexpected symlink under expansion artifacts: "
+                    f"{found.relative_to(expansion_root)}"
+                )
+            if found.is_file():
+                relative_found = found.relative_to(expansion_root)
+                if relative_found not in allowed:
+                    raise SystemExit(
+                        f"unexpected expansion artifact: {relative_found}"
+                    )
+
+
 def _threadpool_environment() -> list[dict[str, object]]:
     """Return stable BLAS/OpenMP metadata without machine-specific paths."""
     try:

tests/test_paper_artifacts.py

@@ -8,7 +8,13 @@
 import subprocess
 from pathlib import Path
 
-from scripts.run_paper_experiments import _json_sha256, source_tree_manifest
+import pytest
+
+from scripts.run_paper_experiments import (
+    _json_sha256,
+    source_tree_manifest,
+    verify_expansion_artifacts,
+)
 
 REPO_ROOT = Path(__file__).resolve().parent.parent
 PAPER_ROOT = REPO_ROOT / "paper"
@@ -446,3 +452,101 @@ def test_paper_citations_are_defined_used_and_unique():
 
     for eprint in eprints:
         assert f"https://arxiv.org/abs/{eprint}" in bibliography
+
+
+def _build_expansion_fixture(root: Path) -> Path:
+    """Create a minimal valid expansion artifact tree with a correct manifest."""
+    expansion = root / "expansion"
+    (expansion / "results").mkdir(parents=True)
+    (expansion / "figures").mkdir()
+    (expansion / "results" / "summary.csv").write_text("a,b\n1,2\n", encoding="ascii")
+    (expansion / "figures" / "plot.pdf").write_bytes(b"%PDF-1.4 fixture")
+    artifacts = {
+        "results/summary.csv": _sha256(expansion / "results" / "summary.csv"),
+        "figures/plot.pdf": _sha256(expansion / "figures" / "plot.pdf"),
+    }
+    manifest = {"git": {"source_commit": "0" * 40}, "artifacts": artifacts}
+    (expansion / "results" / "manifest.json").write_text(
+        json.dumps(manifest), encoding="ascii"
+    )
+    return expansion
+
+
+def test_verify_expansion_artifacts_accepts_valid_tree(tmp_path):
+    expansion = _build_expansion_fixture(tmp_path)
+    verify_expansion_artifacts(expansion)
+
+
+def test_verify_expansion_artifacts_rejects_tampered_artifact(tmp_path):
+    # Regression: the paper release once copied expansion artifacts into the
+    # built PDFs after checking only the manifest's source commit, so a
+    # tampered aggregate (for example an edited generated value) was published
+    # without any digest failure.
+    expansion = _build_expansion_fixture(tmp_path)
+    (expansion / "results" / "summary.csv").write_text("a,b\n9,9\n", encoding="ascii")
+    with pytest.raises(SystemExit, match="digest mismatch"):
+        verify_expansion_artifacts(expansion)
+
+
+def test_verify_expansion_artifacts_rejects_missing_artifact(tmp_path):
+    expansion = _build_expansion_fixture(tmp_path)
+    (expansion / "figures" / "plot.pdf").unlink()
+    with pytest.raises(SystemExit, match="missing"):
+        verify_expansion_artifacts(expansion)
+
+
+def test_verify_expansion_artifacts_rejects_unexpected_file(tmp_path):
+    expansion = _build_expansion_fixture(tmp_path)
+    (expansion / "results" / "extra.csv").write_text("x\n", encoding="ascii")
+    with pytest.raises(SystemExit, match="unexpected expansion artifact"):
+        verify_expansion_artifacts(expansion)
+
+
+def test_verify_expansion_artifacts_rejects_symlink(tmp_path):
+    expansion = _build_expansion_fixture(tmp_path)
+    target = expansion / "results" / "summary.csv"
+    link = expansion / "figures" / "plot.pdf"
+    link.unlink()
+    link.symlink_to(target)
+    with pytest.raises(SystemExit, match="symlink"):
+        verify_expansion_artifacts(expansion)
+
+
+def test_verify_expansion_artifacts_rejects_unsafe_manifest_paths(tmp_path):
+    expansion = _build_expansion_fixture(tmp_path)
+    manifest_path = expansion / "results" / "manifest.json"
+    manifest = json.loads(manifest_path.read_text(encoding="ascii"))
+
+    outside = tmp_path / "outside.txt"
+    outside.write_text("leak\n", encoding="ascii")
+    for unsafe in ("../outside.txt", str(outside)):
+        tampered = dict(manifest)
+        tampered["artifacts"] = dict(manifest["artifacts"])
+        tampered["artifacts"][unsafe] = _sha256(outside)
+        manifest_path.write_text(json.dumps(tampered), encoding="ascii")
+        with pytest.raises(SystemExit, match="unsafe"):
+            verify_expansion_artifacts(expansion)
+
+
+def test_verify_expansion_artifacts_rejects_empty_manifest(tmp_path):
+    expansion = _build_expansion_fixture(tmp_path)
+    manifest_path = expansion / "results" / "manifest.json"
+    manifest_path.write_text(json.dumps({"artifacts": {}}), encoding="ascii")
+    with pytest.raises(SystemExit, match="lists no artifacts"):
+        verify_expansion_artifacts(expansion)
+
+
+def test_release_wrapper_verifies_expansion_artifacts_before_copying():
+    release_script = (REPO_ROOT / "scripts" / "release_paper_artifacts.sh").read_text(
+        encoding="utf-8"
+    )
+    assert "verify_expansion_artifacts" in release_script
+    # The verification must run before the expansion artifacts are copied into
+    # the detached build worktree.
+    assert release_script.index("verify_expansion_artifacts") < release_script.index(
+        'cp -R "${repo_root}/paper/expansion/results"'
+    )
+
+
+def test_committed_expansion_artifacts_validate():
+    verify_expansion_artifacts(PAPER_ROOT / "expansion")