Add CalibForge stage-3 and stage-3-plus-5 RL ablations

.gitattributes

@@ -58,3 +58,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+calibforge/ablations/evidence/stage1-corrected-report.json filter=lfs diff=lfs merge=lfs -text

calibforge/ablations/evidence/archive-audit.json

@@ -0,0 +1,19 @@
+{
+  "retained_tasks": 5372,
+  "patcher_archive_count": 59,
+  "newly_archived": [
+    "contrastive_solver-security_20260610_111702_002",
+    "contrastive_solver-software-engineering_20260604_003113_010",
+    "contrastive_solver-software-engineering_20260611_210349_018",
+    "contrastive_solver-system-administration_20260610_111012_001"
+  ],
+  "other_payloads_identical": false,
+  "retained_comment_only_change": [
+    "contrastive_solver-system-administration_20260610_111702_001"
+  ],
+  "retained_change_reason": "The shared-Dockerfile canonical representative was archived. One retained task now uses its own equivalent Dockerfile; only comments and blank lines differ. Its changed task hash requires corresponding provenance or revalidation before publication.",
+  "original_archived_payloads_verified": true,
+  "source": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/missing-python-archives/source/tasks.parquet",
+  "previous_replacement_plan": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/pandas-verifier-fix/replacement-plan.json",
+  "assembly_requirement": "Use this source and archive for final assembly; keep earlier validated replacement evidence for unchanged retained tasks; revalidate the comment-only changed retained task before publication and apply separate full-run no-op archive decisions. Existing running jobs and frozen reports remain unchanged."
+}

calibforge/ablations/evidence/expected-output-investigation.json

@@ -0,0 +1,470 @@
+{
+  "original_unresolved_count": 58,
+  "items": [
+    {
+      "task_id": "contrastive_solver-model-training_20260604_144210_001",
+      "category": "dependency_or_library",
+      "assessment": "Original verifier installation/import policy must be distinguished from solver dependencies. Scripts match upstream; failures include missing pip, incompatible pinned packages, externally managed Python, missing libgomp, and import/API mismatches. These are not all evidence of an unsolvable task or a runtime PATH regression.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-model-training_20260604_144210_001",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-model-training_20260604_144210_001",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-model-training_20260618_093107_004",
+      "category": "dependency_or_library",
+      "assessment": "Original verifier installation/import policy must be distinguished from solver dependencies. Scripts match upstream; failures include missing pip, incompatible pinned packages, externally managed Python, missing libgomp, and import/API mismatches. These are not all evidence of an unsolvable task or a runtime PATH regression.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-model-training_20260618_093107_004",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-model-training_20260618_093107_004",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "multi_solver-debugging_20260419_112101_001",
+      "category": "native_crash",
+      "assessment": "Instructions explicitly ask to repair crashing/incorrect native C extension or C-library wrapper. Tests invoke that broken native code in the pytest process, producing seven segmentation faults and one abort across this group. Initial crashes are consistent with the task; verifier process isolation is needed for reliable negative grading. Exact memory-corruption mechanisms are not newly proven.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/multi_solver-debugging_20260419_112101_001",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/multi_solver-debugging_20260419_112101_001",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-system-administration_20260606_172554_003",
+      "category": "missing_python",
+      "assessment": "Original Ubuntu Dockerfile does not install Python. Original verifier requires Python. This verifier prerequisite mismatch predates our patch; no Python PATH override can expose an interpreter absent from the image.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-system-administration_20260606_172554_003",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-system-administration_20260606_172554_003",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "multi_solver-software-engineering_20260414_211453_003",
+      "category": "verifier_timeout",
+      "assessment": "No-op verifier exceeded its execution deadline. Captured stdout is absent. Hold out until blocked operation is identified; an intentionally broken initial program may hang. Do not classify as universally unsolvable.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/multi_solver-software-engineering_20260414_211453_003",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/multi_solver-software-engineering_20260414_211453_003",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-debugging_20260604_194036_004",
+      "category": "memory_limit",
+      "assessment": "No-op verifier exceeded the configured task memory limit. Captured stdout is absent. Hold out under this resource profile; neither universal unsolvability nor a verifier-only bug is established.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-debugging_20260604_194036_004",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-debugging_20260604_194036_004",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-optimization_20260604_194036_001",
+      "category": "dependency_or_library",
+      "assessment": "Original verifier installation/import policy must be distinguished from solver dependencies. Scripts match upstream; failures include missing pip, incompatible pinned packages, externally managed Python, missing libgomp, and import/API mismatches. These are not all evidence of an unsolvable task or a runtime PATH regression.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-optimization_20260604_194036_001",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-optimization_20260604_194036_001",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-system-administration_20260604_194036_001",
+      "category": "missing_python",
+      "assessment": "Original Ubuntu Dockerfile does not install Python. Original verifier requires Python. This verifier prerequisite mismatch predates our patch; no Python PATH override can expose an interpreter absent from the image.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-system-administration_20260604_194036_001",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-system-administration_20260604_194036_001",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "multi_solver-software-engineering_20260414_080620_011",
+      "category": "memory_limit",
+      "assessment": "No-op verifier exceeded the configured task memory limit. Captured stdout is absent. Hold out under this resource profile; neither universal unsolvability nor a verifier-only bug is established.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/multi_solver-software-engineering_20260414_080620_011",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/multi_solver-software-engineering_20260414_080620_011",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-model-training_20260601_053159_004",
+      "category": "dependency_or_library",
+      "assessment": "Original verifier installation/import policy must be distinguished from solver dependencies. Scripts match upstream; failures include missing pip, incompatible pinned packages, externally managed Python, missing libgomp, and import/API mismatches. These are not all evidence of an unsolvable task or a runtime PATH regression.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-model-training_20260601_053159_004",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-model-training_20260601_053159_004",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-scientific-computing_20260604_144210_006",
+      "category": "dependency_or_library",
+      "assessment": "Original verifier installation/import policy must be distinguished from solver dependencies. Scripts match upstream; failures include missing pip, incompatible pinned packages, externally managed Python, missing libgomp, and import/API mismatches. These are not all evidence of an unsolvable task or a runtime PATH regression.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-scientific-computing_20260604_144210_006",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-scientific-computing_20260604_144210_006",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "multi_solver-software-engineering_20260413_174325_005",
+      "category": "native_crash",
+      "assessment": "Instructions explicitly ask to repair crashing/incorrect native C extension or C-library wrapper. Tests invoke that broken native code in the pytest process, producing seven segmentation faults and one abort across this group. Initial crashes are consistent with the task; verifier process isolation is needed for reliable negative grading. Exact memory-corruption mechanisms are not newly proven.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/multi_solver-software-engineering_20260413_174325_005",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/multi_solver-software-engineering_20260413_174325_005",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-debugging_20260610_111012_002",
+      "category": "native_crash",
+      "assessment": "Instructions explicitly ask to repair crashing/incorrect native C extension or C-library wrapper. Tests invoke that broken native code in the pytest process, producing seven segmentation faults and one abort across this group. Initial crashes are consistent with the task; verifier process isolation is needed for reliable negative grading. Exact memory-corruption mechanisms are not newly proven.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-debugging_20260610_111012_002",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-debugging_20260610_111012_002",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-machine-learning_20260620_171154_003",
+      "category": "dependency_or_library",
+      "assessment": "Original verifier installation/import policy must be distinguished from solver dependencies. Scripts match upstream; failures include missing pip, incompatible pinned packages, externally managed Python, missing libgomp, and import/API mismatches. These are not all evidence of an unsolvable task or a runtime PATH regression.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-machine-learning_20260620_171154_003",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-machine-learning_20260620_171154_003",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "multi_solver-debugging_20260417_112147_003",
+      "category": "native_crash",
+      "assessment": "Instructions explicitly ask to repair crashing/incorrect native C extension or C-library wrapper. Tests invoke that broken native code in the pytest process, producing seven segmentation faults and one abort across this group. Initial crashes are consistent with the task; verifier process isolation is needed for reliable negative grading. Exact memory-corruption mechanisms are not newly proven.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/multi_solver-debugging_20260417_112147_003",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/multi_solver-debugging_20260417_112147_003",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260528_174918_024",
+      "category": "expected_missing_agent_output",
+      "assessment": "Instructions explicitly require creation of the absent output. Verifier-only prerequisite assertion repair prepared; original tests preserved when the file exists. Acceptance waits for stages 3 and 5.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-software-engineering_20260528_174918_024",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-software-engineering_20260528_174918_024",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-system-administration_20260611_205750_001",
+      "category": "missing_python",
+      "assessment": "Original Ubuntu Dockerfile does not install Python. Original verifier requires Python. This verifier prerequisite mismatch predates our patch; no Python PATH override can expose an interpreter absent from the image.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-system-administration_20260611_205750_001",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-system-administration_20260611_205750_001",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-video-processing_20260607_104421_001",
+      "category": "missing_pytest",
+      "assessment": "Original verifier expects pytest without ensuring it exists in the selected Python environment. Original image installs Python but not pytest in that interpreter; classify as verifier bootstrap mismatch, not proof of task unsolvability.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-video-processing_20260607_104421_001",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-video-processing_20260607_104421_001",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "multi_solver-file-operations_20260413_173854_001",
+      "category": "shell_harness",
+      "assessment": "Original tests/test.sh contains Dockerfile FROM/RUN/WORKDIR/COPY directives instead of a shell verifier: upstream harness defect.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/multi_solver-file-operations_20260413_173854_001",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/multi_solver-file-operations_20260413_173854_001",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-debugging_20260610_111702_002",
+      "category": "native_crash",
+      "assessment": "Instructions explicitly ask to repair crashing/incorrect native C extension or C-library wrapper. Tests invoke that broken native code in the pytest process, producing seven segmentation faults and one abort across this group. Initial crashes are consistent with the task; verifier process isolation is needed for reliable negative grading. Exact memory-corruption mechanisms are not newly proven.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-debugging_20260610_111702_002",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-debugging_20260610_111702_002",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-file-operations_20260509_020109_002",
+      "category": "shell_harness",
+      "assessment": "Upstream bootstrap installs uv successfully, then requires /root/.local/bin/env, which is absent. It retries the successful installation and aborts before pytest. This is an installer/environment assumption mismatch; the log does not show a failed download.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-file-operations_20260509_020109_002",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-file-operations_20260509_020109_002",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-mathematics_20260513_205011_001",
+      "category": "missing_baseline_file",
+      "assessment": "Upstream includes environment/files/discrete_log.py and COPYs it into /app; instructions say it already exists. Not an agent-created-output case. Missing import remains an image/runtime-path investigation; no absence assertion added to hide it.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-mathematics_20260513_205011_001",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-mathematics_20260513_205011_001",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-system-administration_20260604_144210_009",
+      "category": "missing_python",
+      "assessment": "Original Ubuntu Dockerfile does not install Python. Original verifier requires Python. This verifier prerequisite mismatch predates our patch; no Python PATH override can expose an interpreter absent from the image.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-system-administration_20260604_144210_009",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-system-administration_20260604_144210_009",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260507_170334_011",
+      "category": "verifier_timeout",
+      "assessment": "No-op verifier exceeded its execution deadline. Captured stdout is absent. Hold out until blocked operation is identified; an intentionally broken initial program may hang. Do not classify as universally unsolvable.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-software-engineering_20260507_170334_011",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-software-engineering_20260507_170334_011",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-system-administration_20260610_111702_001",
+      "category": "missing_python",
+      "assessment": "Original Ubuntu Dockerfile does not install Python. Original verifier requires Python. This verifier prerequisite mismatch predates our patch; no Python PATH override can expose an interpreter absent from the image.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-system-administration_20260610_111702_001",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-system-administration_20260610_111702_001",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-optimization_20260509_065529_001",
+      "category": "native_crash",
+      "assessment": "Instructions explicitly ask to repair crashing/incorrect native C extension or C-library wrapper. Tests invoke that broken native code in the pytest process, producing seven segmentation faults and one abort across this group. Initial crashes are consistent with the task; verifier process isolation is needed for reliable negative grading. Exact memory-corruption mechanisms are not newly proven.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-optimization_20260509_065529_001",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-optimization_20260509_065529_001",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-scientific-computing_20260509_020109_001",
+      "category": "memory_limit",
+      "assessment": "No-op verifier exceeded the configured task memory limit. Captured stdout is absent. Hold out under this resource profile; neither universal unsolvability nor a verifier-only bug is established.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-scientific-computing_20260509_020109_001",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-scientific-computing_20260509_020109_001",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260422_235124_018",
+      "category": "native_crash",
+      "assessment": "Instructions explicitly ask to repair crashing/incorrect native C extension or C-library wrapper. Tests invoke that broken native code in the pytest process, producing seven segmentation faults and one abort across this group. Initial crashes are consistent with the task; verifier process isolation is needed for reliable negative grading. Exact memory-corruption mechanisms are not newly proven.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-software-engineering_20260422_235124_018",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-software-engineering_20260422_235124_018",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260508_045800_011",
+      "category": "verifier_timeout",
+      "assessment": "No-op verifier exceeded its execution deadline. Captured stdout is absent. Hold out until blocked operation is identified; an intentionally broken initial program may hang. Do not classify as universally unsolvable.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-software-engineering_20260508_045800_011",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-software-engineering_20260508_045800_011",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-data-querying_20260602_105139_001",
+      "category": "dependency_or_library",
+      "assessment": "Original verifier installation/import policy must be distinguished from solver dependencies. Scripts match upstream; failures include missing pip, incompatible pinned packages, externally managed Python, missing libgomp, and import/API mismatches. These are not all evidence of an unsolvable task or a runtime PATH regression.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-data-querying_20260602_105139_001",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-data-querying_20260602_105139_001",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-debugging_20260510_005520_002",
+      "category": "memory_limit",
+      "assessment": "No-op verifier exceeded the configured task memory limit. Captured stdout is absent. Hold out under this resource profile; neither universal unsolvability nor a verifier-only bug is established.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-debugging_20260510_005520_002",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-debugging_20260510_005520_002",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-optimization_20260617_051646_001",
+      "category": "dependency_or_library",
+      "assessment": "Original verifier installation/import policy must be distinguished from solver dependencies. Scripts match upstream; failures include missing pip, incompatible pinned packages, externally managed Python, missing libgomp, and import/API mismatches. These are not all evidence of an unsolvable task or a runtime PATH regression.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-optimization_20260617_051646_001",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-optimization_20260617_051646_001",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260603_181444_011",
+      "category": "expected_missing_agent_output",
+      "assessment": "Instructions explicitly require creation of the absent output. Verifier-only prerequisite assertion repair prepared; original tests preserved when the file exists. Acceptance waits for stages 3 and 5.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-software-engineering_20260603_181444_011",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-software-engineering_20260603_181444_011",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-system-administration_20260610_111702_004",
+      "category": "postgres_unavailable",
+      "assessment": "Instructions require recovering a damaged PostgreSQL database and starting it. Unavailable database under no-op is expected. Repair retains connection probes and original tests but moves failure from fixture setup into test assertions.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-system-administration_20260610_111702_004",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-system-administration_20260610_111702_004",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-data-science_20260604_002443_006",
+      "category": "expected_missing_agent_output",
+      "assessment": "Instructions explicitly require creation of the absent output. Verifier-only prerequisite assertion repair prepared; original tests preserved when the file exists. Acceptance waits for stages 3 and 5.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-data-science_20260604_002443_006",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-data-science_20260604_002443_006",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-machine-learning_20260604_003113_002",
+      "category": "missing_pytest",
+      "assessment": "Original verifier expects pytest without ensuring it exists in the selected Python environment. Original image installs Python but not pytest in that interpreter; classify as verifier bootstrap mismatch, not proof of task unsolvability.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-machine-learning_20260604_003113_002",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-machine-learning_20260604_003113_002",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "multi_solver-debugging_20260414_080620_001",
+      "category": "native_crash",
+      "assessment": "Instructions explicitly ask to repair crashing/incorrect native C extension or C-library wrapper. Tests invoke that broken native code in the pytest process, producing seven segmentation faults and one abort across this group. Initial crashes are consistent with the task; verifier process isolation is needed for reliable negative grading. Exact memory-corruption mechanisms are not newly proven.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/multi_solver-debugging_20260414_080620_001",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/multi_solver-debugging_20260414_080620_001",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "multi_solver-software-engineering_20260414_091921_006",
+      "category": "verifier_timeout",
+      "assessment": "No-op verifier exceeded its execution deadline. Captured stdout is absent. Hold out until blocked operation is identified; an intentionally broken initial program may hang. Do not classify as universally unsolvable.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/multi_solver-software-engineering_20260414_091921_006",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/multi_solver-software-engineering_20260414_091921_006",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260613_152233_017",
+      "category": "expected_missing_agent_output",
+      "assessment": "Instructions explicitly require creation of the absent output. Verifier-only prerequisite assertion repair prepared; original tests preserved when the file exists. Acceptance waits for stages 3 and 5.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-software-engineering_20260613_152233_017",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-software-engineering_20260613_152233_017",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260415_002933_023",
+      "category": "verifier_timeout",
+      "assessment": "No-op verifier exceeded its execution deadline. Captured stdout is absent. Hold out until blocked operation is identified; an intentionally broken initial program may hang. Do not classify as universally unsolvable.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-software-engineering_20260415_002933_023",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-software-engineering_20260415_002933_023",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-data-science_20260614_141608_006",
+      "category": "expected_missing_agent_output",
+      "assessment": "Instructions explicitly require creation of the absent output. Verifier-only prerequisite assertion repair prepared; original tests preserved when the file exists. Acceptance waits for stages 3 and 5.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-data-science_20260614_141608_006",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-data-science_20260614_141608_006",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-data-science_20260503_182123_005",
+      "category": "memory_limit",
+      "assessment": "No-op verifier exceeded the configured task memory limit. Captured stdout is absent. Hold out under this resource profile; neither universal unsolvability nor a verifier-only bug is established.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-data-science_20260503_182123_005",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-data-science_20260503_182123_005",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-data-science_20260601_053159_006",
+      "category": "expected_missing_agent_output",
+      "assessment": "Instructions explicitly require creation of the absent output. Verifier-only prerequisite assertion repair prepared; original tests preserved when the file exists. Acceptance waits for stages 3 and 5.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-data-science_20260601_053159_006",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-data-science_20260601_053159_006",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-model-training_20260611_205750_001",
+      "category": "dependency_or_library",
+      "assessment": "Original verifier installation/import policy must be distinguished from solver dependencies. Scripts match upstream; failures include missing pip, incompatible pinned packages, externally managed Python, missing libgomp, and import/API mismatches. These are not all evidence of an unsolvable task or a runtime PATH regression.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-model-training_20260611_205750_001",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-model-training_20260611_205750_001",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260604_002443_020",
+      "category": "unfinished_task_build",
+      "assessment": "Instructions require repairing the Go/cgo build and starting an HTTP service. Missing libvalidate during no-op is expected unfinished work. Repair runs cached original build/start checks from test bodies; unchanged behavioral checks follow only on successful preparation.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-software-engineering_20260604_002443_020",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-software-engineering_20260604_002443_020",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "multi_solver-software-engineering_20260413_173854_009",
+      "category": "verifier_timeout",
+      "assessment": "No-op verifier exceeded its execution deadline. Captured stdout is absent. Hold out until blocked operation is identified; an intentionally broken initial program may hang. Do not classify as universally unsolvable.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/multi_solver-software-engineering_20260413_173854_009",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/multi_solver-software-engineering_20260413_173854_009",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260610_111702_011",
+      "category": "memory_limit",
+      "assessment": "No-op verifier exceeded the configured task memory limit. Captured stdout is absent. Hold out under this resource profile; neither universal unsolvability nor a verifier-only bug is established.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-software-engineering_20260610_111702_011",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-software-engineering_20260610_111702_011",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-system-administration_20260612_191200_002",
+      "category": "backend_permission",
+      "assessment": "Verifier writes read-only /etc/hosts. This is incompatibility with this unprivileged backend, not an intrinsic upstream-task defect. Hold out for this infrastructure.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-system-administration_20260612_191200_002",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-system-administration_20260612_191200_002",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-data-science_20260615_143301_002",
+      "category": "missing_pytest",
+      "assessment": "Original verifier expects pytest without ensuring it exists in the selected Python environment. Original image installs Python but not pytest in that interpreter; classify as verifier bootstrap mismatch, not proof of task unsolvability.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-data-science_20260615_143301_002",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-data-science_20260615_143301_002",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260606_172622_024",
+      "category": "expected_missing_agent_output",
+      "assessment": "Instructions explicitly require creation of the absent output. Verifier-only prerequisite assertion repair prepared; original tests preserved when the file exists. Acceptance waits for stages 3 and 5.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-software-engineering_20260606_172622_024",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-software-engineering_20260606_172622_024",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-system-administration_20260604_193356_003",
+      "category": "missing_pytest",
+      "assessment": "Original verifier expects pytest without ensuring it exists in the selected Python environment. Original image installs Python but not pytest in that interpreter; classify as verifier bootstrap mismatch, not proof of task unsolvability.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-system-administration_20260604_193356_003",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-system-administration_20260604_193356_003",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260604_002443_024",
+      "category": "expected_missing_agent_output",
+      "assessment": "Instructions explicitly require creation of the absent output. Verifier-only prerequisite assertion repair prepared; original tests preserved when the file exists. Acceptance waits for stages 3 and 5.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-software-engineering_20260604_002443_024",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-software-engineering_20260604_002443_024",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-system-administration_20260510_142854_005",
+      "category": "backend_permission",
+      "assessment": "nginx -t fails binding privileged TCP port 80. This is incompatibility with this unprivileged backend, not an intrinsic upstream-task defect. Hold out for this infrastructure.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-system-administration_20260510_142854_005",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-system-administration_20260510_142854_005",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-system-administration_20260610_112157_003",
+      "category": "missing_python",
+      "assessment": "Original Ubuntu Dockerfile does not install Python. Original verifier requires Python. This verifier prerequisite mismatch predates our patch; no Python PATH override can expose an interpreter absent from the image.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-system-administration_20260610_112157_003",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-system-administration_20260610_112157_003",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-data-science_20260611_210349_008",
+      "category": "dependency_or_library",
+      "assessment": "Original verifier installation/import policy must be distinguished from solver dependencies. Scripts match upstream; failures include missing pip, incompatible pinned packages, externally managed Python, missing libgomp, and import/API mismatches. These are not all evidence of an unsolvable task or a runtime PATH regression.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-data-science_20260611_210349_008",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-data-science_20260611_210349_008",
+      "test_sh_identical_to_upstream": true
+    },
+    {
+      "task_id": "contrastive_solver-scientific-computing_20260501_000112_002",
+      "category": "dependency_or_library",
+      "assessment": "Original verifier installation/import policy must be distinguished from solver dependencies. Scripts match upstream; failures include missing pip, incompatible pinned packages, externally managed Python, missing libgomp, and import/API mismatches. These are not all evidence of an unsolvable task or a runtime PATH regression.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-scientific-computing_20260501_000112_002",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-scientific-computing_20260501_000112_002",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-debugging_20260430_081156_004",
+      "category": "verifier_timeout",
+      "assessment": "No-op verifier exceeded its execution deadline. Captured stdout is absent. Hold out until blocked operation is identified; an intentionally broken initial program may hang. Do not classify as universally unsolvable.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-debugging_20260430_081156_004",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-debugging_20260430_081156_004",
+      "test_sh_identical_to_upstream": false
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260601_053159_018",
+      "category": "memory_limit",
+      "assessment": "No-op verifier exceeded the configured task memory limit. Captured stdout is absent. Hold out under this resource profile; neither universal unsolvability nor a verifier-only bug is established.",
+      "upstream_task_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/expected-output-repairs/upstream/contrastive_solver-software-engineering_20260601_053159_018",
+      "original_log_dir": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage5-unresolved-review/contrastive_solver-software-engineering_20260601_053159_018",
+      "test_sh_identical_to_upstream": true
+    }
+  ],
+  "exclusion_policy": "Hold out until an acceptable verifier result is validated. These categories do not establish universal task unsolvability."
+}

calibforge/ablations/evidence/expected-output-repairs.json

@@ -0,0 +1,109 @@
+{
+  "source": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/pandas-verifier-fix/source/tasks.parquet",
+  "tasks": [
+    {
+      "task_id": "contrastive_solver-data-science_20260601_053159_006",
+      "before_sha256": "de2c553e40993652f4e18fa39fa33e41659122181fa947c39882d8dab1c91652",
+      "after_sha256": "d387e2bd6421320b5b70e2923aeb03a669df1f78fa16bfd85885e0ca9e627ac0",
+      "changed_files": [
+        "tests/test_outputs.py"
+      ],
+      "label": "verifier-missing-output-assertion",
+      "reason": "Assert required agent output /app/consolidate.py exists; retain the original checks when present."
+    },
+    {
+      "task_id": "contrastive_solver-data-science_20260604_002443_006",
+      "before_sha256": "0adf70bb34bd07d716e0618abffd284acd3f2e4d12f20b85c0a80d794ccf5e58",
+      "after_sha256": "4b24197d8c5d5e0413da68aa1e24b7aa61b022f7098297283247953941b30dab",
+      "changed_files": [
+        "tests/test_outputs.py"
+      ],
+      "label": "verifier-missing-output-assertion",
+      "reason": "Assert required agent output /app/pipeline.py exists; retain the original checks when present."
+    },
+    {
+      "task_id": "contrastive_solver-data-science_20260614_141608_006",
+      "before_sha256": "50e43e1b32d00609bfba4c425d7d57260ff7620298943ef87d705db63ede43a8",
+      "after_sha256": "a50a4f23da3f19ca7b028d1ccb886ff374c13f26f88e518bedb4929d501c5225",
+      "changed_files": [
+        "tests/test_outputs.py"
+      ],
+      "label": "verifier-missing-output-assertion",
+      "reason": "Assert required agent output /app/csv2parquet.py exists; retain the original checks when present."
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260528_174918_024",
+      "before_sha256": "12bd05661ed9c2fa477160762ce98b2f024f5104ec1d2528a6ed2f46a6470146",
+      "after_sha256": "f1b2d18d014a0479c59d80052c7a3701ac3048d0a89b3bbab104734ad5db9882",
+      "changed_files": [
+        "tests/test_outputs.py"
+      ],
+      "label": "verifier-missing-output-assertion",
+      "reason": "Assert required agent output /app/server.py exists; retain the original checks when present."
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260603_181444_011",
+      "before_sha256": "2ec1a48c283c8e661c02e5ae122abbb371f1730dc835f3256cf975e2ddbccdc4",
+      "after_sha256": "8df6b07368618a7cc10774c229be9d55beb0fea38e96e98723aa7febdb66b6ad",
+      "changed_files": [
+        "tests/test_outputs.py"
+      ],
+      "label": "verifier-missing-output-assertion",
+      "reason": "Assert required agent output /app/table_format.py exists; retain the original checks when present."
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260604_002443_020",
+      "before_sha256": "151bdd12f18b443422d07469bcaf03ac3920b4369d23c274c6dbc1b9b21655fe",
+      "after_sha256": "893d524968a13958b961f8528b337080b920ca0a52d30e6b7c67bbccd6db03db",
+      "changed_files": [
+        "tests/test_outputs.py"
+      ],
+      "label": "verifier-expected-unsolved-state-assertion",
+      "reason": "The agent must repair the Go/cgo build and start the service; failed compilation or service startup is an expected unsolved state."
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260604_002443_024",
+      "before_sha256": "431a00e7c3d1684689b93a7632ce47ab2a9e79d89e2fab8c2ac651c2cc7c7aba",
+      "after_sha256": "29b24c73ffd924915d3e5a8aee9a28239dbd458294afa0c562b43fb228c0fe54",
+      "changed_files": [
+        "tests/test_outputs.py"
+      ],
+      "label": "verifier-missing-output-assertion",
+      "reason": "Assert required agent output /app/regex_engine.py exists; retain the original checks when present."
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260606_172622_024",
+      "before_sha256": "f52d266ccafe3751e9cb48baf02eb356a760bca4cf6a3b26c5d3e3a9d06bb0bd",
+      "after_sha256": "ee28f2c9ef4868674e242c256123df332b5fe398b445c664ce590281698159d5",
+      "changed_files": [
+        "tests/test_outputs.py"
+      ],
+      "label": "verifier-missing-output-assertion",
+      "reason": "Assert required agent output /app/gc.c exists; retain the original checks when present."
+    },
+    {
+      "task_id": "contrastive_solver-software-engineering_20260613_152233_017",
+      "before_sha256": "77a3aefadb60dc78b4a763396be530cbef59c4f50a039114e7e0ce83993364ab",
+      "after_sha256": "7b33b034da924ccd425a00965f4d10e2f7d49c3a334905859174d1316cc251e6",
+      "changed_files": [
+        "tests/test_outputs.py"
+      ],
+      "label": "verifier-missing-output-assertion",
+      "reason": "Assert required agent output /app/calc/calc.c exists; retain the original checks when present."
+    },
+    {
+      "task_id": "contrastive_solver-system-administration_20260610_111702_004",
+      "before_sha256": "d1548d55016cf07e224c4b09b8c10f67b187dde411e044e713b59eb1e29ba2d9",
+      "after_sha256": "0f65fdbf88f5fe521459b5762dee1bbde5e44a6e798a91d554ab528b2e85e7aa",
+      "changed_files": [
+        "tests/test_outputs.py"
+      ],
+      "label": "verifier-expected-unsolved-state-assertion",
+      "reason": "The agent must recover and start PostgreSQL; absence of a usable connection is an expected unsolved state."
+    }
+  ],
+  "count": 10,
+  "only_verifiers_changed": true,
+  "status": "All ten passed stage 3 and stage 5",
+  "validation_evidence": "calibforge/ablations/evidence/expected-output-reruns.json"
+}

calibforge/ablations/evidence/expected-output-reruns.json

@@ -0,0 +1,102 @@
+{
+  "check_counts": {},
+  "contract_sha256": "68349e876d038666f49f4850d510fef52465b81b0e754ddfe11ae0efb785b0e1",
+  "failures": [],
+  "oracle_validated": false,
+  "passed_all": 10,
+  "passed_task_ids": [
+    "contrastive_solver-data-science_20260601_053159_006",
+    "contrastive_solver-data-science_20260604_002443_006",
+    "contrastive_solver-data-science_20260614_141608_006",
+    "contrastive_solver-software-engineering_20260528_174918_024",
+    "contrastive_solver-software-engineering_20260603_181444_011",
+    "contrastive_solver-software-engineering_20260604_002443_020",
+    "contrastive_solver-software-engineering_20260604_002443_024",
+    "contrastive_solver-software-engineering_20260606_172622_024",
+    "contrastive_solver-software-engineering_20260613_152233_017",
+    "contrastive_solver-system-administration_20260610_111702_004"
+  ],
+  "per_task": {
+    "contrastive_solver-data-science_20260601_053159_006": {
+      "1": "not_evaluated",
+      "3": "passed",
+      "4": "not_evaluated",
+      "5": "passed"
+    },
+    "contrastive_solver-data-science_20260604_002443_006": {
+      "1": "not_evaluated",
+      "3": "passed",
+      "4": "not_evaluated",
+      "5": "passed"
+    },
+    "contrastive_solver-data-science_20260614_141608_006": {
+      "1": "not_evaluated",
+      "3": "passed",
+      "4": "not_evaluated",
+      "5": "passed"
+    },
+    "contrastive_solver-software-engineering_20260528_174918_024": {
+      "1": "not_evaluated",
+      "3": "passed",
+      "4": "not_evaluated",
+      "5": "passed"
+    },
+    "contrastive_solver-software-engineering_20260603_181444_011": {
+      "1": "not_evaluated",
+      "3": "passed",
+      "4": "not_evaluated",
+      "5": "passed"
+    },
+    "contrastive_solver-software-engineering_20260604_002443_020": {
+      "1": "not_evaluated",
+      "3": "passed",
+      "4": "not_evaluated",
+      "5": "passed"
+    },
+    "contrastive_solver-software-engineering_20260604_002443_024": {
+      "1": "not_evaluated",
+      "3": "passed",
+      "4": "not_evaluated",
+      "5": "passed"
+    },
+    "contrastive_solver-software-engineering_20260606_172622_024": {
+      "1": "not_evaluated",
+      "3": "passed",
+      "4": "not_evaluated",
+      "5": "passed"
+    },
+    "contrastive_solver-software-engineering_20260613_152233_017": {
+      "1": "not_evaluated",
+      "3": "passed",
+      "4": "not_evaluated",
+      "5": "passed"
+    },
+    "contrastive_solver-system-administration_20260610_111702_004": {
+      "1": "not_evaluated",
+      "3": "passed",
+      "4": "not_evaluated",
+      "5": "passed"
+    }
+  },
+  "per_task_checks": {},
+  "required_stages": [
+    3,
+    5
+  ],
+  "skipped_optional_checks": [],
+  "stage_counts": {
+    "1": {
+      "not_evaluated": 10
+    },
+    "3": {
+      "passed": 10
+    },
+    "4": {
+      "not_evaluated": 10
+    },
+    "5": {
+      "passed": 10
+    }
+  },
+  "task_count": 10
+}

calibforge/ablations/evidence/missing-output-reruns.json

@@ -0,0 +1,66 @@
+{
+  "check_counts": {},
+  "contract_sha256": "e6d85cabd1a94401b7e0596c02e97a224ae1168ccbc0c48f7b0245325902f98e",
+  "failures": [],
+  "oracle_validated": false,
+  "passed_all": 2,
+  "passed_task_ids": [
+    "contrastive_solver-data-science_20260610_112157_008",
+    "contrastive_solver-security_20260604_003113_006"
+  ],
+  "per_task": {
+    "contrastive_solver-data-science_20260610_112157_008": {
+      "1": "passed",
+      "3": "passed",
+      "4": "not_evaluated",
+      "5": "passed"
+    },
+    "contrastive_solver-security_20260604_003113_006": {
+      "1": "passed",
+      "3": "passed",
+      "4": "not_evaluated",
+      "5": "passed"
+    }
+  },
+  "per_task_checks": {},
+  "required_stages": [
+    3,
+    5,
+    1
+  ],
+  "skipped_optional_checks": [
+    {
+      "check": "check_ai_detection.py",
+      "evidence": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/user-verifier-fixes/targeted-validation/results/submissions/694a7acd7c4c/report/stage-1-605b0455c7d0.json",
+      "log": null,
+      "reason": "no GPTZERO_API_KEY configured",
+      "stage": 1,
+      "status": "skipped",
+      "task_id": "contrastive_solver-data-science_20260610_112157_008"
+    },
+    {
+      "check": "check_ai_detection.py",
+      "evidence": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/user-verifier-fixes/targeted-validation/results/submissions/694a7acd7c4c/report/stage-1-605b0455c7d0.json",
+      "log": null,
+      "reason": "no GPTZERO_API_KEY configured",
+      "stage": 1,
+      "status": "skipped",
+      "task_id": "contrastive_solver-security_20260604_003113_006"
+    }
+  ],
+  "stage_counts": {
+    "1": {
+      "passed": 2
+    },
+    "3": {
+      "passed": 2
+    },
+    "4": {
+      "not_evaluated": 2
+    },
+    "5": {
+      "passed": 2
+    }
+  },
+  "task_count": 2
+}

calibforge/ablations/evidence/nproc-affinity-audit.json

@@ -0,0 +1,91 @@
+{
+  "job_id": "1017578",
+  "cluster": "helma",
+  "node": "h31-62",
+  "allocation_cpus": 48,
+  "node_logical_cpus": 384,
+  "method": "Actual five cached task SIFs; Apptainer exec in Slurm steps using trial (2 CPUs) and build (4 CPUs, cpu-bind=none) resource settings. No compilation workload rerun.",
+  "findings": [
+    {
+      "task": "contrastive_solver-security_20260508_045740_002",
+      "mode": "trial",
+      "requested_cpus": 2,
+      "nproc": 2,
+      "nproc_all": 384,
+      "cpu_affinity": "136-137"
+    },
+    {
+      "task": "contrastive_solver-security_20260508_045740_002",
+      "mode": "build",
+      "requested_cpus": 4,
+      "nproc": 4,
+      "nproc_all": 384,
+      "cpu_affinity": "136-139"
+    },
+    {
+      "task": "contrastive_solver-software-engineering_20260510_053611_008",
+      "mode": "trial",
+      "requested_cpus": 2,
+      "nproc": 2,
+      "nproc_all": 384,
+      "cpu_affinity": "136-137"
+    },
+    {
+      "task": "contrastive_solver-software-engineering_20260510_053611_008",
+      "mode": "build",
+      "requested_cpus": 4,
+      "nproc": 4,
+      "nproc_all": 384,
+      "cpu_affinity": "136-139"
+    },
+    {
+      "task": "contrastive_solver-software-engineering_20260611_210349_008",
+      "mode": "trial",
+      "requested_cpus": 2,
+      "nproc": 2,
+      "nproc_all": 384,
+      "cpu_affinity": "136-137"
+    },
+    {
+      "task": "contrastive_solver-software-engineering_20260611_210349_008",
+      "mode": "build",
+      "requested_cpus": 4,
+      "nproc": 4,
+      "nproc_all": 384,
+      "cpu_affinity": "136-139"
+    },
+    {
+      "task": "contrastive_solver-system-administration_20260604_004411_008",
+      "mode": "trial",
+      "requested_cpus": 2,
+      "nproc": 2,
+      "nproc_all": 384,
+      "cpu_affinity": "136-137"
+    },
+    {
+      "task": "contrastive_solver-system-administration_20260604_004411_008",
+      "mode": "build",
+      "requested_cpus": 4,
+      "nproc": 4,
+      "nproc_all": 384,
+      "cpu_affinity": "136-139"
+    },
+    {
+      "task": "contrastive_solver-system-administration_20260604_004411_009",
+      "mode": "trial",
+      "requested_cpus": 2,
+      "nproc": 2,
+      "nproc_all": 384,
+      "cpu_affinity": "136-137"
+    },
+    {
+      "task": "contrastive_solver-system-administration_20260604_004411_009",
+      "mode": "build",
+      "requested_cpus": 4,
+      "nproc": 4,
+      "nproc_all": 384,
+      "cpu_affinity": "136-139"
+    }
+  ],
+  "conclusion": "Bare nproc respects the Slurm step CPU affinity in all ten probes; no full-node CPU expansion observed. This is scoped to the tested Helma Slurm/Apptainer execution path."
+}

calibforge/ablations/evidence/pandas-rerun.json

@@ -0,0 +1,50 @@
+{
+  "check_counts": {},
+  "contract_sha256": "555852c5e294513f8a1c901a70f99c479b56245809036371edd646e5cb6e0311",
+  "failures": [],
+  "oracle_validated": false,
+  "passed_all": 1,
+  "passed_task_ids": [
+    "contrastive_solver-data-processing_20260604_003814_003"
+  ],
+  "per_task": {
+    "contrastive_solver-data-processing_20260604_003814_003": {
+      "1": "passed",
+      "3": "passed",
+      "4": "not_evaluated",
+      "5": "passed"
+    }
+  },
+  "per_task_checks": {},
+  "required_stages": [
+    3,
+    5,
+    1
+  ],
+  "skipped_optional_checks": [
+    {
+      "check": "check_ai_detection.py",
+      "evidence": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/pandas-verifier-fix/targeted-validation/results/submissions/6b048500bd9a/report/stage-1-a719e293576b.json",
+      "log": null,
+      "reason": "no GPTZERO_API_KEY configured",
+      "stage": 1,
+      "status": "skipped",
+      "task_id": "contrastive_solver-data-processing_20260604_003814_003"
+    }
+  ],
+  "stage_counts": {
+    "1": {
+      "passed": 1
+    },
+    "3": {
+      "passed": 1
+    },
+    "4": {
+      "not_evaluated": 1
+    },
+    "5": {
+      "passed": 1
+    }
+  },
+  "task_count": 1
+}

calibforge/ablations/evidence/stage1-checker-final.py

@@ -0,0 +1,890 @@
+#!/usr/bin/env python3
+"""Run pinned Terminal-Bench checks with training-task defaults and optional GPTZero."""
+from __future__ import annotations
+
+import argparse
+from concurrent.futures import ThreadPoolExecutor, as_completed
+import hashlib
+import json
+import os
+from pathlib import Path
+import re
+import shlex
+import shutil
+import subprocess
+import sys
+import tempfile
+import time
+import threading
+
+sys.path.insert(0, str(Path(__file__).resolve().parents[2]))
+from validation.data.selection import discover_tasks
+from validation.checks.supplied_references import discoverable_references
+
+TERMINAL_BENCH = Path(__file__).resolve().parents[1] / 'upstream/terminal_bench'
+# These are policy decisions in our wrapper; upstream files remain unmodified.
+POLICY = {
+    'check-canary.sh': 'Terminal-Bench-specific canary GUID',
+    'check-task-fields.sh': 'benchmark author metadata, taxonomy and README sections',
+    'check-task-timeout.sh': 'benchmark timeout caps',
+    'check-instruction-suffix.sh': 'benchmark-specific instruction suffix',
+    'check-instruction-headings.sh': 'benchmark prose-only instruction style',
+    'check-gpu-types.sh': 'Modal-specific GPU allowlist',
+    'check-resource-sizes.sh': 'benchmark CPU/memory size allowlist',
+    'check-allow-internet.sh': 'benchmark requires default internet access',
+    'check-no-allow-internet-true.sh': 'benchmark forbids explicit internet opt-in',
+    'check-task-slug.sh': 'benchmark limit of three slug tokens',
+    'check-task-package-name.sh': 'requires terminal-bench/<task> package namespace',
+    'check-separate-verifier.sh': 'requires separate verifier mode for every task',
+    'check-pytest-version.sh': 'benchmark-wide exact pytest/CTRF versions',
+}
+PR_ONLY = {'check-task-changelog.sh': 'training tasks do not require Terminal-Bench PR changelogs'}
+TRAINING_EXCLUSIONS = {
+    'check-test-sh-sanity.sh': 'training permits shared system Python and image-installed verifier dependencies; uv is not required, and stages 4/5 check execution',
+    'check-separate-verifier.sh': 'training permits grading in the agent environment, including installed packages and changed system state; separate verification is optional',
+    'check-allow-internet.sh': 'network policy is declared by the task and checked at runtime',
+    'check-no-allow-internet-true.sh': 'explicit task network policies are allowed',
+    'check-pytest-version.sh': 'training tasks may use other pinned pytest/CTRF versions',
+    'check-gpu-types.sh': 'Modal GPU naming conventions do not apply to the Helma execution profile',
+    'check-canary.sh': 'training tasks do not require a benchmark canary string',
+    'check-instruction-headings.sh': 'Markdown headings are allowed in training instructions',
+    'check-task-fields.sh': 'training tasks do not require TB author GitHub metadata, taxonomy or explanation sections',
+    'check-task-package-name.sh': 'training task package names need not use the terminal-bench namespace',
+    'check-task-slug.sh': 'training task names may contain more than three hyphen-separated tokens',
+}
+CHECKER_UNIT_TESTS = ('test-author-github.py', 'test-instruction-headings.sh',
+                      'test-resource-sizes.sh', 'test-task-changelog.sh')
+AI_CHECK = 'check_ai_detection.py'
+LOCAL_CHECKS = {'check-task-toml-schema.py': Path(__file__).with_name('task_toml_schema.py')}
+
+
+
+def load_checks(profile, upstream=None, exclude=()):
+    manifest = json.loads((TERMINAL_BENCH / 'UPSTREAM.json').read_text())
+    # Detect accidental edits or incomplete copies before executing anything.
+    for name, digest in manifest['files'].items():
+        if hashlib.sha256(((upstream or TERMINAL_BENCH) / name).read_bytes()).hexdigest() != digest:
+            raise ValueError(f'upstream file differs from pinned copy: {name}')
+    names = sorted(Path(p).name for p in manifest['files'] if p.startswith('scripts/checks/'))
+    names = sorted([*names, *LOCAL_CHECKS])
+    excluded = {**PR_ONLY, **(POLICY if profile == 'portable' else TRAINING_EXCLUSIONS if profile == 'training' else {}),
+                'rubric_review.py': 'LLM rubric review is opt-in via stage 2, never a default static check'}
+    inactive = {'rubric_review.py', *CHECKER_UNIT_TESTS}
+    for value in exclude:
+        # NAME=reason records why; a reason may contain commas, so it is one item.
+        value, _, reason = value.partition('=')
+        for requested in value.split(','):
+            requested = requested.strip()
+            aliases = {'ai-detection': 'check_ai_detection.py', 'rubric-review': 'rubric_review.py',
+                       'task-toml-schema': 'check-task-toml-schema.py',
+                       'check-task-toml-schema': 'check-task-toml-schema.py'}
+            name = aliases.get(requested, requested)
+            if name not in inactive and name != AI_CHECK and name not in LOCAL_CHECKS:
+                name = name if name.endswith('.sh') else name + '.sh'
+                name = name if name.startswith('check-') else 'check-' + name
+            if name not in names and name not in inactive:
+                raise ValueError(f'unknown static check: {requested}; use --list')
+            excluded[name] = (reason.strip() or 'explicitly excluded' if name in names else
+                'upstream checker unit test, not dataset validation' if name in CHECKER_UNIT_TESTS else
+                'not part of the static suite (LLM review is opt-in)')
+    return manifest, [n for n in names if n not in excluded], excluded
+
+
+def validate_input(task):
+    import tomllib
+    for name in ('instruction.md', 'task.toml', 'tests/test.sh'):
+        if not (task / name).is_file():
+            raise ValueError(f'missing {name}')
+    if not (task / 'environment').is_dir():
+        raise ValueError('missing environment/')
+    with (task / 'task.toml').open('rb') as stream:
+        tomllib.load(stream)
+    if any(c.isspace() or c in '*?[]' for c in str(task)):
+        raise ValueError(f'task directory path must not contain whitespace or glob characters: {task}')
+
+
+UNSAFE = re.compile(r'[\s*?\[\]]')
+
+
+def safe_copy(task, scratch):
+    """Several upstream scripts split paths as shell words and expand globs, so a file
+    named `Clase 4/[id].ts` would be skipped or misread and the check could pass wrongly.
+    Such tasks are checked on a copy whose offending names have those characters
+    replaced by '_'. The task itself is unchanged. Returns (copy, renamed) or (task, [])."""
+    renamed = sorted(str(p.relative_to(task)) for p in task.rglob('*') if UNSAFE.search(str(p.relative_to(task))))
+    if not renamed:
+        return task, []
+    copy = Path(scratch) / 'renamed' / task.name
+    if copy.exists():
+        shutil.rmtree(copy)
+    for path in task.rglob('*'):
+        target = copy / UNSAFE.sub('_', str(path.relative_to(task)))
+        if path.is_dir():
+            target.mkdir(parents=True, exist_ok=True)
+        else:
+            target.parent.mkdir(parents=True, exist_ok=True)
+            shutil.copyfile(path, target)
+    return copy, renamed
+
+
+PATH_CHECK = 'check-task-absolute-path.sh'
+SHELL_FENCES = {'', 'bash', 'sh', 'shell', 'zsh', 'console', 'text', 'txt'}
+ADAPTATIONS = {PATH_CHECK: 'Relative-path findings are advisory warnings and do not fail stage 1. Runs on a copy of the task whose instruction.md has its source-code blocks removed '
+                           '(fenced blocks tagged with a programming language); masks complete absolute paths '
+                           'and JavaScript console calls/sed substitutions so their substrings are not mistaken for paths; '
+                           'masks complete non-file URLs, quoted absolute paths with spaces, simple inline commands rooted by cd /absolute/path &&, '
+                           'and literal relative symlink targets with explicit absolute link locations; '
+                           'skips all Markdown fenced blocks, recognizes $HOME/${HOME}/~/ paths, and accepts adjacent literal cd and command lines; '
+                           'accepts explicit named-file-in-directory clauses, pure parent-navigation commands, and relative command tokens for uniquely absolute-named executables; '
+                           'unresolved relative file references outside fenced blocks are otherwise kept',
+               'check-test-file-references.sh': 'masks complete non-file URLs, XML hostnames and excluded system paths; fixes full-token extraction and shell redirections, preserving basenames without inventing /app paths; accepts conventional boot artifacts, explicit numeric X filename ranges, explicit label filename templates resolved from supplied label:glob configurations, and references discovered through named supplied files/directories; reads literal writes and copies/moves in explicitly invoked local setup shell scripts without executing them, with source evidence',
+               'check-pip-pinning.sh': 'recognizes SHA-256-pinned HTTP(S) requirements as single shell arguments; masks unquoted shell redirections and argument forwarding in generated offline installer heredocs, retaining actual package installations',
+               'check-nproc.sh': 'training permits measurement-only variables and the exact audited InferredBugs Python 2.7.18 Dockerfile build on Maven Java 8/11/17 (Helma Slurm affinity probes 934209/934274); also permits four content-pinned SETA solutions tested with 1/2 CPUs (Helma probe 948213); other worker selection remains checked; not a Docker quota-only portability guarantee',
+               'file names': 'a task with whitespace or *?[] in a file name is checked on a copy where those characters '
+                             'are replaced by _, because the upstream scripts split paths at spaces and expand globs; '
+                             'the renamed files are listed per task'}
+ADAPTATIONS['check-dockerfile-references.sh'] = 'Ignore full-line Dockerfile comments; executable references remain checked on a scratch copy.'
+ADAPTATIONS['check-dockerfile-sanity.sh'] = 'Inspect apt install arguments within RUN commands, including continuations and quoted pins; do not scan unrelated ENV assignments or embedded source following apt.'
+ADAPTATIONS['check-nproc.sh'] += ' Also permits five content-pinned CalibForge image/script pairs measured at 2/4 CPUs in Helma job 1017578; nproc --all still saw 384 node CPUs.'
+ADAPTATIONS['check-task-toml-schema.py'] = (
+    'Local deterministic replacement for the task_toml_schema rubric: validates against pinned Harbor models '
+    'and rejects unrecognized fields recursively; Harbor free-form metadata/env mappings remain allowed.')
+
+
+def without_source_code(instruction):
+    """Drop fenced blocks tagged with a programming language: file names inside code
+    to read or complete are not paths the task tells the agent to use.
+
+    Source code can itself contain Markdown fences and '#' lines, so the first bare
+    fence is not always the end of the block. The block ends at the first bare fence
+    that is followed by a heading or by the end of the text; if there is none before
+    the next tagged block, it ends at the first bare fence."""
+    lines, kept, i = instruction.split('\n'), [], 0
+    fence = lambda line: re.fullmatch(r'\s*```\s*([A-Za-z0-9_+#.-]*)\s*', line)
+    def before_heading(j):
+        following = next((l for l in lines[j + 1:] if l.strip()), None)
+        return following is None or re.match(r'#{1,6} ', following) is not None
+    while i < len(lines):
+        match = fence(lines[i])
+        if not match or match.group(1).lower() in SHELL_FENCES:
+            kept.append(lines[i])
+            i += 1
+            continue
+        bare = []
+        for j in range(i + 1, len(lines)):
+            inner = fence(lines[j])
+            if inner and inner.group(1):
+                break                # the next tagged block starts here
+            if inner:
+                bare.append(j)
+        closing = next((j for j in bare if before_heading(j)), bare[0] if bare else None)
+        if closing is None:          # unterminated block: leave the text for the check to see
+            kept.append(lines[i])
+            i += 1
+            continue
+        kept.append(f'[{match.group(1)} source code removed for the path check]')
+        i = closing + 1
+    return '\n'.join(kept)
+
+
+def without_urls(text):
+    # Mask whole tokens before upstream extracts filename-like suffixes.
+    text = re.sub(r'\b(?![Ff][Ii][Ll][Ee]://)[A-Za-z][A-Za-z0-9+.-]*://[^\s`\"\'<>]+', '[URL]', text)
+    # Bare host/path form, e.g. mirrors.ubuntu.com/mirrors.txt.
+    return re.sub(r'\b(?:[A-Za-z0-9-]+\.)+(?:com|org|net|edu|gov|io)/[^\s`\"\'<>]+', '[URL]', text)
+
+
+def without_fenced_blocks(text):
+    """Skip Markdown fences of any language, including untagged and shell blocks."""
+    kept, opening = [], None
+    for line in text.splitlines(keepends=True):
+        match = re.match(r'^ {0,3}(`{3,}|~{3,})(.*)$', line.rstrip('\n'))
+        if opening is None:
+            if match:
+                opening = match[1]
+                kept.append('[fenced block omitted from path check]\n')
+            else:
+                kept.append(line)
+        elif (match and match[1][0] == opening[0]
+              and len(match[1]) >= len(opening) and not match[2].strip()):
+            opening = None
+    return ''.join(kept)
+
+
+# Specific conventional interfaces, not an exemption for everything under /boot.
+CONVENTIONAL_REFERENCE_PATHS = (
+    r'/boot/grub/grub\.cfg',
+    r'/boot/initrd\.img-[0-9][A-Za-z0-9_.+-]*',
+)
+
+
+def reference_check_script(source):
+    """Correct lexical extraction on a temporary copy of pinned upstream."""
+    old = "grep -E '^/(app|home|tests|tmp|usr|var|etc)/'"
+    if source.count(old) != 1 or source.count('/[a-zA-Z0-9_./]+\\.') != 1:
+        raise ValueError('upstream file-reference extractor changed')
+    source = source.replace(old, "grep -E '^/'")
+    # A quoted basename supplies no working directory. Keep it as a basename.
+    source = source.replace("sed 's|^|/app/|'", 'cat')
+    # Upstream uses optional quote markers (?) with basic sed regex syntax.
+    # Extended regex syntax is required to strip the redirection / -o prefix.
+    source = source.replace("sed 's/^>\\s*", "sed -E 's/^>\\s*")
+    source = source.replace("sed 's/^-o\\s*", "sed -E 's/^-o\\s*")
+    # Consume the full basename, including suffixes after .img (kernel versions).
+    lines = source.splitlines(keepends=True)
+    for i, line in enumerate(lines):
+        if '/[a-zA-Z0-9_./]+\\.' in line:
+            line = line.replace('/[a-zA-Z0-9_./]+\\.', '/[a-zA-Z0-9_./-]+\\.')
+            line = line.replace("grep -oE '/", "grep -oE '(^|[[:space:]=])/")
+            lines[i] = line.replace("wad)'", "wad)[a-zA-Z0-9_.+-]*'").rstrip('\n') + " | sed 's|^[^/]||'\n"
+    return ''.join(lines)
+
+
+def reference_check_text(text):
+    text = without_urls(text)
+    text = re.sub(r'file://(?=/)', '', text)
+    text = re.sub(r'<host>[^<\n]+</host>', '<host>[hostname]</host>', text)
+    # Upstream deliberately excludes these system roots, but its second regex
+    # can truncate a hyphenated path into e.g. /xsettings.xml and flag it again.
+    text = re.sub(r'/(?:tests|tmp|usr|var|etc)/[^\s`\"\'<>;]+', '[system path]', text)
+    for path in CONVENTIONAL_REFERENCE_PATHS:
+        text = re.sub(r'(?<![\w/])' + path + r'(?![\w./+-])', '[conventional boot artifact]', text)
+    return text
+
+
+def numeric_reference_patterns(instruction, sources):
+    """Accept an X filename template only with an explicit numeric X range."""
+    bounds = re.search(r'\b(?:where\s+)?X\s+is\s+(\d+)\s*[-–]\s*(\d+)\b', instruction)
+    if not bounds:
+        return {}
+    low, high = map(int, bounds.groups())
+    result = {}
+    for match in re.finditer(r'\b([A-Za-z0-9_.-]*_X(?:_[A-Za-z0-9_.-]+)?\.[A-Za-z0-9]+)\b', instruction):
+        template = match.group(1)
+        expression = re.escape(template).replace('_X', r'_(\d+)')
+        for candidate in re.finditer(r'(?<![\w.-])' + expression + r'(?![\w.-])', sources):
+            if low <= int(candidate.group(1)) <= high:
+                result[candidate.group(0)] = {'instruction_pattern': template, 'numeric_range': [low, high]}
+    return result
+
+
+def pip_check_line(line):
+    """Adapt shell syntax on the check copy, never rewriting the installation."""
+    from packaging.requirements import Requirement, InvalidRequirement
+    from urllib.parse import urlsplit
+    # Keep quotes intact so quoted '>' and spaces inside requirements are not
+    # mistaken for shell operators or separate package arguments.
+    pattern = r'''(?:\d+)?(?:>>?|<<?)&?|&&|\|\||[;|&]|(?:[^\s'"\\<>;&|]+|\\[^\n]|'[^']*'|"(?:\\.|[^"\\])*")+'''
+    tokens = list(re.finditer(pattern, line))
+    cursor = 0
+    for token in tokens:
+        if line[cursor:token.start()].strip():
+            return line  # Unsupported/malformed shell syntax: keep the finding.
+        cursor = token.end()
+    if line[cursor:].strip():
+        return line
+    edits, i = [], 0
+    while i < len(tokens):
+        token = tokens[i]
+        raw = token.group()
+        if raw.startswith('#'):
+            break
+        if re.fullmatch(r'(?:\d+)?(?:>>?|<)&?', raw) and i + 1 < len(tokens):
+            destination = tokens[i + 1]
+            if destination.group() not in ('&&', '||', ';', '|', '&'):
+                edits.append((token.start(), destination.end(), ' '))
+                i += 2
+                continue
+        try:
+            value, = shlex.split(raw)
+        except ValueError:
+            i += 1
+            continue
+        url = value
+        name = 'hash-pinned-artifact'
+        try:
+            requirement = Requirement(value)
+            if requirement.url and not requirement.marker:
+                url, name = requirement.url, requirement.name
+        except InvalidRequirement:
+            pass
+        try:
+            parsed = urlsplit(url)
+        except ValueError:
+            i += 1
+            continue
+        if (parsed.scheme in ('http', 'https') and parsed.netloc
+                and not any(c in url for c in '$`\\')
+                and re.fullmatch(r'sha256=[0-9a-fA-F]{64}', parsed.fragment)):
+            # Upstream understands == pins, but splits direct references at
+            # spaces. This placeholder exists only in its scratch input.
+            edits.append((token.start(), token.end(), name + '==0'))
+        i += 1
+    for start, end, replacement in reversed(edits):
+        line = line[:start] + replacement + line[end:]
+    return line
+
+
+def pip_check_text(text):
+    # Generated offline installers are tools accepting user-specified packages,
+    # not an unpinned install into the task environment. Only exempt forwarding
+    # inside a quoted heredoc; retain concrete installs inside those heredocs.
+    lines, delimiter = [], None
+    for line in text.splitlines(keepends=True):
+        if delimiter and line.strip() == delimiter:
+            delimiter = None
+        elif delimiter and re.fullmatch(
+                r'\s*pip3? install --no-index --find-links="\$SCRIPT_DIR" "\$@"\s*', line):
+            line = '# generated offline installer forwards caller arguments\n'
+        if delimiter is None:
+            match = re.search(r"<<\s*['\"]([A-Za-z_][A-Za-z0-9_]*)['\"]", line)
+            if match:
+                delimiter = match.group(1)
+        lines.append(pip_check_line(line))
+    return ''.join(lines)
+
+
+# Content-pinned CPU-affinity audit: Helma job 1017578, all five images at 2/4 CPUs.
+CALIBFORGE_REVIEWED_NPROC = {'contrastive_solver-security_20260508_045740_002': {'file': 'environment/Dockerfile',
+                                                     'sha256': {'environment/Dockerfile': '8554c71778e6d80171e69483cafc1c53f016d16607b586eb8d259936c2996ad1'}},
+ 'contrastive_solver-software-engineering_20260510_053611_008': {'file': 'environment/Dockerfile',
+                                                                 'sha256': {'environment/Dockerfile': 'fe371f2e4d5ccf5ac295269324bf2d7dbfb6d3e10377e84910f457f384f365cb'}},
+ 'contrastive_solver-software-engineering_20260611_210349_008': {'file': 'tests/test.sh',
+                                                                 'sha256': {'environment/Dockerfile': '4f6194d3d652fd8cb9d9de5681211adf5ba57146718f2fc0db9d977d11f8d8b7',
+                                                                            'tests/test.sh': 'b7f4a23eaffed3576d649078f6bb09f89b84e2a5573063b53552799af644560a'}},
+ 'contrastive_solver-system-administration_20260604_004411_008': {'file': 'environment/Dockerfile',
+                                                                  'sha256': {'environment/Dockerfile': '47c7d9e917e98d3965d48a380c1d82a2fd774505857ccfdcc6bfdaacba388db9'}},
+ 'contrastive_solver-system-administration_20260604_004411_009': {'file': 'environment/Dockerfile',
+                                                                  'sha256': {'environment/Dockerfile': 'bbe5c1425ac6323702e29c0faae4d27efa23de0c6202797491ed5343887a2373'}}}
+
+
+def dockerfile_without_comments(text):
+    """Ignore full-line Dockerfile comments, retaining inline arguments/data."""
+    kept, heredocs = [], []
+    for line in text.splitlines(keepends=True):
+        if heredocs:
+            kept.append(line)
+            if line.strip() == heredocs[0]:
+                heredocs.pop(0)
+            continue
+        if line.lstrip().startswith('#'):
+            continue
+        kept.append(line)
+        # Heredoc payload is data, not Dockerfile comments.
+        heredocs.extend(re.findall(r"<<-?\s*['\"]?([A-Za-z_][A-Za-z0-9_]*)['\"]?", line))
+    return ''.join(kept)
+
+
+def dockerfile_sanity_text(text):
+    """Give upstream only apt command arguments, not the next 20 source lines.
+
+    Shell tokenization preserves quoted pins and joins continued RUN commands.
+    Unparseable shell is kept for conservative upstream checking.
+    """
+    text = dockerfile_without_comments(text)
+    logical = re.sub(r'\\\n', ' ', text)
+    commands = []
+    for line in logical.splitlines():
+        if not re.match(r'^\s*RUN\s', line, re.I):
+            continue
+        if re.search(r'\bapt(?:-get)?\b', line) and ('<<' in line or re.match(r'^\s*RUN\s*\[', line, re.I) or re.search(r'\b(?:sh|bash)\s+-c', line)):
+            return text  # Preserve conservative checking of unsupported shell forms.
+        try:
+            lexer = shlex.shlex(line, posix=True, punctuation_chars=';&|()<>' )
+            lexer.whitespace_split = True
+            tokens = list(lexer)
+        except ValueError:
+            return text
+        for i, token in enumerate(tokens):
+            if token.rsplit('/', 1)[-1] not in ('apt', 'apt-get'):
+                continue
+            args = []
+            for arg in tokens[i + 1:]:
+                if arg and all(c in ';&|()<>' for c in arg):
+                    break
+                args.append(arg)
+            # Keep update/cleanup advisory behavior, but expose version pins
+            # only in install arguments. Epochs/integer pins count too.
+            if 'install' in args:
+                if (i and tokens[i - 1] not in ('RUN', 'run', '&&', '||', ';', '|', 'sudo', 'env', 'then', 'do', '{', '(', '!')
+                        and not re.fullmatch(r'[A-Za-z_][A-Za-z0-9_]*=.*', tokens[i - 1])):
+                    return text  # Do not silently exempt unknown command wrappers.
+                packages = args[args.index('install') + 1:]
+                pinned = [a for a in packages if re.fullmatch(r'[a-zA-Z0-9][a-zA-Z0-9+.:_-]*=[^=\s]+', a)]
+                commands.append('RUN apt install ' + ('pinned-package=1.0' if pinned else 'packages'))
+            elif 'update' in args:
+                commands.append('RUN apt update')
+    if 'rm -rf /var/lib/apt/lists' in text:
+        commands.append('RUN rm -rf /var/lib/apt/lists/*')
+    return '\n'.join(commands) + '\n'
+
+
+def calibforge_nproc_text(text, task, relative):
+    """Allow only the exact image/script pairs measured in Helma job 1017578."""
+    record = CALIBFORGE_REVIEWED_NPROC.get(task.name)
+    if not record or relative != record['file']:
+        return text
+    for filename, digest in record['sha256'].items():
+        path = task / filename
+        if not path.is_file() or hashlib.sha256(path.read_bytes()).hexdigest() != digest:
+            return text
+    return text.replace('$(nproc)', 'VERIFIED_CPU_AFFINITY')
+
+
+def nproc_check_text(text, *, dockerfile=False):
+    """Conservatively recognize measurement-only variables; not a shell parser.
+
+    Also recognize the exact Python 2 build audited under Slurm CPU affinity.
+    Other build flags and unknown uses retain the original check.
+    """
+    if dockerfile and re.search(r'^FROM maven:3\.9-eclipse-temurin-(?:8|11|17)$', text, re.M):
+        # Match the build context and complete command, not make/nproc generally.
+        # Mask only on the check's scratch copy; the actual task is unchanged.
+        reviewed = (
+            ' && tar -xzf "$d/python2.tgz" -C "$d" && cd "$d/Python-2.7.18" \\\n'
+            ' && ./configure --prefix=/opt/python2 --disable-shared --without-ensurepip >/dev/null '
+            '&& make -j"$(nproc)" >/dev/null && make install >/dev/null \\\n'
+            ' && cd / && rm -rf "$d" && /opt/python2/bin/python2.7 -c "import zlib"'
+        )
+        text = text.replace(reviewed, reviewed.replace('$(nproc)', 'VERIFIED_CPU_AFFINITY'))
+    lines = text.splitlines(keepends=True)
+    for i, line in enumerate(lines):
+        assignment = re.fullmatch(r'\s*([A-Za-z_]\w*)="?\$\(nproc\)"?\s*', line)
+        if not assignment:
+            continue
+        var = assignment.group(1)
+        refs = re.compile(r'\$(?:' + re.escape(var) + r'\b|\{' + re.escape(var) + r'\})')
+        uses = [s.strip() for s in lines if refs.search(s) and not s.lstrip().startswith('#')]
+        def measurement(s):
+            # JSON fields: no command substitutions, backticks or shell chains.
+            if s.startswith(('{"', '"')) and not re.search(r'\$\(|`|[;&|]', s):
+                return True
+            if re.fullmatch(r'if \(\( \$\(echo "\$\w+ > \$' + re.escape(var) + r'" \| bc -l\) \)\); then', s):
+                return True
+            return bool(re.fullmatch(r'alerts(?:\+)?=\(?"[^\n]*"\)?', s)) and not re.search(r'\$\(|`|[;&|]', s)
+        if uses and all(measurement(s) for s in uses):
+            lines[i] = line.replace('$(nproc)', 'CPU_MEASUREMENT')
+    return ''.join(lines)
+
+
+def adapted_check_copy(task, scratch, name, profile):
+    transforms = {'check-test-file-references.sh': reference_check_text,
+                  'check-pip-pinning.sh': pip_check_text,
+                  'check-dockerfile-references.sh': dockerfile_without_comments,
+                  'check-dockerfile-sanity.sh': dockerfile_sanity_text}
+    if profile == 'training':
+        transforms['check-nproc.sh'] = nproc_check_text
+    if name not in transforms:
+        return task
+    copy = Path(scratch) / name / task.name
+    # Only files consumed by these checks. Avoid copying potentially large setup
+    # archives for each adaptation.
+    paths = ['instruction.md', 'task.toml', 'environment/Dockerfile',
+             'tests/Dockerfile', 'tests/test.sh', 'solution/solve.sh']
+    paths.extend(str(p.relative_to(task)) for p in (task / 'tests').rglob('test_*.py'))
+    for relative in paths:
+        source = task / relative
+        if source.is_file():
+            target = copy / relative
+            target.parent.mkdir(parents=True, exist_ok=True)
+            text = source.read_text(errors='replace')
+            if name == 'check-nproc.sh' and relative not in ('instruction.md', 'task.toml'):
+                if profile == 'training' and relative == 'solution/solve.sh':
+                    from data.seta.patch import reviewed_nproc_text
+                    dockerfile = task / 'environment/Dockerfile'
+                    text = reviewed_nproc_text(text, task.name,
+                                               dockerfile.read_bytes() if dockerfile.is_file() else b'')
+                text = calibforge_nproc_text(text, task, relative)
+                text = nproc_check_text(text, dockerfile=relative == 'environment/Dockerfile')
+            elif relative not in ('instruction.md', 'task.toml'):
+                text = transforms[name](text)
+            target.write_text(text)
+    if name == 'check-test-file-references.sh':
+        evidence = discoverable_references(task)
+        if (copy / 'instruction.md').is_file():
+            sources = '\n'.join((copy / p).read_text(errors='replace') for p in paths
+                                if p not in ('instruction.md', 'task.toml') and (copy / p).is_file())
+            evidence.update(numeric_reference_patterns((copy / 'instruction.md').read_text(), sources))
+        (copy / 'discovered-references.json').write_text(json.dumps(evidence, indent=2))
+        if (copy / 'instruction.md').is_file():
+            with (copy / 'instruction.md').open('a') as stream:
+                stream.write('\nSupplied entry points reveal these references:\n' + '\n'.join(evidence) + '\n')
+    return copy
+
+
+def named_path_examples(text):
+    """Recognize explicit location clauses and reuse unique executable locations."""
+    locations = {}
+    def remember(path):
+        if not any(c in path for c in '$*?[]{}'):
+            locations.setdefault(path.rsplit('/', 1)[-1], set()).add(path)
+    for match in re.finditer(r'''(?<![\w./])/(?!/)[A-Za-z0-9_.+@/-]+(?=$|[\s`"'<>|;,:!?)])''', text):
+        remember(match[0].rstrip('.,:'))
+
+    # Join only this explicit grammatical construction, never nearby paths.
+    clause = re.compile(
+        r'''\b(?:file|script|executable|utility|tool)\s+(?:named|called)\s+'''
+        r'''(?P<quote>[`"']?)(?P<name>[A-Za-z0-9_-][A-Za-z0-9_.+-]*)(?P=quote)'''
+        r'''\s+in\s+(?P<dirquote>[`"']?)(?P<directory>/[A-Za-z0-9_.+@/-]+)(?P=dirquote)(?=$|[\s.,:;!?])''', re.I)
+    def specified(match):
+        directory = match['directory'].rstrip('.,:')
+        remember(directory.rstrip('/') + '/' + match['name'])
+        start, end = match.span('name')
+        start, end = start - match.start(), end - match.start()
+        return match[0][:start] + '[explicitly located filename]' + match[0][end:]
+    text = clause.sub(specified, text)
+
+    def invocation(match):
+        value = match[1]
+        # Mask only ./NAME at command position. Arguments remain checked.
+        token = re.match(r'\./(?P<name>[A-Za-z0-9_-][A-Za-z0-9_.+-]*)(?=\s|$)', value)
+        if token and len(locations.get(token['name'], set())) == 1:
+            return '`[explicitly located executable]' + value[token.end():] + '`'
+        return match[0]
+    return re.sub(r'`([^`\n]+)`', invocation, text)
+
+
+def explicit_path_examples(text):
+    """Mask locally specified command/link examples, without inferring global cwd."""
+    def literal(value):
+        return bool(value) and not any(c in value for c in '$`*?[]{}<>\n')
+
+    def inline(match):
+        value = match.group(1)
+        try:
+            tokens = list(shlex.shlex(value, posix=True, punctuation_chars=';&|<>'))
+        except ValueError:
+            return match.group(0)
+        if re.fullmatch(r'cd\s+(?:--\s+)?\.\.(?:/\.\.)*/?', value.strip()):
+            return '[parent navigation]'
+        # Only a single command after &&. Extra shell operators, dynamic
+        # expressions and another directory change remain review findings.
+        args = tokens[1:] if tokens[:1] == ['cd'] else []
+        if args[:1] == ['--']:
+            args = args[1:]
+        if (len(args) >= 3 and args[0].startswith('/') and args[1] == '&&'
+                and args[2] not in ('cd', 'pushd', 'popd', 'eval')
+                and '-c' not in args[2:]
+                and all(literal(t) and not any(c in t for c in ';&|()') for t in [args[0], *args[2:]])):
+            return '[command with explicit directory]'
+        # ln -s TARGET /absolute/LINK defines the relative target's base.
+        if (len(tokens) == 4 and tokens[:2] == ['ln', '-s']
+                and tokens[2].startswith(('./', '../')) and tokens[3].startswith('/')
+                and all(literal(t) for t in tokens[2:])):
+            return '[symlink with explicit location]'
+        return match.group(0)
+
+    # Two adjacent command lines can establish the same local base as &&.
+    # Do not carry that directory across paragraphs or unrelated prose.
+    def adjacent(match):
+        commands = [line.strip().strip('`') for line in match[0].splitlines()]
+        combined = '`' + commands[0] + ' && ' + commands[1] + '`'
+        result = inline(re.fullmatch(r'`([^`\n]+)`', combined))
+        return result if result != combined else match[0]
+    text = re.sub(r'(?m)^ {0,3}`?cd [^\n`]+`?\n {0,3}(?:`[^`\n]+`|[^`\n]+)$', adjacent, text)
+    text = re.sub(r'`([^`\n]+)`', inline, text)
+    absolute = r'''(?:`/[^`\n]+`|"/[^"\n]+"|'/[^'\n]+'|/[^\s`"'<>|;]+)'''
+    relative = r'''(?:`\.{1,2}/[^`\n]+`|"\.{1,2}/[^"\n]+"|'\.{1,2}/[^'\n]+'|\.{1,2}/[^\s`"'<>|;]+)'''
+    mapping = re.compile(r'(?P<link>' + absolute + r')\s*->\s*(?P<target>' + relative + r')')
+    paragraphs = re.split(r'(\n\s*\n)', text)
+    for i, paragraph in enumerate(paragraphs):
+        if not re.search(r'\b(?:symlink|symbolic\s+link)s?\b', paragraph, re.I):
+            continue
+        established = set()
+        def link(match):
+            location = match['link'].strip('`"\'')
+            target = match['target'].strip('`"\'')
+            if literal(location) and literal(target):
+                established.update((target, target.rsplit('/', 1)[0] + '/'))
+                return match['link'] + ' -> [relative symlink target]'
+            return match.group(0)
+        paragraph = mapping.sub(link, paragraph)
+        # The same paragraph may reiterate the literal target or its directory.
+        # Only these exact inline strings inherit the established link location.
+        paragraphs[i] = re.sub(r'`([^`\n]+)`',
+                               lambda m: '[specified symlink reference]' if m[1] in established else m[0],
+                               paragraph)
+    return ''.join(paragraphs)
+
+
+def path_check_text(instruction):
+    """Adapt known lexical false positives without changing pinned upstream code."""
+    text = without_fenced_blocks(without_source_code(instruction))
+    text = without_urls(text)
+    text = named_path_examples(text)
+    text = explicit_path_examples(text)
+    # HOME is case-sensitive in shells. Unknown variables remain unresolved.
+    text = re.sub(r'''(?<![\w$])(?:\$HOME|\$\{HOME\}|~)/[^\s`"'<>|;]+''',
+                  '[home-anchored path]', text)
+    # A relative command with an explicit working directory on the same line
+    # is unambiguous. Do not infer a global cwd from unrelated absolute paths.
+    text = re.sub(r'`(\./[^`\n]+)`(?= from `/[^`\n]+`)', '[rooted command]', text)
+    # Quoted absolute paths can contain spaces; consume before bare tokens.
+    text = re.sub(r'`/[^`\n]+`', '`[absolute path]`', text)
+    # Consume the WHOLE absolute token, including @ and hyphens in systemd units.
+    # Replacing tokens individually also prevents upstream's global substring
+    # filter from excusing a relative path merely because an absolute one exists.
+    text = re.sub(r'''(?<![\w./])/(?!/)[^\s`"'<>|;]+''', '[absolute path]', text)
+    lines = []
+    method = r'console\.(?:log|warn|error|info|debug|trace|table)'
+    for line in text.splitlines(keepends=True):
+        code_context = re.search(r'\b(?:JavaScript|regex|calls?|references?|strings?|literals?|statements?)\b', line, re.I)
+        def inline(match):
+            value = match.group(1)
+            # A sed substitution is an expression, not a directory reference.
+            if re.fullmatch(r's/[^\n]*/[^\n]*/[gip0-9]*', value):
+                return '`[sed expression]`'
+            if re.search(method + r'\s*\(', value) or (code_context and re.fullmatch(method, value)):
+                return '`' + re.sub(method, '[JavaScript method]', value) + '`'
+            return match.group(0)
+        line = re.sub(r'`([^`\n]+)`', inline, line)
+        if code_context:
+            line = re.sub(r'(["\'])(' + method + r')\1', '[JavaScript method]', line)
+        lines.append(line)
+    return ''.join(lines)
+
+
+def path_check_copy(task, scratch):
+    copy = Path(scratch) / 'path-check' / task.name
+    (copy / 'environment').mkdir(parents=True, exist_ok=True)
+    (copy / 'instruction.md').write_text(path_check_text((task / 'instruction.md').read_text(errors='replace')))
+    for name in ('task.toml', 'environment/Dockerfile'):
+        if (task / name).is_file():
+            shutil.copyfile(task / name, copy / name)
+    return copy
+
+
+def rebuild_summary(out):
+    """Reconstruct completed outcomes; ignore only an unfinished final journal line."""
+    out = Path(out)
+    summary = out / 'summary.json'
+    report = json.loads(summary.read_text())
+    expected = [Path(path).name for path in report['selected_tasks']]
+    expected_names = set(expected)
+    entries = {}
+    incomplete_tail = False
+    with (out / 'outcomes.jsonl').open() as stream:
+        for line in stream:
+            if not line.endswith('\n'):
+                incomplete_tail = True
+                break
+            entry = json.loads(line)
+            name = entry['task']
+            if name not in expected_names or name in entries:
+                raise ValueError(f'unknown or duplicate journal task: {name}')
+            entries[name] = entry
+    report['tasks'] = [entries[name] for name in expected if name in entries]
+    report['complete'] = len(entries) == len(expected) and not incomplete_tail
+    report['passed'] = report['complete'] and all(t['status'] == 'passed' for t in report['tasks'])
+    report['incomplete_journal_tail'] = incomplete_tail
+    pending = summary.with_suffix('.json.tmp')
+    pending.write_text(json.dumps(report, indent=2) + '\n')
+    pending.replace(summary)
+    return report
+
+
+def run_checks(tasks, out, profile='training', timeout=300, upstream=None, exclude=(), concurrency=1,
+               resume=None, resume_record=None, accept_previous_path_check=False):
+    if concurrency < 1:
+        raise ValueError('concurrency must be positive')
+    if sys.version_info < (3, 11):
+        raise ValueError('Terminal-Bench checks require Python 3.11+; activate your prep environment')
+    manifest, checks, excluded = load_checks(profile, upstream, exclude)
+    if not checks:
+        raise ValueError('no static checks selected')
+    for command in ('bash', 'grep', 'sed', 'awk', 'find', 'sort', 'uniq', 'mktemp', 'dirname', 'basename', 'cat', 'tr', 'rm'):
+        if not shutil.which(command):
+            raise ValueError(f'missing required executable: {command}')
+    out.mkdir(parents=True, exist_ok=True)
+    if (out / 'outcomes.jsonl').exists():
+        raise ValueError('output already has task outcomes; use a new output directory or --rebuild-summary')
+    report = {'upstream': manifest['repository'], 'commit': manifest['commit'],
+              'concurrency': concurrency, 'profile': profile, 'selected_tasks': [str(t) for t in tasks],
+              'checks': checks, 'excluded_checks': excluded, 'tasks': [],
+              'adaptations': {name: text for name, text in ADAPTATIONS.items() if name in checks or name == 'file names'},
+              'checker_unit_tests_not_run': list(CHECKER_UNIT_TESTS),
+              'conditional_checks': {AI_CHECK: 'runs only when GPTZERO_API_KEY is configured; missing key is a non-failing skip'},
+              'complete': False, 'passed': False}
+    imported = {}
+    if resume:
+        from validation.checkpoints.static_resume import load
+        imported, report['resumed_from'] = load(resume, tasks, manifest, checks, profile, resume_record,
+                                               accept_previous_path_check)
+        print(f"Static checkpoint: importing {report['resumed_from']['imported_checks']} checks; "
+              f"rerunning changed checks {report['resumed_from']['rerun_changed_checks']}", flush=True)
+    for name, reason in excluded.items():
+        print(f'SKIP {name}: {reason}', flush=True)
+    if AI_CHECK in checks and not os.environ.get('GPTZERO_API_KEY', '').strip():
+        print('SKIP check_ai_detection.py: no GPTZERO_API_KEY configured (not a failure)', flush=True)
+    summary = out / 'summary.json'
+    summary.write_text(json.dumps(report, indent=2) + '\n')
+    log = out / 'checks.log'
+    log_lock = threading.Lock()
+    static_root = os.environ.get('ZIH_STATIC_TMPDIR')
+    with tempfile.TemporaryDirectory(prefix='tb-checks-', dir=static_root or '/tmp') as scratch, \
+            log.open('w') as combined_log, (out / 'outcomes.jsonl').open('x') as journal:
+        # Upstream invokes python3. Use this interpreter, not an unrelated
+        # system Python that may lack tomllib. No dependency installation needed.
+        bindir = Path(scratch) / 'bin'
+        bindir.mkdir()
+        check_python = os.environ.get('ZIH_STATIC_PYTHON', sys.executable)
+        (bindir / 'python3').symlink_to(check_python)
+        scripts = (upstream or TERMINAL_BENCH) / 'scripts/checks'
+        reference_script = Path(scratch) / 'adapted-scripts/check-test-file-references.sh'
+        if reference_script.name in checks:
+            reference_script.parent.mkdir()
+            reference_script.write_text(reference_check_script((scripts / reference_script.name).read_text()))
+        if static_root:
+            local_scripts = Path(scratch) / 'scripts'
+            shutil.copytree(scripts, local_scripts)
+            scripts = local_scripts
+        env = {**os.environ, 'PATH': str(bindir) + os.pathsep + os.environ.get('PATH', '')}
+        for key in ('FIX_DIRS', 'BASE_DIR', 'BASH_ENV', 'ENV'):
+            env.pop(key, None)
+        def check_task_body(task, scratch):
+            entry = {'task': task.name, 'path': str(task), 'checks': []}
+            try:
+                validate_input(task)
+            except (ValueError, OSError) as exc:
+                entry.update(status='error', error=str(exc))
+            else:
+                pending_checks = set(checks) - set(imported.get(task.name, {}))
+                if not pending_checks or (pending_checks <= {AI_CHECK} and not os.environ.get('GPTZERO_API_KEY', '').strip()):
+                    # Complete checkpointed tasks need no staging copy or subprocesses.
+                    # The optional AI check is still handled below using current credentials.
+                    renamed = []
+                else:
+                    if static_root:
+                        staged = Path(scratch) / 'input' / task.name
+                        shutil.copytree(task, staged)
+                        task = staged
+                    task, renamed = safe_copy(task, scratch)
+                if renamed:
+                    entry['renamed_for_checks'] = renamed
+                for name in checks:
+                    if name in imported.get(task.name, {}):
+                        entry['checks'].append(imported[task.name][name])
+                        continue
+                    if name == AI_CHECK and not os.environ.get('GPTZERO_API_KEY', '').strip():
+                        entry['checks'].append({'check': name, 'status': 'skipped', 'optional': True,
+                            'reason': 'no GPTZERO_API_KEY configured', 'exit_code': None, 'log': None})
+                        continue
+                    started = time.monotonic()
+                    target = path_check_copy(task, scratch) if name == PATH_CHECK else adapted_check_copy(task, scratch, name, profile)
+                    if name == 'check-test-file-references.sh':
+                        evidence = json.loads((target / 'discovered-references.json').read_text())
+                        if evidence:
+                            entry['discoverable_reference_evidence'] = evidence
+                    # Buffer each check separately so parallel outputs never interleave.
+                    with tempfile.TemporaryFile(mode='w+', encoding='utf-8', errors='replace', dir=scratch) as stream:
+                        # The scripts take under a second; a timeout means the node or the
+                        # file system stalled (job 916252), so one more attempt is made.
+                        for attempt in (1, 2):
+                            try:
+                                script = LOCAL_CHECKS.get(name) or (reference_script if name == reference_script.name else scripts / name)
+                                interpreter = sys.executable if name in LOCAL_CHECKS else check_python if name.endswith('.py') else 'bash'
+                                result = subprocess.run([interpreter, str(script), str(target)],
+                                    cwd=scratch, env=env, stdout=stream, stderr=subprocess.STDOUT, timeout=timeout)
+                                status = 'passed' if result.returncode == 0 else 'failed'
+                                rc = result.returncode
+                                break
+                            except subprocess.TimeoutExpired:
+                                status, rc = 'error', None
+                                stream.write(f'\nTimed out after {timeout} seconds (attempt {attempt})\n')
+                                stream.flush()
+                        stream.seek(0)
+                        if name == PATH_CHECK and rc == 1:
+                            if re.search(r'relative paths used \(should be absolute under /[^)]*\): ', stream.read()):
+                                status = 'warning'
+                            stream.seek(0)
+                        if name == AI_CHECK and rc == 0:
+                            text = stream.read()
+                            if 'skipped' in text.lower() or 'No files to check' in text:
+                                status = 'skipped'
+                            stream.seek(0)
+                        with log_lock:
+                            combined_log.write(f'\n=== {entry["task"]} / {name} ===\n')
+                            shutil.copyfileobj(stream, combined_log)
+                            combined_log.write(f'\n=== result: {status}, exit_code: {rc} ===\n')
+                            combined_log.flush()
+                    entry['checks'].append({'check': name, 'status': status, 'optional': name == AI_CHECK, 'exit_code': rc,
+                                            'log': str(log.resolve()), 'duration_seconds': round(time.monotonic() - started, 3)})
+                    if status != 'passed':
+                        print(f'{task.name}: {name}: {status} (see {log})', flush=True)
+                entry['warnings'] = [{'tag': 'relative-instruction-path', 'check': c['check'], 'log': c.get('log')} for c in entry['checks'] if c['status'] == 'warning']
+                entry['status'] = 'passed' if all(c['status'] in ('passed', 'warning') or (c['status'] == 'skipped' and c.get('optional')) for c in entry['checks']) else 'failed'
+            return entry
+        def check_task(task):
+            if not static_root:
+                return check_task_body(task, scratch)
+            # Bound live task copies in RAM; oversized tasks use durable scratch.
+            # Allow for staging plus renamed/path-check copies per concurrent task.
+            parent = scratch
+            try:
+                validate_input(task)
+                size = sum(p.stat().st_size for p in task.rglob('*') if p.is_file())
+                limit = int(os.environ.get('ZIH_STATIC_MAX_BYTES', '1073741824')) // (3 * concurrency)
+                if size > limit:
+                    parent = os.environ['TMPDIR']
+            except (ValueError, OSError) as exc:
+                return {'task': task.name, 'path': str(task), 'checks': [], 'status': 'error', 'error': str(exc)}
+            # Delete only this task's temporary copies immediately after its checks.
+            with tempfile.TemporaryDirectory(prefix='static-task-', dir=parent) as task_scratch:
+                return check_task_body(task, task_scratch)
+        with ThreadPoolExecutor(max_workers=concurrency) as pool:
+            futures = [pool.submit(check_task, task) for task in tasks]
+            for future in as_completed(futures):
+                entry = future.result()
+                journal.write(json.dumps(entry) + '\n')
+                journal.flush()
+                print(f"{entry['task']}: {entry['status']}", flush=True)
+    report = rebuild_summary(out)
+    print(f'{len(checks)} upstream checks per task; {len(excluded)} explicitly excluded. Report: {summary}')
+    return 0 if report['passed'] else 1
+
+
+def main():
+    ap = argparse.ArgumentParser(description=__doc__)
+    ap.add_argument('root', nargs='?', type=Path)
+    ap.add_argument('--profile', choices=('training', 'portable', 'terminal-bench'), default='training')
+    ap.add_argument('--out', type=Path, default=Path('verify-out/terminal-bench'))
+    ap.add_argument('--limit', type=int)
+    ap.add_argument('--concurrency', type=int, default=1, help='parallel static tasks')
+    ap.add_argument('--timeout', type=int, default=120, help='seconds per static script per task')
+    ap.add_argument('--list', action='store_true', help='list included and excluded checks')
+    ap.add_argument('--exclude', action='append', default=[], help='check ID or filename, optionally NAME=reason; repeat or comma-separate')
+    ap.add_argument('--dry-run', action='store_true')
+    ap.add_argument('--rebuild-summary', action='store_true', help='reconstruct --out/summary.json from saved task outcomes without rerunning checks')
+    a = ap.parse_args()
+    try:
+        if a.rebuild_summary:
+            report = rebuild_summary(a.out)
+            print(f"Recovered {len(report['tasks'])} task outcomes; complete={report['complete']}")
+            return 0 if report['passed'] else 1
+        if a.timeout <= 0 or (a.limit is not None and a.limit <= 0):
+            raise ValueError('--limit and --timeout must be positive')
+        manifest, checks, excluded = load_checks(a.profile, exclude=a.exclude)
+        if a.list or a.dry_run:
+            print(f"Terminal-Bench {manifest['commit']} ({a.profile})")
+            for name in checks:
+                print(('SKIP ' + name + ': no GPTZERO_API_KEY configured (not a failure)')
+                      if name == AI_CHECK and not os.environ.get('GPTZERO_API_KEY', '').strip()
+                      else f"{'CONDITIONAL' if name == AI_CHECK else 'RUN '} {name}")
+            for name, reason in excluded.items():
+                print(f'SKIP {name}: {reason}')
+        if a.list:
+            return 0
+        if a.root is None:
+            raise ValueError('provide a task or task directory')
+        tasks = discover_tasks(a.root)[:a.limit]
+        if a.dry_run:
+            for task in tasks:
+                print(f'Would check {task}')
+            return 0
+        return run_checks(tasks, a.out, a.profile, a.timeout, exclude=a.exclude, concurrency=a.concurrency)
+    except (ValueError, OSError) as exc:
+        ap.exit(1, f'{exc}\n')
+
+
+if __name__ == '__main__':
+    raise SystemExit(main())

calibforge/ablations/evidence/stage1-checker.py

@@ -0,0 +1,889 @@
+#!/usr/bin/env python3
+"""Run pinned Terminal-Bench checks with training-task defaults and optional GPTZero."""
+from __future__ import annotations
+
+import argparse
+from concurrent.futures import ThreadPoolExecutor, as_completed
+import hashlib
+import json
+import os
+from pathlib import Path
+import re
+import shlex
+import shutil
+import subprocess
+import sys
+import tempfile
+import time
+import threading
+
+sys.path.insert(0, str(Path(__file__).resolve().parents[2]))
+from validation.data.selection import discover_tasks
+from validation.checks.supplied_references import discoverable_references
+
+TERMINAL_BENCH = Path(__file__).resolve().parents[1] / 'upstream/terminal_bench'
+# These are policy decisions in our wrapper; upstream files remain unmodified.
+POLICY = {
+    'check-canary.sh': 'Terminal-Bench-specific canary GUID',
+    'check-task-fields.sh': 'benchmark author metadata, taxonomy and README sections',
+    'check-task-timeout.sh': 'benchmark timeout caps',
+    'check-instruction-suffix.sh': 'benchmark-specific instruction suffix',
+    'check-instruction-headings.sh': 'benchmark prose-only instruction style',
+    'check-gpu-types.sh': 'Modal-specific GPU allowlist',
+    'check-resource-sizes.sh': 'benchmark CPU/memory size allowlist',
+    'check-allow-internet.sh': 'benchmark requires default internet access',
+    'check-no-allow-internet-true.sh': 'benchmark forbids explicit internet opt-in',
+    'check-task-slug.sh': 'benchmark limit of three slug tokens',
+    'check-task-package-name.sh': 'requires terminal-bench/<task> package namespace',
+    'check-separate-verifier.sh': 'requires separate verifier mode for every task',
+    'check-pytest-version.sh': 'benchmark-wide exact pytest/CTRF versions',
+}
+PR_ONLY = {'check-task-changelog.sh': 'training tasks do not require Terminal-Bench PR changelogs'}
+TRAINING_EXCLUSIONS = {
+    'check-test-sh-sanity.sh': 'training permits shared system Python and image-installed verifier dependencies; uv is not required, and stages 4/5 check execution',
+    'check-separate-verifier.sh': 'training permits grading in the agent environment, including installed packages and changed system state; separate verification is optional',
+    'check-allow-internet.sh': 'network policy is declared by the task and checked at runtime',
+    'check-no-allow-internet-true.sh': 'explicit task network policies are allowed',
+    'check-pytest-version.sh': 'training tasks may use other pinned pytest/CTRF versions',
+    'check-gpu-types.sh': 'Modal GPU naming conventions do not apply to the Helma execution profile',
+    'check-canary.sh': 'training tasks do not require a benchmark canary string',
+    'check-instruction-headings.sh': 'Markdown headings are allowed in training instructions',
+    'check-task-fields.sh': 'training tasks do not require TB author GitHub metadata, taxonomy or explanation sections',
+    'check-task-package-name.sh': 'training task package names need not use the terminal-bench namespace',
+    'check-task-slug.sh': 'training task names may contain more than three hyphen-separated tokens',
+}
+CHECKER_UNIT_TESTS = ('test-author-github.py', 'test-instruction-headings.sh',
+                      'test-resource-sizes.sh', 'test-task-changelog.sh')
+AI_CHECK = 'check_ai_detection.py'
+LOCAL_CHECKS = {'check-task-toml-schema.py': Path(__file__).with_name('task_toml_schema.py')}
+
+
+
+def load_checks(profile, upstream=None, exclude=()):
+    manifest = json.loads((TERMINAL_BENCH / 'UPSTREAM.json').read_text())
+    # Detect accidental edits or incomplete copies before executing anything.
+    for name, digest in manifest['files'].items():
+        if hashlib.sha256(((upstream or TERMINAL_BENCH) / name).read_bytes()).hexdigest() != digest:
+            raise ValueError(f'upstream file differs from pinned copy: {name}')
+    names = sorted(Path(p).name for p in manifest['files'] if p.startswith('scripts/checks/'))
+    names = sorted([*names, *LOCAL_CHECKS])
+    excluded = {**PR_ONLY, **(POLICY if profile == 'portable' else TRAINING_EXCLUSIONS if profile == 'training' else {}),
+                'rubric_review.py': 'LLM rubric review is opt-in via stage 2, never a default static check'}
+    inactive = {'rubric_review.py', *CHECKER_UNIT_TESTS}
+    for value in exclude:
+        # NAME=reason records why; a reason may contain commas, so it is one item.
+        value, _, reason = value.partition('=')
+        for requested in value.split(','):
+            requested = requested.strip()
+            aliases = {'ai-detection': 'check_ai_detection.py', 'rubric-review': 'rubric_review.py',
+                       'task-toml-schema': 'check-task-toml-schema.py',
+                       'check-task-toml-schema': 'check-task-toml-schema.py'}
+            name = aliases.get(requested, requested)
+            if name not in inactive and name != AI_CHECK and name not in LOCAL_CHECKS:
+                name = name if name.endswith('.sh') else name + '.sh'
+                name = name if name.startswith('check-') else 'check-' + name
+            if name not in names and name not in inactive:
+                raise ValueError(f'unknown static check: {requested}; use --list')
+            excluded[name] = (reason.strip() or 'explicitly excluded' if name in names else
+                'upstream checker unit test, not dataset validation' if name in CHECKER_UNIT_TESTS else
+                'not part of the static suite (LLM review is opt-in)')
+    return manifest, [n for n in names if n not in excluded], excluded
+
+
+def validate_input(task):
+    import tomllib
+    for name in ('instruction.md', 'task.toml', 'tests/test.sh'):
+        if not (task / name).is_file():
+            raise ValueError(f'missing {name}')
+    if not (task / 'environment').is_dir():
+        raise ValueError('missing environment/')
+    with (task / 'task.toml').open('rb') as stream:
+        tomllib.load(stream)
+    if any(c.isspace() or c in '*?[]' for c in str(task)):
+        raise ValueError(f'task directory path must not contain whitespace or glob characters: {task}')
+
+
+UNSAFE = re.compile(r'[\s*?\[\]]')
+
+
+def safe_copy(task, scratch):
+    """Several upstream scripts split paths as shell words and expand globs, so a file
+    named `Clase 4/[id].ts` would be skipped or misread and the check could pass wrongly.
+    Such tasks are checked on a copy whose offending names have those characters
+    replaced by '_'. The task itself is unchanged. Returns (copy, renamed) or (task, [])."""
+    renamed = sorted(str(p.relative_to(task)) for p in task.rglob('*') if UNSAFE.search(str(p.relative_to(task))))
+    if not renamed:
+        return task, []
+    copy = Path(scratch) / 'renamed' / task.name
+    if copy.exists():
+        shutil.rmtree(copy)
+    for path in task.rglob('*'):
+        target = copy / UNSAFE.sub('_', str(path.relative_to(task)))
+        if path.is_dir():
+            target.mkdir(parents=True, exist_ok=True)
+        else:
+            target.parent.mkdir(parents=True, exist_ok=True)
+            shutil.copyfile(path, target)
+    return copy, renamed
+
+
+PATH_CHECK = 'check-task-absolute-path.sh'
+SHELL_FENCES = {'', 'bash', 'sh', 'shell', 'zsh', 'console', 'text', 'txt'}
+ADAPTATIONS = {PATH_CHECK: 'Relative-path findings are advisory warnings and do not fail stage 1. Runs on a copy of the task whose instruction.md has its source-code blocks removed '
+                           '(fenced blocks tagged with a programming language); masks complete absolute paths '
+                           'and JavaScript console calls/sed substitutions so their substrings are not mistaken for paths; '
+                           'masks complete non-file URLs, quoted absolute paths with spaces, simple inline commands rooted by cd /absolute/path &&, '
+                           'and literal relative symlink targets with explicit absolute link locations; '
+                           'skips all Markdown fenced blocks, recognizes $HOME/${HOME}/~/ paths, and accepts adjacent literal cd and command lines; '
+                           'accepts explicit named-file-in-directory clauses, pure parent-navigation commands, and relative command tokens for uniquely absolute-named executables; '
+                           'unresolved relative file references outside fenced blocks are otherwise kept',
+               'check-test-file-references.sh': 'masks complete non-file URLs, XML hostnames and excluded system paths; fixes full-token extraction and shell redirections, preserving basenames without inventing /app paths; accepts conventional boot artifacts, explicit numeric X filename ranges, explicit label filename templates resolved from supplied label:glob configurations, and references discovered through named supplied files/directories; reads literal writes and copies/moves in explicitly invoked local setup shell scripts without executing them, with source evidence',
+               'check-pip-pinning.sh': 'recognizes SHA-256-pinned HTTP(S) requirements as single shell arguments; masks unquoted shell redirections and argument forwarding in generated offline installer heredocs, retaining actual package installations',
+               'check-nproc.sh': 'training permits measurement-only variables and the exact audited InferredBugs Python 2.7.18 Dockerfile build on Maven Java 8/11/17 (Helma Slurm affinity probes 934209/934274); also permits four content-pinned SETA solutions tested with 1/2 CPUs (Helma probe 948213); other worker selection remains checked; not a Docker quota-only portability guarantee',
+               'file names': 'a task with whitespace or *?[] in a file name is checked on a copy where those characters '
+                             'are replaced by _, because the upstream scripts split paths at spaces and expand globs; '
+                             'the renamed files are listed per task'}
+ADAPTATIONS['check-dockerfile-references.sh'] = 'Ignore full-line Dockerfile comments; executable references remain checked on a scratch copy.'
+ADAPTATIONS['check-dockerfile-sanity.sh'] = 'Inspect apt install arguments within RUN commands, including continuations and quoted pins; do not scan unrelated ENV assignments or embedded source following apt.'
+ADAPTATIONS['check-nproc.sh'] += ' Also permits five content-pinned CalibForge image/script pairs measured at 2/4 CPUs in Helma job 1017578; nproc --all still saw 384 node CPUs.'
+ADAPTATIONS['check-task-toml-schema.py'] = (
+    'Local deterministic replacement for the task_toml_schema rubric: validates against pinned Harbor models '
+    'and rejects unrecognized fields recursively; Harbor free-form metadata/env mappings remain allowed.')
+
+
+def without_source_code(instruction):
+    """Drop fenced blocks tagged with a programming language: file names inside code
+    to read or complete are not paths the task tells the agent to use.
+
+    Source code can itself contain Markdown fences and '#' lines, so the first bare
+    fence is not always the end of the block. The block ends at the first bare fence
+    that is followed by a heading or by the end of the text; if there is none before
+    the next tagged block, it ends at the first bare fence."""
+    lines, kept, i = instruction.split('\n'), [], 0
+    fence = lambda line: re.fullmatch(r'\s*```\s*([A-Za-z0-9_+#.-]*)\s*', line)
+    def before_heading(j):
+        following = next((l for l in lines[j + 1:] if l.strip()), None)
+        return following is None or re.match(r'#{1,6} ', following) is not None
+    while i < len(lines):
+        match = fence(lines[i])
+        if not match or match.group(1).lower() in SHELL_FENCES:
+            kept.append(lines[i])
+            i += 1
+            continue
+        bare = []
+        for j in range(i + 1, len(lines)):
+            inner = fence(lines[j])
+            if inner and inner.group(1):
+                break                # the next tagged block starts here
+            if inner:
+                bare.append(j)
+        closing = next((j for j in bare if before_heading(j)), bare[0] if bare else None)
+        if closing is None:          # unterminated block: leave the text for the check to see
+            kept.append(lines[i])
+            i += 1
+            continue
+        kept.append(f'[{match.group(1)} source code removed for the path check]')
+        i = closing + 1
+    return '\n'.join(kept)
+
+
+def without_urls(text):
+    # Mask whole tokens before upstream extracts filename-like suffixes.
+    text = re.sub(r'\b(?![Ff][Ii][Ll][Ee]://)[A-Za-z][A-Za-z0-9+.-]*://[^\s`\"\'<>]+', '[URL]', text)
+    # Bare host/path form, e.g. mirrors.ubuntu.com/mirrors.txt.
+    return re.sub(r'\b(?:[A-Za-z0-9-]+\.)+(?:com|org|net|edu|gov|io)/[^\s`\"\'<>]+', '[URL]', text)
+
+
+def without_fenced_blocks(text):
+    """Skip Markdown fences of any language, including untagged and shell blocks."""
+    kept, opening = [], None
+    for line in text.splitlines(keepends=True):
+        match = re.match(r'^ {0,3}(`{3,}|~{3,})(.*)$', line.rstrip('\n'))
+        if opening is None:
+            if match:
+                opening = match[1]
+                kept.append('[fenced block omitted from path check]\n')
+            else:
+                kept.append(line)
+        elif (match and match[1][0] == opening[0]
+              and len(match[1]) >= len(opening) and not match[2].strip()):
+            opening = None
+    return ''.join(kept)
+
+
+# Specific conventional interfaces, not an exemption for everything under /boot.
+CONVENTIONAL_REFERENCE_PATHS = (
+    r'/boot/grub/grub\.cfg',
+    r'/boot/initrd\.img-[0-9][A-Za-z0-9_.+-]*',
+)
+
+
+def reference_check_script(source):
+    """Correct lexical extraction on a temporary copy of pinned upstream."""
+    old = "grep -E '^/(app|home|tests|tmp|usr|var|etc)/'"
+    if source.count(old) != 1 or source.count('/[a-zA-Z0-9_./]+\\.') != 1:
+        raise ValueError('upstream file-reference extractor changed')
+    source = source.replace(old, "grep -E '^/'")
+    # A quoted basename supplies no working directory. Keep it as a basename.
+    source = source.replace("sed 's|^|/app/|'", 'cat')
+    # Upstream uses optional quote markers (?) with basic sed regex syntax.
+    # Extended regex syntax is required to strip the redirection / -o prefix.
+    source = source.replace("sed 's/^>\\s*", "sed -E 's/^>\\s*")
+    source = source.replace("sed 's/^-o\\s*", "sed -E 's/^-o\\s*")
+    # Consume the full basename, including suffixes after .img (kernel versions).
+    lines = source.splitlines(keepends=True)
+    for i, line in enumerate(lines):
+        if '/[a-zA-Z0-9_./]+\\.' in line:
+            line = line.replace('/[a-zA-Z0-9_./]+\\.', '/[a-zA-Z0-9_./-]+\\.')
+            line = line.replace("grep -oE '/", "grep -oE '(^|[[:space:]=])/")
+            lines[i] = line.replace("wad)'", "wad)[a-zA-Z0-9_.+-]*'").rstrip('\n') + " | sed 's|^[^/]||'\n"
+    return ''.join(lines)
+
+
+def reference_check_text(text):
+    text = without_urls(text)
+    text = re.sub(r'file://(?=/)', '', text)
+    text = re.sub(r'<host>[^<\n]+</host>', '<host>[hostname]</host>', text)
+    # Upstream deliberately excludes these system roots, but its second regex
+    # can truncate a hyphenated path into e.g. /xsettings.xml and flag it again.
+    text = re.sub(r'/(?:tests|tmp|usr|var|etc)/[^\s`\"\'<>;]+', '[system path]', text)
+    for path in CONVENTIONAL_REFERENCE_PATHS:
+        text = re.sub(r'(?<![\w/])' + path + r'(?![\w./+-])', '[conventional boot artifact]', text)
+    return text
+
+
+def numeric_reference_patterns(instruction, sources):
+    """Accept an X filename template only with an explicit numeric X range."""
+    bounds = re.search(r'\b(?:where\s+)?X\s+is\s+(\d+)\s*[-–]\s*(\d+)\b', instruction)
+    if not bounds:
+        return {}
+    low, high = map(int, bounds.groups())
+    result = {}
+    for match in re.finditer(r'\b([A-Za-z0-9_.-]*_X(?:_[A-Za-z0-9_.-]+)?\.[A-Za-z0-9]+)\b', instruction):
+        template = match.group(1)
+        expression = re.escape(template).replace('_X', r'_(\d+)')
+        for candidate in re.finditer(r'(?<![\w.-])' + expression + r'(?![\w.-])', sources):
+            if low <= int(candidate.group(1)) <= high:
+                result[candidate.group(0)] = {'instruction_pattern': template, 'numeric_range': [low, high]}
+    return result
+
+
+def pip_check_line(line):
+    """Adapt shell syntax on the check copy, never rewriting the installation."""
+    from packaging.requirements import Requirement, InvalidRequirement
+    from urllib.parse import urlsplit
+    # Keep quotes intact so quoted '>' and spaces inside requirements are not
+    # mistaken for shell operators or separate package arguments.
+    pattern = r'''(?:\d+)?(?:>>?|<<?)&?|&&|\|\||[;|&]|(?:[^\s'"\\<>;&|]+|\\[^\n]|'[^']*'|"(?:\\.|[^"\\])*")+'''
+    tokens = list(re.finditer(pattern, line))
+    cursor = 0
+    for token in tokens:
+        if line[cursor:token.start()].strip():
+            return line  # Unsupported/malformed shell syntax: keep the finding.
+        cursor = token.end()
+    if line[cursor:].strip():
+        return line
+    edits, i = [], 0
+    while i < len(tokens):
+        token = tokens[i]
+        raw = token.group()
+        if raw.startswith('#'):
+            break
+        if re.fullmatch(r'(?:\d+)?(?:>>?|<)&?', raw) and i + 1 < len(tokens):
+            destination = tokens[i + 1]
+            if destination.group() not in ('&&', '||', ';', '|', '&'):
+                edits.append((token.start(), destination.end(), ' '))
+                i += 2
+                continue
+        try:
+            value, = shlex.split(raw)
+        except ValueError:
+            i += 1
+            continue
+        url = value
+        name = 'hash-pinned-artifact'
+        try:
+            requirement = Requirement(value)
+            if requirement.url and not requirement.marker:
+                url, name = requirement.url, requirement.name
+        except InvalidRequirement:
+            pass
+        try:
+            parsed = urlsplit(url)
+        except ValueError:
+            i += 1
+            continue
+        if (parsed.scheme in ('http', 'https') and parsed.netloc
+                and not any(c in url for c in '$`\\')
+                and re.fullmatch(r'sha256=[0-9a-fA-F]{64}', parsed.fragment)):
+            # Upstream understands == pins, but splits direct references at
+            # spaces. This placeholder exists only in its scratch input.
+            edits.append((token.start(), token.end(), name + '==0'))
+        i += 1
+    for start, end, replacement in reversed(edits):
+        line = line[:start] + replacement + line[end:]
+    return line
+
+
+def pip_check_text(text):
+    # Generated offline installers are tools accepting user-specified packages,
+    # not an unpinned install into the task environment. Only exempt forwarding
+    # inside a quoted heredoc; retain concrete installs inside those heredocs.
+    lines, delimiter = [], None
+    for line in text.splitlines(keepends=True):
+        if delimiter and line.strip() == delimiter:
+            delimiter = None
+        elif delimiter and re.fullmatch(
+                r'\s*pip3? install --no-index --find-links="\$SCRIPT_DIR" "\$@"\s*', line):
+            line = '# generated offline installer forwards caller arguments\n'
+        if delimiter is None:
+            match = re.search(r"<<\s*['\"]([A-Za-z_][A-Za-z0-9_]*)['\"]", line)
+            if match:
+                delimiter = match.group(1)
+        lines.append(pip_check_line(line))
+    return ''.join(lines)
+
+
+# Content-pinned CPU-affinity audit: Helma job 1017578, all five images at 2/4 CPUs.
+CALIBFORGE_REVIEWED_NPROC = {'contrastive_solver-security_20260508_045740_002': {'file': 'environment/Dockerfile',
+                                                     'sha256': {'environment/Dockerfile': '8554c71778e6d80171e69483cafc1c53f016d16607b586eb8d259936c2996ad1'}},
+ 'contrastive_solver-software-engineering_20260510_053611_008': {'file': 'environment/Dockerfile',
+                                                                 'sha256': {'environment/Dockerfile': 'fe371f2e4d5ccf5ac295269324bf2d7dbfb6d3e10377e84910f457f384f365cb'}},
+ 'contrastive_solver-software-engineering_20260611_210349_008': {'file': 'tests/test.sh',
+                                                                 'sha256': {'environment/Dockerfile': '4f6194d3d652fd8cb9d9de5681211adf5ba57146718f2fc0db9d977d11f8d8b7',
+                                                                            'tests/test.sh': 'b7f4a23eaffed3576d649078f6bb09f89b84e2a5573063b53552799af644560a'}},
+ 'contrastive_solver-system-administration_20260604_004411_008': {'file': 'environment/Dockerfile',
+                                                                  'sha256': {'environment/Dockerfile': '47c7d9e917e98d3965d48a380c1d82a2fd774505857ccfdcc6bfdaacba388db9'}},
+ 'contrastive_solver-system-administration_20260604_004411_009': {'file': 'environment/Dockerfile',
+                                                                  'sha256': {'environment/Dockerfile': 'bbe5c1425ac6323702e29c0faae4d27efa23de0c6202797491ed5343887a2373'}}}
+
+
+def dockerfile_without_comments(text):
+    """Ignore full-line Dockerfile comments, retaining inline arguments/data."""
+    kept, heredocs = [], []
+    for line in text.splitlines(keepends=True):
+        if heredocs:
+            kept.append(line)
+            if line.strip() == heredocs[0]:
+                heredocs.pop(0)
+            continue
+        if line.lstrip().startswith('#'):
+            continue
+        kept.append(line)
+        # Heredoc payload is data, not Dockerfile comments.
+        heredocs.extend(re.findall(r"<<-?\s*['\"]?([A-Za-z_][A-Za-z0-9_]*)['\"]?", line))
+    return ''.join(kept)
+
+
+def dockerfile_sanity_text(text):
+    """Give upstream only apt command arguments, not the next 20 source lines.
+
+    Shell tokenization preserves quoted pins and joins continued RUN commands.
+    Unparseable shell is kept for conservative upstream checking.
+    """
+    text = dockerfile_without_comments(text)
+    logical = re.sub(r'\\\n', ' ', text)
+    commands = []
+    for line in logical.splitlines():
+        if not re.match(r'^\s*RUN\s', line, re.I):
+            continue
+        if re.search(r'\bapt(?:-get)?\b', line) and ('<<' in line or re.match(r'^\s*RUN\s*\[', line, re.I) or re.search(r'\b(?:sh|bash)\s+-c', line)):
+            return text  # Preserve conservative checking of unsupported shell forms.
+        try:
+            lexer = shlex.shlex(line, posix=True, punctuation_chars=';&|()<>' )
+            lexer.whitespace_split = True
+            tokens = list(lexer)
+        except ValueError:
+            return text
+        for i, token in enumerate(tokens):
+            if token.rsplit('/', 1)[-1] not in ('apt', 'apt-get'):
+                continue
+            if i and tokens[i - 1] not in ('RUN', 'run', '&&', '||', ';', '|', 'sudo', 'env', 'then', 'do'):
+                continue
+            args = []
+            for arg in tokens[i + 1:]:
+                if arg and all(c in ';&|()<>' for c in arg):
+                    break
+                args.append(arg)
+            # Keep update/cleanup advisory behavior, but expose version pins
+            # only in install arguments. Epochs/integer pins count too.
+            if 'install' in args:
+                packages = args[args.index('install') + 1:]
+                pinned = [a for a in packages if re.fullmatch(r'[a-zA-Z0-9][a-zA-Z0-9+.:_-]*=[^=\s]+', a)]
+                commands.append('RUN apt install ' + ('pinned-package=1.0' if pinned else 'packages'))
+            elif 'update' in args:
+                commands.append('RUN apt update')
+    if 'rm -rf /var/lib/apt/lists' in text:
+        commands.append('RUN rm -rf /var/lib/apt/lists/*')
+    return '\n'.join(commands) + '\n'
+
+
+def calibforge_nproc_text(text, task, relative):
+    """Allow only the exact image/script pairs measured in Helma job 1017578."""
+    record = CALIBFORGE_REVIEWED_NPROC.get(task.name)
+    if not record or relative != record['file']:
+        return text
+    for filename, digest in record['sha256'].items():
+        path = task / filename
+        if not path.is_file() or hashlib.sha256(path.read_bytes()).hexdigest() != digest:
+            return text
+    return text.replace('$(nproc)', 'VERIFIED_CPU_AFFINITY')
+
+
+def nproc_check_text(text, *, dockerfile=False):
+    """Conservatively recognize measurement-only variables; not a shell parser.
+
+    Also recognize the exact Python 2 build audited under Slurm CPU affinity.
+    Other build flags and unknown uses retain the original check.
+    """
+    if dockerfile and re.search(r'^FROM maven:3\.9-eclipse-temurin-(?:8|11|17)$', text, re.M):
+        # Match the build context and complete command, not make/nproc generally.
+        # Mask only on the check's scratch copy; the actual task is unchanged.
+        reviewed = (
+            ' && tar -xzf "$d/python2.tgz" -C "$d" && cd "$d/Python-2.7.18" \\\n'
+            ' && ./configure --prefix=/opt/python2 --disable-shared --without-ensurepip >/dev/null '
+            '&& make -j"$(nproc)" >/dev/null && make install >/dev/null \\\n'
+            ' && cd / && rm -rf "$d" && /opt/python2/bin/python2.7 -c "import zlib"'
+        )
+        text = text.replace(reviewed, reviewed.replace('$(nproc)', 'VERIFIED_CPU_AFFINITY'))
+    lines = text.splitlines(keepends=True)
+    for i, line in enumerate(lines):
+        assignment = re.fullmatch(r'\s*([A-Za-z_]\w*)="?\$\(nproc\)"?\s*', line)
+        if not assignment:
+            continue
+        var = assignment.group(1)
+        refs = re.compile(r'\$(?:' + re.escape(var) + r'\b|\{' + re.escape(var) + r'\})')
+        uses = [s.strip() for s in lines if refs.search(s) and not s.lstrip().startswith('#')]
+        def measurement(s):
+            # JSON fields: no command substitutions, backticks or shell chains.
+            if s.startswith(('{"', '"')) and not re.search(r'\$\(|`|[;&|]', s):
+                return True
+            if re.fullmatch(r'if \(\( \$\(echo "\$\w+ > \$' + re.escape(var) + r'" \| bc -l\) \)\); then', s):
+                return True
+            return bool(re.fullmatch(r'alerts(?:\+)?=\(?"[^\n]*"\)?', s)) and not re.search(r'\$\(|`|[;&|]', s)
+        if uses and all(measurement(s) for s in uses):
+            lines[i] = line.replace('$(nproc)', 'CPU_MEASUREMENT')
+    return ''.join(lines)
+
+
+def adapted_check_copy(task, scratch, name, profile):
+    transforms = {'check-test-file-references.sh': reference_check_text,
+                  'check-pip-pinning.sh': pip_check_text,
+                  'check-dockerfile-references.sh': dockerfile_without_comments,
+                  'check-dockerfile-sanity.sh': dockerfile_sanity_text}
+    if profile == 'training':
+        transforms['check-nproc.sh'] = nproc_check_text
+    if name not in transforms:
+        return task
+    copy = Path(scratch) / name / task.name
+    # Only files consumed by these checks. Avoid copying potentially large setup
+    # archives for each adaptation.
+    paths = ['instruction.md', 'task.toml', 'environment/Dockerfile',
+             'tests/Dockerfile', 'tests/test.sh', 'solution/solve.sh']
+    paths.extend(str(p.relative_to(task)) for p in (task / 'tests').rglob('test_*.py'))
+    for relative in paths:
+        source = task / relative
+        if source.is_file():
+            target = copy / relative
+            target.parent.mkdir(parents=True, exist_ok=True)
+            text = source.read_text(errors='replace')
+            if name == 'check-nproc.sh' and relative not in ('instruction.md', 'task.toml'):
+                if profile == 'training' and relative == 'solution/solve.sh':
+                    from data.seta.patch import reviewed_nproc_text
+                    dockerfile = task / 'environment/Dockerfile'
+                    text = reviewed_nproc_text(text, task.name,
+                                               dockerfile.read_bytes() if dockerfile.is_file() else b'')
+                text = calibforge_nproc_text(text, task, relative)
+                text = nproc_check_text(text, dockerfile=relative == 'environment/Dockerfile')
+            elif relative not in ('instruction.md', 'task.toml'):
+                text = transforms[name](text)
+            target.write_text(text)
+    if name == 'check-test-file-references.sh':
+        evidence = discoverable_references(task)
+        if (copy / 'instruction.md').is_file():
+            sources = '\n'.join((copy / p).read_text(errors='replace') for p in paths
+                                if p not in ('instruction.md', 'task.toml') and (copy / p).is_file())
+            evidence.update(numeric_reference_patterns((copy / 'instruction.md').read_text(), sources))
+        (copy / 'discovered-references.json').write_text(json.dumps(evidence, indent=2))
+        if (copy / 'instruction.md').is_file():
+            with (copy / 'instruction.md').open('a') as stream:
+                stream.write('\nSupplied entry points reveal these references:\n' + '\n'.join(evidence) + '\n')
+    return copy
+
+
+def named_path_examples(text):
+    """Recognize explicit location clauses and reuse unique executable locations."""
+    locations = {}
+    def remember(path):
+        if not any(c in path for c in '$*?[]{}'):
+            locations.setdefault(path.rsplit('/', 1)[-1], set()).add(path)
+    for match in re.finditer(r'''(?<![\w./])/(?!/)[A-Za-z0-9_.+@/-]+(?=$|[\s`"'<>|;,:!?)])''', text):
+        remember(match[0].rstrip('.,:'))
+
+    # Join only this explicit grammatical construction, never nearby paths.
+    clause = re.compile(
+        r'''\b(?:file|script|executable|utility|tool)\s+(?:named|called)\s+'''
+        r'''(?P<quote>[`"']?)(?P<name>[A-Za-z0-9_-][A-Za-z0-9_.+-]*)(?P=quote)'''
+        r'''\s+in\s+(?P<dirquote>[`"']?)(?P<directory>/[A-Za-z0-9_.+@/-]+)(?P=dirquote)(?=$|[\s.,:;!?])''', re.I)
+    def specified(match):
+        directory = match['directory'].rstrip('.,:')
+        remember(directory.rstrip('/') + '/' + match['name'])
+        start, end = match.span('name')
+        start, end = start - match.start(), end - match.start()
+        return match[0][:start] + '[explicitly located filename]' + match[0][end:]
+    text = clause.sub(specified, text)
+
+    def invocation(match):
+        value = match[1]
+        # Mask only ./NAME at command position. Arguments remain checked.
+        token = re.match(r'\./(?P<name>[A-Za-z0-9_-][A-Za-z0-9_.+-]*)(?=\s|$)', value)
+        if token and len(locations.get(token['name'], set())) == 1:
+            return '`[explicitly located executable]' + value[token.end():] + '`'
+        return match[0]
+    return re.sub(r'`([^`\n]+)`', invocation, text)
+
+
+def explicit_path_examples(text):
+    """Mask locally specified command/link examples, without inferring global cwd."""
+    def literal(value):
+        return bool(value) and not any(c in value for c in '$`*?[]{}<>\n')
+
+    def inline(match):
+        value = match.group(1)
+        try:
+            tokens = list(shlex.shlex(value, posix=True, punctuation_chars=';&|<>'))
+        except ValueError:
+            return match.group(0)
+        if re.fullmatch(r'cd\s+(?:--\s+)?\.\.(?:/\.\.)*/?', value.strip()):
+            return '[parent navigation]'
+        # Only a single command after &&. Extra shell operators, dynamic
+        # expressions and another directory change remain review findings.
+        args = tokens[1:] if tokens[:1] == ['cd'] else []
+        if args[:1] == ['--']:
+            args = args[1:]
+        if (len(args) >= 3 and args[0].startswith('/') and args[1] == '&&'
+                and args[2] not in ('cd', 'pushd', 'popd', 'eval')
+                and '-c' not in args[2:]
+                and all(literal(t) and not any(c in t for c in ';&|()') for t in [args[0], *args[2:]])):
+            return '[command with explicit directory]'
+        # ln -s TARGET /absolute/LINK defines the relative target's base.
+        if (len(tokens) == 4 and tokens[:2] == ['ln', '-s']
+                and tokens[2].startswith(('./', '../')) and tokens[3].startswith('/')
+                and all(literal(t) for t in tokens[2:])):
+            return '[symlink with explicit location]'
+        return match.group(0)
+
+    # Two adjacent command lines can establish the same local base as &&.
+    # Do not carry that directory across paragraphs or unrelated prose.
+    def adjacent(match):
+        commands = [line.strip().strip('`') for line in match[0].splitlines()]
+        combined = '`' + commands[0] + ' && ' + commands[1] + '`'
+        result = inline(re.fullmatch(r'`([^`\n]+)`', combined))
+        return result if result != combined else match[0]
+    text = re.sub(r'(?m)^ {0,3}`?cd [^\n`]+`?\n {0,3}(?:`[^`\n]+`|[^`\n]+)$', adjacent, text)
+    text = re.sub(r'`([^`\n]+)`', inline, text)
+    absolute = r'''(?:`/[^`\n]+`|"/[^"\n]+"|'/[^'\n]+'|/[^\s`"'<>|;]+)'''
+    relative = r'''(?:`\.{1,2}/[^`\n]+`|"\.{1,2}/[^"\n]+"|'\.{1,2}/[^'\n]+'|\.{1,2}/[^\s`"'<>|;]+)'''
+    mapping = re.compile(r'(?P<link>' + absolute + r')\s*->\s*(?P<target>' + relative + r')')
+    paragraphs = re.split(r'(\n\s*\n)', text)
+    for i, paragraph in enumerate(paragraphs):
+        if not re.search(r'\b(?:symlink|symbolic\s+link)s?\b', paragraph, re.I):
+            continue
+        established = set()
+        def link(match):
+            location = match['link'].strip('`"\'')
+            target = match['target'].strip('`"\'')
+            if literal(location) and literal(target):
+                established.update((target, target.rsplit('/', 1)[0] + '/'))
+                return match['link'] + ' -> [relative symlink target]'
+            return match.group(0)
+        paragraph = mapping.sub(link, paragraph)
+        # The same paragraph may reiterate the literal target or its directory.
+        # Only these exact inline strings inherit the established link location.
+        paragraphs[i] = re.sub(r'`([^`\n]+)`',
+                               lambda m: '[specified symlink reference]' if m[1] in established else m[0],
+                               paragraph)
+    return ''.join(paragraphs)
+
+
+def path_check_text(instruction):
+    """Adapt known lexical false positives without changing pinned upstream code."""
+    text = without_fenced_blocks(without_source_code(instruction))
+    text = without_urls(text)
+    text = named_path_examples(text)
+    text = explicit_path_examples(text)
+    # HOME is case-sensitive in shells. Unknown variables remain unresolved.
+    text = re.sub(r'''(?<![\w$])(?:\$HOME|\$\{HOME\}|~)/[^\s`"'<>|;]+''',
+                  '[home-anchored path]', text)
+    # A relative command with an explicit working directory on the same line
+    # is unambiguous. Do not infer a global cwd from unrelated absolute paths.
+    text = re.sub(r'`(\./[^`\n]+)`(?= from `/[^`\n]+`)', '[rooted command]', text)
+    # Quoted absolute paths can contain spaces; consume before bare tokens.
+    text = re.sub(r'`/[^`\n]+`', '`[absolute path]`', text)
+    # Consume the WHOLE absolute token, including @ and hyphens in systemd units.
+    # Replacing tokens individually also prevents upstream's global substring
+    # filter from excusing a relative path merely because an absolute one exists.
+    text = re.sub(r'''(?<![\w./])/(?!/)[^\s`"'<>|;]+''', '[absolute path]', text)
+    lines = []
+    method = r'console\.(?:log|warn|error|info|debug|trace|table)'
+    for line in text.splitlines(keepends=True):
+        code_context = re.search(r'\b(?:JavaScript|regex|calls?|references?|strings?|literals?|statements?)\b', line, re.I)
+        def inline(match):
+            value = match.group(1)
+            # A sed substitution is an expression, not a directory reference.
+            if re.fullmatch(r's/[^\n]*/[^\n]*/[gip0-9]*', value):
+                return '`[sed expression]`'
+            if re.search(method + r'\s*\(', value) or (code_context and re.fullmatch(method, value)):
+                return '`' + re.sub(method, '[JavaScript method]', value) + '`'
+            return match.group(0)
+        line = re.sub(r'`([^`\n]+)`', inline, line)
+        if code_context:
+            line = re.sub(r'(["\'])(' + method + r')\1', '[JavaScript method]', line)
+        lines.append(line)
+    return ''.join(lines)
+
+
+def path_check_copy(task, scratch):
+    copy = Path(scratch) / 'path-check' / task.name
+    (copy / 'environment').mkdir(parents=True, exist_ok=True)
+    (copy / 'instruction.md').write_text(path_check_text((task / 'instruction.md').read_text(errors='replace')))
+    for name in ('task.toml', 'environment/Dockerfile'):
+        if (task / name).is_file():
+            shutil.copyfile(task / name, copy / name)
+    return copy
+
+
+def rebuild_summary(out):
+    """Reconstruct completed outcomes; ignore only an unfinished final journal line."""
+    out = Path(out)
+    summary = out / 'summary.json'
+    report = json.loads(summary.read_text())
+    expected = [Path(path).name for path in report['selected_tasks']]
+    expected_names = set(expected)
+    entries = {}
+    incomplete_tail = False
+    with (out / 'outcomes.jsonl').open() as stream:
+        for line in stream:
+            if not line.endswith('\n'):
+                incomplete_tail = True
+                break
+            entry = json.loads(line)
+            name = entry['task']
+            if name not in expected_names or name in entries:
+                raise ValueError(f'unknown or duplicate journal task: {name}')
+            entries[name] = entry
+    report['tasks'] = [entries[name] for name in expected if name in entries]
+    report['complete'] = len(entries) == len(expected) and not incomplete_tail
+    report['passed'] = report['complete'] and all(t['status'] == 'passed' for t in report['tasks'])
+    report['incomplete_journal_tail'] = incomplete_tail
+    pending = summary.with_suffix('.json.tmp')
+    pending.write_text(json.dumps(report, indent=2) + '\n')
+    pending.replace(summary)
+    return report
+
+
+def run_checks(tasks, out, profile='training', timeout=300, upstream=None, exclude=(), concurrency=1,
+               resume=None, resume_record=None, accept_previous_path_check=False):
+    if concurrency < 1:
+        raise ValueError('concurrency must be positive')
+    if sys.version_info < (3, 11):
+        raise ValueError('Terminal-Bench checks require Python 3.11+; activate your prep environment')
+    manifest, checks, excluded = load_checks(profile, upstream, exclude)
+    if not checks:
+        raise ValueError('no static checks selected')
+    for command in ('bash', 'grep', 'sed', 'awk', 'find', 'sort', 'uniq', 'mktemp', 'dirname', 'basename', 'cat', 'tr', 'rm'):
+        if not shutil.which(command):
+            raise ValueError(f'missing required executable: {command}')
+    out.mkdir(parents=True, exist_ok=True)
+    if (out / 'outcomes.jsonl').exists():
+        raise ValueError('output already has task outcomes; use a new output directory or --rebuild-summary')
+    report = {'upstream': manifest['repository'], 'commit': manifest['commit'],
+              'concurrency': concurrency, 'profile': profile, 'selected_tasks': [str(t) for t in tasks],
+              'checks': checks, 'excluded_checks': excluded, 'tasks': [],
+              'adaptations': {name: text for name, text in ADAPTATIONS.items() if name in checks or name == 'file names'},
+              'checker_unit_tests_not_run': list(CHECKER_UNIT_TESTS),
+              'conditional_checks': {AI_CHECK: 'runs only when GPTZERO_API_KEY is configured; missing key is a non-failing skip'},
+              'complete': False, 'passed': False}
+    imported = {}
+    if resume:
+        from validation.checkpoints.static_resume import load
+        imported, report['resumed_from'] = load(resume, tasks, manifest, checks, profile, resume_record,
+                                               accept_previous_path_check)
+        print(f"Static checkpoint: importing {report['resumed_from']['imported_checks']} checks; "
+              f"rerunning changed checks {report['resumed_from']['rerun_changed_checks']}", flush=True)
+    for name, reason in excluded.items():
+        print(f'SKIP {name}: {reason}', flush=True)
+    if AI_CHECK in checks and not os.environ.get('GPTZERO_API_KEY', '').strip():
+        print('SKIP check_ai_detection.py: no GPTZERO_API_KEY configured (not a failure)', flush=True)
+    summary = out / 'summary.json'
+    summary.write_text(json.dumps(report, indent=2) + '\n')
+    log = out / 'checks.log'
+    log_lock = threading.Lock()
+    static_root = os.environ.get('ZIH_STATIC_TMPDIR')
+    with tempfile.TemporaryDirectory(prefix='tb-checks-', dir=static_root or '/tmp') as scratch, \
+            log.open('w') as combined_log, (out / 'outcomes.jsonl').open('x') as journal:
+        # Upstream invokes python3. Use this interpreter, not an unrelated
+        # system Python that may lack tomllib. No dependency installation needed.
+        bindir = Path(scratch) / 'bin'
+        bindir.mkdir()
+        check_python = os.environ.get('ZIH_STATIC_PYTHON', sys.executable)
+        (bindir / 'python3').symlink_to(check_python)
+        scripts = (upstream or TERMINAL_BENCH) / 'scripts/checks'
+        reference_script = Path(scratch) / 'adapted-scripts/check-test-file-references.sh'
+        if reference_script.name in checks:
+            reference_script.parent.mkdir()
+            reference_script.write_text(reference_check_script((scripts / reference_script.name).read_text()))
+        if static_root:
+            local_scripts = Path(scratch) / 'scripts'
+            shutil.copytree(scripts, local_scripts)
+            scripts = local_scripts
+        env = {**os.environ, 'PATH': str(bindir) + os.pathsep + os.environ.get('PATH', '')}
+        for key in ('FIX_DIRS', 'BASE_DIR', 'BASH_ENV', 'ENV'):
+            env.pop(key, None)
+        def check_task_body(task, scratch):
+            entry = {'task': task.name, 'path': str(task), 'checks': []}
+            try:
+                validate_input(task)
+            except (ValueError, OSError) as exc:
+                entry.update(status='error', error=str(exc))
+            else:
+                pending_checks = set(checks) - set(imported.get(task.name, {}))
+                if not pending_checks or (pending_checks <= {AI_CHECK} and not os.environ.get('GPTZERO_API_KEY', '').strip()):
+                    # Complete checkpointed tasks need no staging copy or subprocesses.
+                    # The optional AI check is still handled below using current credentials.
+                    renamed = []
+                else:
+                    if static_root:
+                        staged = Path(scratch) / 'input' / task.name
+                        shutil.copytree(task, staged)
+                        task = staged
+                    task, renamed = safe_copy(task, scratch)
+                if renamed:
+                    entry['renamed_for_checks'] = renamed
+                for name in checks:
+                    if name in imported.get(task.name, {}):
+                        entry['checks'].append(imported[task.name][name])
+                        continue
+                    if name == AI_CHECK and not os.environ.get('GPTZERO_API_KEY', '').strip():
+                        entry['checks'].append({'check': name, 'status': 'skipped', 'optional': True,
+                            'reason': 'no GPTZERO_API_KEY configured', 'exit_code': None, 'log': None})
+                        continue
+                    started = time.monotonic()
+                    target = path_check_copy(task, scratch) if name == PATH_CHECK else adapted_check_copy(task, scratch, name, profile)
+                    if name == 'check-test-file-references.sh':
+                        evidence = json.loads((target / 'discovered-references.json').read_text())
+                        if evidence:
+                            entry['discoverable_reference_evidence'] = evidence
+                    # Buffer each check separately so parallel outputs never interleave.
+                    with tempfile.TemporaryFile(mode='w+', encoding='utf-8', errors='replace', dir=scratch) as stream:
+                        # The scripts take under a second; a timeout means the node or the
+                        # file system stalled (job 916252), so one more attempt is made.
+                        for attempt in (1, 2):
+                            try:
+                                script = LOCAL_CHECKS.get(name) or (reference_script if name == reference_script.name else scripts / name)
+                                interpreter = sys.executable if name in LOCAL_CHECKS else check_python if name.endswith('.py') else 'bash'
+                                result = subprocess.run([interpreter, str(script), str(target)],
+                                    cwd=scratch, env=env, stdout=stream, stderr=subprocess.STDOUT, timeout=timeout)
+                                status = 'passed' if result.returncode == 0 else 'failed'
+                                rc = result.returncode
+                                break
+                            except subprocess.TimeoutExpired:
+                                status, rc = 'error', None
+                                stream.write(f'\nTimed out after {timeout} seconds (attempt {attempt})\n')
+                                stream.flush()
+                        stream.seek(0)
+                        if name == PATH_CHECK and rc == 1:
+                            if re.search(r'relative paths used \(should be absolute under /[^)]*\): ', stream.read()):
+                                status = 'warning'
+                            stream.seek(0)
+                        if name == AI_CHECK and rc == 0:
+                            text = stream.read()
+                            if 'skipped' in text.lower() or 'No files to check' in text:
+                                status = 'skipped'
+                            stream.seek(0)
+                        with log_lock:
+                            combined_log.write(f'\n=== {entry["task"]} / {name} ===\n')
+                            shutil.copyfileobj(stream, combined_log)
+                            combined_log.write(f'\n=== result: {status}, exit_code: {rc} ===\n')
+                            combined_log.flush()
+                    entry['checks'].append({'check': name, 'status': status, 'optional': name == AI_CHECK, 'exit_code': rc,
+                                            'log': str(log.resolve()), 'duration_seconds': round(time.monotonic() - started, 3)})
+                    if status != 'passed':
+                        print(f'{task.name}: {name}: {status} (see {log})', flush=True)
+                entry['warnings'] = [{'tag': 'relative-instruction-path', 'check': c['check'], 'log': c.get('log')} for c in entry['checks'] if c['status'] == 'warning']
+                entry['status'] = 'passed' if all(c['status'] in ('passed', 'warning') or (c['status'] == 'skipped' and c.get('optional')) for c in entry['checks']) else 'failed'
+            return entry
+        def check_task(task):
+            if not static_root:
+                return check_task_body(task, scratch)
+            # Bound live task copies in RAM; oversized tasks use durable scratch.
+            # Allow for staging plus renamed/path-check copies per concurrent task.
+            parent = scratch
+            try:
+                validate_input(task)
+                size = sum(p.stat().st_size for p in task.rglob('*') if p.is_file())
+                limit = int(os.environ.get('ZIH_STATIC_MAX_BYTES', '1073741824')) // (3 * concurrency)
+                if size > limit:
+                    parent = os.environ['TMPDIR']
+            except (ValueError, OSError) as exc:
+                return {'task': task.name, 'path': str(task), 'checks': [], 'status': 'error', 'error': str(exc)}
+            # Delete only this task's temporary copies immediately after its checks.
+            with tempfile.TemporaryDirectory(prefix='static-task-', dir=parent) as task_scratch:
+                return check_task_body(task, task_scratch)
+        with ThreadPoolExecutor(max_workers=concurrency) as pool:
+            futures = [pool.submit(check_task, task) for task in tasks]
+            for future in as_completed(futures):
+                entry = future.result()
+                journal.write(json.dumps(entry) + '\n')
+                journal.flush()
+                print(f"{entry['task']}: {entry['status']}", flush=True)
+    report = rebuild_summary(out)
+    print(f'{len(checks)} upstream checks per task; {len(excluded)} explicitly excluded. Report: {summary}')
+    return 0 if report['passed'] else 1
+
+
+def main():
+    ap = argparse.ArgumentParser(description=__doc__)
+    ap.add_argument('root', nargs='?', type=Path)
+    ap.add_argument('--profile', choices=('training', 'portable', 'terminal-bench'), default='training')
+    ap.add_argument('--out', type=Path, default=Path('verify-out/terminal-bench'))
+    ap.add_argument('--limit', type=int)
+    ap.add_argument('--concurrency', type=int, default=1, help='parallel static tasks')
+    ap.add_argument('--timeout', type=int, default=120, help='seconds per static script per task')
+    ap.add_argument('--list', action='store_true', help='list included and excluded checks')
+    ap.add_argument('--exclude', action='append', default=[], help='check ID or filename, optionally NAME=reason; repeat or comma-separate')
+    ap.add_argument('--dry-run', action='store_true')
+    ap.add_argument('--rebuild-summary', action='store_true', help='reconstruct --out/summary.json from saved task outcomes without rerunning checks')
+    a = ap.parse_args()
+    try:
+        if a.rebuild_summary:
+            report = rebuild_summary(a.out)
+            print(f"Recovered {len(report['tasks'])} task outcomes; complete={report['complete']}")
+            return 0 if report['passed'] else 1
+        if a.timeout <= 0 or (a.limit is not None and a.limit <= 0):
+            raise ValueError('--limit and --timeout must be positive')
+        manifest, checks, excluded = load_checks(a.profile, exclude=a.exclude)
+        if a.list or a.dry_run:
+            print(f"Terminal-Bench {manifest['commit']} ({a.profile})")
+            for name in checks:
+                print(('SKIP ' + name + ': no GPTZERO_API_KEY configured (not a failure)')
+                      if name == AI_CHECK and not os.environ.get('GPTZERO_API_KEY', '').strip()
+                      else f"{'CONDITIONAL' if name == AI_CHECK else 'RUN '} {name}")
+            for name, reason in excluded.items():
+                print(f'SKIP {name}: {reason}')
+        if a.list:
+            return 0
+        if a.root is None:
+            raise ValueError('provide a task or task directory')
+        tasks = discover_tasks(a.root)[:a.limit]
+        if a.dry_run:
+            for task in tasks:
+                print(f'Would check {task}')
+            return 0
+        return run_checks(tasks, a.out, a.profile, a.timeout, exclude=a.exclude, concurrency=a.concurrency)
+    except (ValueError, OSError) as exc:
+        ap.exit(1, f'{exc}\n')
+
+
+if __name__ == '__main__':
+    raise SystemExit(main())

calibforge/ablations/evidence/stage1-corrected-report.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c00b60d9c12ec156d65de48bd07ad61d6bed85ceea9950d00348e504ae6b4dd4
+size 27612947

calibforge/ablations/evidence/stage1-summary.json

@@ -0,0 +1,20 @@
+{
+  "tasks_checked": 5372,
+  "stage1_passed": 4498,
+  "stage1_excluded": 874,
+  "failed_checks": {
+    "check-pip-pinning.sh": 871,
+    "check-task-toml-schema.py": 2,
+    "check-dockerfile-sanity.sh": 1
+  },
+  "source": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage1-current/contract.stage1-tasks/0000.parquet",
+  "parquet_sha256": "0682a10c5a0c932d406749490f4d7c2761904e14c97046f9ec5fba25066644aa",
+  "policy": "User requested exclusion of all 871 unresolved pip-pinning tasks. Pip pinning remains a required check. Other genuine static failures are also held out. Earlier stage3 and stage3_stage5 ablations are unchanged.",
+  "provenance": {
+    "original_report": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage1-current/array/report/stage-1-merged.json",
+    "targeted_rerun": "/hnvme/workspace/y500bb12-optiagent/calibforge-manual-20261014/stage1-checker-corrections/rerun/summary.json",
+    "reused_checks": "All other checks retain their original results on the identical frozen task snapshot.",
+    "original_contract_sha256": "fb8eb298e4341021b969d61a28c3ccd389bfb01e6d2dfb73d5a205a80529f46d",
+    "checker_sha256": "bb094bb42b436caac10efa274a03bd37680c245e5163b193fb58453c77a9455e"
+  }
+}

calibforge/ablations/stage3/tasks.parquet

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+version https://git-lfs.github.com/spec/v1
+oid sha256:7cc9e05078b0a347e7df38ecad0a529ad1d306f804f742036cd73ea442405a8d
+size 524537154

calibforge/ablations/stage3_stage5/tasks.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:eba1918b1b7ae904014ef1430008d4a71480c6a1d9a86224c363cdf7ca8f8692
+size 517168366

calibforge/ablations/variants.json

@@ -0,0 +1,95 @@
+{
+  "variants": {
+    "stage3": {
+      "tasks": 5377,
+      "parquet_sha256": "7cc9e05078b0a347e7df38ecad0a529ad1d306f804f742036cd73ea442405a8d"
+    },
+    "stage3_stage5": {
+      "tasks": 5320,
+      "parquet_sha256": "eba1918b1b7ae904014ef1430008d4a71480c6a1d9a86224c363cdf7ca8f8692"
+    }
+  },
+  "stage5_removed_count": 57,
+  "stage5_removed_ids": [
+    "contrastive_solver-data-querying_20260602_105139_001",
+    "contrastive_solver-data-science_20260503_182123_005",
+    "contrastive_solver-data-science_20260611_210349_008",
+    "contrastive_solver-data-science_20260615_143301_002",
+    "contrastive_solver-debugging_20260430_081156_004",
+    "contrastive_solver-debugging_20260510_005520_002",
+    "contrastive_solver-debugging_20260604_194036_004",
+    "contrastive_solver-debugging_20260610_111012_002",
+    "contrastive_solver-debugging_20260610_111702_002",
+    "contrastive_solver-file-operations_20260509_020109_002",
+    "contrastive_solver-machine-learning_20260604_003113_002",
+    "contrastive_solver-machine-learning_20260620_171154_003",
+    "contrastive_solver-mathematics_20260513_205011_001",
+    "contrastive_solver-model-training_20260601_053159_004",
+    "contrastive_solver-model-training_20260604_144210_001",
+    "contrastive_solver-model-training_20260611_205750_001",
+    "contrastive_solver-model-training_20260618_093107_004",
+    "contrastive_solver-optimization_20260509_065529_001",
+    "contrastive_solver-optimization_20260604_194036_001",
+    "contrastive_solver-optimization_20260617_051646_001",
+    "contrastive_solver-scientific-computing_20260501_000112_002",
+    "contrastive_solver-scientific-computing_20260509_020109_001",
+    "contrastive_solver-scientific-computing_20260604_144210_006",
+    "contrastive_solver-security_20260610_111702_002",
+    "contrastive_solver-software-engineering_20260415_002933_023",
+    "contrastive_solver-software-engineering_20260422_235124_018",
+    "contrastive_solver-software-engineering_20260424_090344_024",
+    "contrastive_solver-software-engineering_20260507_170334_011",
+    "contrastive_solver-software-engineering_20260508_045800_011",
+    "contrastive_solver-software-engineering_20260601_053159_018",
+    "contrastive_solver-software-engineering_20260604_003113_010",
+    "contrastive_solver-software-engineering_20260610_111702_011",
+    "contrastive_solver-software-engineering_20260611_210349_018",
+    "contrastive_solver-system-administration_20260510_142854_005",
+    "contrastive_solver-system-administration_20260604_144210_009",
+    "contrastive_solver-system-administration_20260604_193356_003",
+    "contrastive_solver-system-administration_20260604_194036_001",
+    "contrastive_solver-system-administration_20260606_172554_003",
+    "contrastive_solver-system-administration_20260610_111012_001",
+    "contrastive_solver-system-administration_20260610_111702_001",
+    "contrastive_solver-system-administration_20260610_112157_003",
+    "contrastive_solver-system-administration_20260611_205750_001",
+    "contrastive_solver-system-administration_20260612_191200_002",
+    "contrastive_solver-video-processing_20260607_104421_001",
+    "multi_solver-debugging_20260414_080620_001",
+    "multi_solver-debugging_20260417_112147_003",
+    "multi_solver-debugging_20260419_112101_001",
+    "multi_solver-file-operations_20260413_173854_001",
+    "multi_solver-software-engineering_20260413_173854_009",
+    "multi_solver-software-engineering_20260413_174325_005",
+    "multi_solver-software-engineering_20260414_080620_011",
+    "multi_solver-software-engineering_20260414_091921_006",
+    "multi_solver-software-engineering_20260414_211453_003",
+    "multi_solver-software-engineering_20260414_211453_025",
+    "multi_solver-software-engineering_20260414_211532_024",
+    "multi_solver-software-engineering_20260416_020953_009",
+    "multi_solver-system-administration_20260415_123352_009"
+  ],
+  "verifier_repairs_between_variants": [
+    "contrastive_solver-data-processing_20260604_003814_003",
+    "contrastive_solver-data-science_20260601_053159_006",
+    "contrastive_solver-data-science_20260604_002443_006",
+    "contrastive_solver-data-science_20260610_112157_008",
+    "contrastive_solver-data-science_20260614_141608_006",
+    "contrastive_solver-security_20260604_003113_006",
+    "contrastive_solver-software-engineering_20260528_174918_024",
+    "contrastive_solver-software-engineering_20260603_181444_011",
+    "contrastive_solver-software-engineering_20260604_002443_020",
+    "contrastive_solver-software-engineering_20260604_002443_024",
+    "contrastive_solver-software-engineering_20260606_172622_024",
+    "contrastive_solver-software-engineering_20260613_152233_017",
+    "contrastive_solver-system-administration_20260610_111702_004"
+  ],
+  "stage1_repaired_variant": {
+    "status": "Corrected stage-1 selection complete: 4498 passed, 874 excluded (871 pip pins, 1 apt pins, 2 schema failures). Combined stage1/3/5 Parquet pending.",
+    "plan": "Preserve matched task IDs for the repair-effect ablation; record exclusions separately instead of silently conflating repair and filtering."
+  },
+  "stage2_variant": {
+    "status": "not run",
+    "plan": "Keep rubric-filtered selection separate from both base variants; record criterion verdicts, model, rubric, image and setup evidence."
+  }
+}