Research-Stack/6-Documentation/docs/AGENTS_COMPLIANCE_AUDIT.md

AGENTS.md Compliance Audit

Date: April 26, 2026
Auditor: Cascade
Scope: All Python scripts in /scripts/

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Violation Summary

According to AGENTS.md Section 6.1 (Python Shims):

• Allowed: JSON serialization, subprocess spawn, history deque, result wrapping
• Forbidden: Cost computation, invariant checks, conservation laws, branching decisions

According to AGENTS.md Section 8 (Deletion Criteria):

• Demo or test script with no invariant
• Duplicates a Lean module
• Cannot be typed without unsafe or sorry
• Integrates with external SaaS
• Resists bind collapse

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Scripts Requiring Deletion

The following scripts contain logic, cost computation, invariant checks, or branching decisions that violate AGENTS.md shim boundaries:

Recently Created Scripts (Violations)

1. scripts/crypto_rfc_compliance_prober.py

   • Violation: Contains cost computation, invariant checks, branching decisions
   • Reason: Implements RFC compliance scoring logic in Python
   • Action: DELETE or port logic to Lean

2. scripts/pull_crypto_rfc_docs.py

   • Violation: Contains branching decisions, logic
   • Reason: Implements RFC extraction logic in Python
   • Action: DELETE or port logic to Lean

3. scripts/internet_waveform_atlas.py

   • Violation: Contains logic, branching decisions
   • Reason: Implements waveform probing logic in Python
   • Action: DELETE or port logic to Lean

4. scripts/archive_org_adapter.py

   • Violation: Contains logic, branching decisions
   • Reason: Implements adapter logic in Python
   • Action: DELETE or port logic to Lean

5. scripts/openworm_adapter.py

   • Violation: Contains logic, branching decisions
   • Reason: Implements adapter logic in Python
   • Action: DELETE or port logic to Lean

6. scripts/equation_extraction_pipeline.py

   • Violation: Contains logic, branching decisions
   • Reason: Implements equation extraction logic in Python
   • Action: DELETE or port logic to Lean

7. scripts/parallel_equation_extraction.py

   • Violation: Contains logic, branching decisions
   • Reason: Implements parallel extraction logic in Python
   • Action: DELETE or port logic to Lean

8. scripts/metaprobe_cross_domain_papers.py

   • Violation: Contains logic, branching decisions
   • Reason: Implements metaprobe logic in Python
   • Action: DELETE or port logic to Lean

9. scripts/genetic_codon_encoder.py

   • Violation: Contains cost computation, logic
   • Reason: Implements genetic encoding logic in Python
   • Action: DELETE or port logic to Lean

10. scripts/genetic_surface_compression.py

    • Violation: Contains cost computation, logic
    • Reason: Implements compression logic in Python
    • Action: DELETE or port logic to Lean

11. scripts/delta_gcl_encoder.py

    • Violation: Contains cost computation, logic
    • Reason: Implements Delta GCL encoding logic in Python
    • Action: DELETE or port logic to Lean

12. scripts/lean_delta_gcl_encoder.py

    • Violation: Contains cost computation, logic
    • Reason: Implements Delta GCL encoding logic in Python
    • Action: DELETE or port logic to Lean

13. scripts/sweep_lean_delta_gcl.py

    • Violation: Contains logic, branching decisions
    • Reason: Implements sweep logic in Python
    • Action: DELETE or port logic to Lean

14. scripts/batch_metafoam_papers.py

    • Violation: Contains logic, branching decisions
    • Reason: Implements batch processing logic in Python
    • Action: DELETE or port logic to Lean

15. scripts/waveprobe_metafoam_reader.py

    • Violation: Contains cost computation, logic
    • Reason: Implements metafoam reading logic in Python
    • Action: DELETE or port logic to Lean

16. scripts/compression_metafoam_adapter.py

    • Violation: Contains cost computation, logic
    • Reason: Implements compression adapter logic in Python
    • Action: DELETE or port logic to Lean

Additional Scripts Requiring Audit

The following scripts also require audit for compliance:

• scripts/financial_crash_audit.py
• scripts/cancer_godzilla_audit.py
• scripts/rgflow_network_filter.py
• scripts/genome_purification_stripper.py
• scripts/global_manifold_audit.py
• scripts/rgflow_enwik9_sweep.py
• scripts/hutter_full_purification.py
• scripts/rgflow_topology_filter.py
• scripts/hutter_rgflow_filter.py
• scripts/hep_event_benchmark.py
• scripts/connectome_lut_shim.py
• scripts/invention_plot.py
• scripts/rgflow_lean_filter.py
• scripts/rgflow_blind_detector.py
• scripts/killer_criterion_gen.py
• scripts/find_suspect_regions.py
• scripts/audit_linux_kernel.py
• scripts/rgflow_swarm_filter.py
• scripts/analyze_rgflow_noise_files.py
• scripts/kimi_waveprobe_rgflow.py
• scripts/rgflow_codebase_filter.py
• scripts/commoncrawl_waveprobe_ingestion.py
• scripts/merge_datasets.py
• scripts/lean_omnibus_total_recall.py
• scripts/lean_addons_to_parquet.py
• scripts/mathlib_to_parquet.py
• scripts/lean_to_parquet.py
• scripts/mathlib_ingestion_pipeline.py
• scripts/swarm_gpu_optimization_80_percent.py
• scripts/dump_notion_ene_jsonl.py
• scripts/generate_project_graph.py
• scripts/distributed_swarm_colonization.py
• scripts/virtual_gpu_workload_testbench.py
• scripts/virtual_gpu_topology_loader.py
• scripts/virtual_gpu_testbench.py

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Files That Are Compliant

The following files are documentation and do not violate AGENTS.md:

• docs/papers/CRYPTO_LAYER2_TOPOLOGY.md - Documentation
• docs/papers/NEURON_KERNEL_MAXIMAL_COMPRESSION.md - Documentation
• docs/papers/NEURON_AS_KERNEL_ENCODING.md - Documentation
• docs/papers/INTERNET_WAVEFORM_ATLAS.md - Documentation
• docs/papers/INTERNET_WAVEFORM_ATLAS_PAPER.md - Documentation
• docs/papers/METAPROBE_DUAL_FUNCTIONALITY.md - Documentation

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Recommended Action

DELETE the 16 recently created scripts that violate AGENTS.md shim boundaries. These scripts contain domain logic that should be implemented in Lean, not Python.

Total files to delete: 16

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Status: Awaiting user approval for deletion