{
  "permissions": {
    "allow": [
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" -c:*)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" examples/test_journal_optimization.py)",
      "Bash(while true)",
      "Bash(do sleep 30)",
      "Bash(if pgrep -f \"test_journal_optimization.py\")",
      "Bash(/dev/null)",
      "Bash(then echo \"Still running...\")",
      "Bash(else echo \"Completed!\")",
      "Bash(break)",
      "Bash(fi)",
      "Bash(done)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" -m pytest tests/test_plugin_system.py -v)",
      "Bash(C:Usersantoianaconda3envsatomizerpython.exe tests/test_hooks_with_bracket.py)",
      "Bash(dir:*)",
      "Bash(nul)",
      "Bash(findstr:*)",
      "Bash(test:*)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_research_agent.py)",
      "Bash(powershell -Command:*)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_knowledge_base_search.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_code_generation.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_complete_research_workflow.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_interactive_session.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/atomizer/python.exe\" tests/test_interactive_session.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/atomizer/python.exe\" optimization_engine/workflow_decomposer.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/atomizer/python.exe\" optimization_engine/capability_matcher.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/atomizer/python.exe\" tests/test_phase_2_5_intelligent_gap_detection.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_step_classifier.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_cbar_genetic_algorithm.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" -m pip install anthropic --quiet)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/atomizer/python.exe\" -m pip install anthropic --quiet)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" optimization_engine/hook_generator.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" hook_weighted_objective_norm_stress_norm_disp.py test_input.json)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" optimization_engine/pynastran_research_agent.py)",
      "Bash(git init:*)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" optimization_engine/extractor_orchestrator.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_phase_3_1_integration.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_bracket_llm_runner.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\":*)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_bracket_full_optimization.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/interactive_optimization_setup.py)",
      "Bash(tee:*)",
      "Bash(tree:*)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_timestamp_verification.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" run_optimization.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" studies/bracket_displacement_maximizing/test_fix.py)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" run_substudy.py coarse_exploration)",
      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" -c \"import json; h = json.load(open(''c:/Users/antoi/Documents/Atomaste/Atomizer/studies/bracket_displacement_maximizing/substudies/coarse_exploration/optimization_history_incremental.json'')); best = min(h, key=lambda x: x[''objective'']); print(f''Best Trial: {best[\"\"trial_number\"\"]}''); print(f''Parameters: tip={best[\"\"design_variables\"\"][\"\"tip_thickness\"\"]:.2f}mm, angle={best[\"\"design_variables\"\"][\"\"support_angle\"\"]:.2f}°''); print(f''Max Displacement: {best[\"\"results\"\"][\"\"max_displacement\"\"]:.6f}mm''); print(f''Objective: {best[\"\"objective\"\"]:.6f}'')\")"
    ],
    "deny": [],
    "ask": []
  }
}