CHANGELOG.md
CITATION.cff
LICENSE
MANIFEST.in
README.md
pyproject.toml
run_stable_daemon.sh
start_research.sh
.github/CODE_OF_CONDUCT.md
.github/CONTRIBUTING.md
.github/PULL_REQUEST_TEMPLATE.md
.github/SECURITY.md
ai_scientist/__init__.py
ai_scientist/adaptive_learning_engine.py
ai_scientist/agent_guidance_coordinator.py
ai_scientist/agent_interface.py
ai_scientist/autonomous_evolution.py
ai_scientist/baseline_system.py
ai_scientist/daemon_feedback_integration.py
ai_scientist/enhanced_feedback_system.py
ai_scientist/improvement_reporter.py
ai_scientist/innovation_enhancer.py
ai_scientist/llm.py
ai_scientist/paper_metadata.py
ai_scientist/perform_auto_improvement.py
ai_scientist/perform_icbinb_writeup.py
ai_scientist/perform_ideation_temp_free.py
ai_scientist/perform_llm_review.py
ai_scientist/perform_plotting.py
ai_scientist/perform_vlm_review.py
ai_scientist/perform_writeup.py
ai_scientist/professional_writing_system.py
ai_scientist/review_strategies.py
ai_scientist/self_learning_knowledge_base.py
ai_scientist/vlm.py
ai_scientist/writeup_guardrails.py
ai_scientist/writing_audit.py
ai_scientist/writing_prompt_profiles.py
ai_scientist/writing_skill_pack.py
ai_scientist/writing_strategies.py
ai_scientist/apps/__init__.py
ai_scientist/apps/ara.py
ai_scientist/apps/auth.py
ai_scientist/apps/batch.py
ai_scientist/apps/batch_cli.py
ai_scientist/apps/batch_experiment_artifacts.py
ai_scientist/apps/bfts.py
ai_scientist/apps/daemon.py
ai_scientist/apps/daemon_control.py
ai_scientist/apps/daemon_dashboard.py
ai_scientist/apps/daemon_reports.py
ai_scientist/apps/daemon_sources.py
ai_scientist/apps/feedback.py
ai_scientist/apps/manager.py
ai_scientist/apps/manager_cli.py
ai_scientist/apps/manager_ranking.py
ai_scientist/apps/manager_reports.py
ai_scientist/apps/preflight.py
ai_scientist/apps/project.py
ai_scientist/apps/project_cli.py
ai_scientist/apps/validate.py
ai_scientist/apps/zhipu.py
ai_scientist/blank_icbinb_latex/fancyhdr.sty
ai_scientist/blank_icbinb_latex/iclr2025.bib
ai_scientist/blank_icbinb_latex/iclr2025.bst
ai_scientist/blank_icbinb_latex/iclr2025.sty
ai_scientist/blank_icbinb_latex/math_commands.tex
ai_scientist/blank_icbinb_latex/natbib.sty
ai_scientist/blank_icbinb_latex/template.tex
ai_scientist/blank_icml_latex/algorithm.sty
ai_scientist/blank_icml_latex/algorithmic.sty
ai_scientist/blank_icml_latex/icml2025.bst
ai_scientist/blank_icml_latex/icml2025.sty
ai_scientist/blank_icml_latex/template.tex
ai_scientist/config/__init__.py
ai_scientist/config/paths.py
ai_scientist/experiments/__init__.py
ai_scientist/experiments/ara_ab/__init__.py
ai_scientist/experiments/ara_ab/harness.py
ai_scientist/fewshot_examples/132_automated_relational.json
ai_scientist/fewshot_examples/132_automated_relational.txt
ai_scientist/fewshot_examples/2_carpe_diem.json
ai_scientist/fewshot_examples/2_carpe_diem.txt
ai_scientist/fewshot_examples/attention.json
ai_scientist/fewshot_examples/attention.txt
ai_scientist/ideas/i_cant_believe_its_not_better.json
ai_scientist/ideas/i_cant_believe_its_not_better.md
ai_scientist/ideas/i_cant_believe_its_not_better.py
ai_scientist/ideas/i_cant_believe_its_not_betterrealworld.json
ai_scientist/ideas/i_cant_believe_its_not_betterrealworld.py
ai_scientist/ideas/my_research_topic.json
ai_scientist/ideas/my_research_topic.md
ai_scientist/protocol/SPEC.md
ai_scientist/protocol/__init__.py
ai_scientist/protocol/constants.py
ai_scientist/protocol/graph.py
ai_scientist/protocol/hashing.py
ai_scientist/protocol/llm_trace.py
ai_scientist/protocol/objects.py
ai_scientist/protocol/schemas.py
ai_scientist/protocol/validator.py
ai_scientist/protocol/schemas/bundle_manifest.schema.json
ai_scientist/protocol/schemas/claim.schema.json
ai_scientist/protocol/schemas/context_pack.schema.json
ai_scientist/protocol/schemas/exploration_graph.schema.json
ai_scientist/protocol/schemas/gc_plan.schema.json
ai_scientist/protocol/schemas/gc_receipt.schema.json
ai_scientist/protocol/schemas/llm_call.schema.json
ai_scientist/protocol/schemas/manifest.schema.json
ai_scientist/protocol/schemas/manifest_lock.schema.json
ai_scientist/protocol/schemas/manifest_revision.schema.json
ai_scientist/protocol/schemas/metric_marker.schema.json
ai_scientist/protocol/schemas/node.schema.json
ai_scientist/protocol/schemas/reexec_batch.schema.json
ai_scientist/protocol/schemas/reference_manifest.schema.json
ai_scientist/protocol/schemas/research_event.schema.json
ai_scientist/protocol/schemas/storage_report.schema.json
ai_scientist/protocol/schemas/verify_report.schema.json
ai_scientist/resources/__init__.py
ai_scientist/resources/configs/__init__.py
ai_scientist/resources/configs/bfts_deep.yaml
ai_scientist/resources/configs/bfts_default.yaml
ai_scientist/tools/__init__.py
ai_scientist/tools/base_tool.py
ai_scientist/tools/semantic_scholar.py
ai_scientist/treesearch/__init__.py
ai_scientist/treesearch/agent_manager.py
ai_scientist/treesearch/bfts_utils.py
ai_scientist/treesearch/interpreter.py
ai_scientist/treesearch/journal.py
ai_scientist/treesearch/journal2report.py
ai_scientist/treesearch/log_summarization.py
ai_scientist/treesearch/parallel_agent.py
ai_scientist/treesearch/perform_experiments_bfts_with_agentmanager.py
ai_scientist/treesearch/backend/__init__.py
ai_scientist/treesearch/backend/backend_anthropic.py
ai_scientist/treesearch/backend/backend_openai.py
ai_scientist/treesearch/backend/backend_zhipu.py
ai_scientist/treesearch/backend/utils.py
ai_scientist/treesearch/utils/__init__.py
ai_scientist/treesearch/utils/config.py
ai_scientist/treesearch/utils/data_preview.py
ai_scientist/treesearch/utils/metric.py
ai_scientist/treesearch/utils/response.py
ai_scientist/treesearch/utils/serialize.py
ai_scientist/treesearch/utils/tree_export.py
ai_scientist/treesearch/utils/viz_templates/template.html
ai_scientist/treesearch/utils/viz_templates/template.js
ai_scientist/utils/ara_artifact.py
ai_scientist/utils/ara_catalog.py
ai_scientist/utils/ara_compact.py
ai_scientist/utils/ara_context.py
ai_scientist/utils/ara_diff.py
ai_scientist/utils/ara_events.py
ai_scientist/utils/ara_graph.py
ai_scientist/utils/ara_log.py
ai_scientist/utils/ara_manifest_lock.py
ai_scientist/utils/ara_metric_parser.py
ai_scientist/utils/ara_minimal.py
ai_scientist/utils/ara_pipeline.py
ai_scientist/utils/ara_reexec.py
ai_scientist/utils/ara_refs.py
ai_scientist/utils/ara_seed.py
ai_scientist/utils/ara_storage.py
ai_scientist/utils/atomic_io.py
ai_scientist/utils/auth_session.py
ai_scientist/utils/claim_coverage.py
ai_scientist/utils/claim_registry.py
ai_scientist/utils/critic_workflow.py
ai_scientist/utils/daemon_feedback.py
ai_scientist/utils/decision_log.py
ai_scientist/utils/deferred_imports.py
ai_scientist/utils/deterministic_evaluator.py
ai_scientist/utils/epistemic_graph.py
ai_scientist/utils/evaluation_governance.py
ai_scientist/utils/evolution_controller.py
ai_scientist/utils/evolution_gate.py
ai_scientist/utils/evolution_program.py
ai_scientist/utils/experiment_registry.py
ai_scientist/utils/experiment_report.py
ai_scientist/utils/experiment_run_lock.py
ai_scientist/utils/experiment_todo_progress.py
ai_scientist/utils/fallback_audit.py
ai_scientist/utils/figure_spec.py
ai_scientist/utils/gate_preconditions.py
ai_scientist/utils/guardrail_artifacts.py
ai_scientist/utils/high_quality_pipeline.py
ai_scientist/utils/hypothesis_archive.py
ai_scientist/utils/idea_ranking.py
ai_scientist/utils/integrity_forensics.py
ai_scientist/utils/integrity_workflow.py
ai_scientist/utils/latex_lint.py
ai_scientist/utils/launcher_cli.py
ai_scientist/utils/launcher_workflow.py
ai_scientist/utils/llm_budget.py
ai_scientist/utils/manuscript_state.py
ai_scientist/utils/optional_dependencies.py
ai_scientist/utils/pareto_pool.py
ai_scientist/utils/pipeline_contracts.py
ai_scientist/utils/pipeline_helpers.py
ai_scientist/utils/process_alignment.py
ai_scientist/utils/provider_registry.py
ai_scientist/utils/quality_workflow.py
ai_scientist/utils/readiness_benchmark.py
ai_scientist/utils/repair_attempts.py
ai_scientist/utils/repair_reflection.py
ai_scientist/utils/repair_verifier.py
ai_scientist/utils/research_integrity.py
ai_scientist/utils/research_planning.py
ai_scientist/utils/review_execution.py
ai_scientist/utils/review_jobs.py
ai_scientist/utils/review_repair_planner.py
ai_scientist/utils/review_workflow.py
ai_scientist/utils/run_index.py
ai_scientist/utils/runtime_bootstrap.py
ai_scientist/utils/sample_gate.py
ai_scientist/utils/science_constitution.py
ai_scientist/utils/self_evolution.py
ai_scientist/utils/self_review_optimizer.py
ai_scientist/utils/source_planning.py
ai_scientist/utils/stage_standards.py
ai_scientist/utils/submission_history.py
ai_scientist/utils/token_tracker.py
ai_scientist/utils/truth_contracts.py
ai_scientist/utils/workflow_cli.py
ai_scientist/utils/workflow_execution_policy.py
ai_scientist/utils/workflow_modes.py
ai_scientist/utils/workflow_runtime.py
ai_scientist/utils/workflow_selection.py
ai_scientist/utils/writeup_workflow.py
compat/auth_cli.py
compat/continuous_paper_generator.py
compat/continuous_research_daemon.py
compat/feedback_cli.py
compat/launch_scientist_bfts.py
compat/launch_scientist_zhipu.py
compat/preflight_check.py
compat/research_manager.py
compat/run_ara_fork.py
compat/run_project.py
compat/validate_repo.py
compat/xscientist.egg-info/PKG-INFO
compat/xscientist.egg-info/SOURCES.txt
compat/xscientist.egg-info/dependency_links.txt
compat/xscientist.egg-info/entry_points.txt
compat/xscientist.egg-info/requires.txt
compat/xscientist.egg-info/top_level.txt
configs/bfts/bfts_config.yaml
configs/bfts/bfts_config_deep.yaml
configs/bfts/bfts_config_enhanced.yaml
configs/daemon/daemon_control.example.json
configs/daemon/daemon_control.schema.json
configs/daemon/daemon_profile.example.json
configs/daemon/daemon_profile.schema.json
configs/daemon/stable_daemon_profile.example.json
configs/daemon/stable_daemon_profile.local.example.json
configs/daemon/stable_day_daemon_profile.example.json
configs/daemon/stable_night_daemon_profile.example.json
configs/environment/example.env
configs/research/research_config.example.yaml
configs/sources/source_priority.example.json
configs/sources/source_queue.example.toml
configs/sources/source_queue.schema.json
configs/sources/stable_source_priority.example.json
docs/ARA_STORAGE_LIFECYCLE.md
docs/ARCHITECTURE.md
docs/CONFIG_REFERENCE.md
docs/DEEPREVIEWER_ALIGNMENT.md
docs/ENGINEERING.md
docs/EPISTEMIC_GRAPH_SPEC.md
docs/EVALUATION_GOVERNANCE.md
docs/EVOLUTION_GATE.md
docs/LOGIN_GUARDRAIL.md
docs/LONG_RUNNING_GUIDE.md
docs/OPERATIONS_CHECKLIST.md
docs/PERFORMANCE_GATES.md
docs/README.zh.md
docs/RESEARCH_DISCOVERY.md
docs/RESEARCH_INTEGRITY.md
docs/SCIENCE_CONSTITUTION.md
docs/SELF_EVOLUTION_ARCHITECTURE.md
docs/SOURCE_ORCHESTRATION.md
docs/logo_v1.png
docs/guides/ADAPTIVE_LEARNING_README.md
docs/guides/AUTONOMOUS_EVOLUTION_README.md
docs/guides/AUTO_IMPROVEMENT_README.md
docs/guides/DEEP_OPTIMIZATION_README.md
docs/guides/FEEDBACK_QUICKSTART.md
docs/guides/OPTIMIZATION_SUMMARY.md
docs/guides/OUTPUT_DIRECTORIES.md
docs/guides/PAPER_METADATA_README.md
docs/guides/PROFESSIONAL_WRITING_README.md
docs/guides/PROJECT_USAGE.md
docs/guides/RESEARCH_GENERATOR_README.md
docs/guides/SDK_AND_API.md
examples/example_topic.md
requirements/constraints-ci.txt
requirements/smoke.txt
scripts/__init__.py
scripts/daemon/__init__.py
scripts/daemon/run_daemon_profile.py
scripts/daemon/run_daemon_rehearsal.py
tools/__init__.py
tools/build_distribution.py
tools/check_distribution.py
tools/check_release.py
tools/engineering_checks.py
tools/performance_regression.py
tools/repository_validation.py
xscientist/__init__.py
xscientist/__main__.py
xscientist/_version.py
xscientist/cli.py
xscientist/client.py
xscientist/entrypoints.py
xscientist/models.py
xscientist/service.py
xscientist/service_jobs.py