.env.example
LICENSE
MANIFEST.in
README.md
config.py
pyproject.toml
setup.py
adapters/__init__.py
adapters/config_parser_settings.py
adapters/docling_parser.py
adapters/factory.py
adapters/output_export.py
adapters/pymupdf_parser.py
agents/__init__.py
agents/analysis_context.py
agents/analysis_snapshot.py
agents/coder.py
agents/coder_quality.py
agents/planner.py
agents/reader.py
agents/reporter.py
agents/reviewer.py
agents/runner.py
application/__init__.py
application/facade.py
application/version.py
application/lifecycle/__init__.py
application/lifecycle/clean.py
application/lifecycle/common.py
application/lifecycle/doctor.py
application/lifecycle/init.py
application/lifecycle/init_wizard.py
application/lifecycle/llm_doctor.py
conf/config.yaml
conf/analysis/default.yaml
conf/coder/default.yaml
conf/discovery/default.yaml
conf/execution_planning/default.yaml
conf/llm/default.yaml
conf/logging/default.yaml
conf/parser/default.yaml
conf/planner/default.yaml
conf/reporter/default.yaml
conf/reviewer/default.yaml
conf/runner/default.yaml
conf/tracking/default.yaml
conf/workflow/default.yaml
configuration/__init__.py
configuration/bootstrap.py
configuration/hydra_provider.py
configuration/legacy_provider.py
configuration/models.py
configuration/paths.py
configuration/provider.py
discovery/__init__.py
discovery/empty.py
discovery/workflow.py
execution/__init__.py
execution/execution_planner.py
execution_planning/__init__.py
execution_planning/builder.py
execution_planning/workflow.py
interfaces/__init__.py
interfaces/api/__init__.py
interfaces/cli/__init__.py
interfaces/cli/app.py
interfaces/cli/common.py
interfaces/cli/commands/__init__.py
interfaces/cli/commands/analyze.py
interfaces/cli/commands/clean.py
interfaces/cli/commands/config.py
interfaces/cli/commands/discover.py
interfaces/cli/commands/doctor.py
interfaces/cli/commands/execute.py
interfaces/cli/commands/init.py
interfaces/cli/commands/model.py
interfaces/cli/commands/plan.py
interfaces/cli/commands/reproduce.py
interfaces/cli/commands/version.py
interfaces/mcp/__init__.py
interfaces/sdk/__init__.py
interfaces/sdk/client.py
llm/__init__.py
llm/anthropic_provider.py
llm/coder_mock_provider.py
llm/compat.py
llm/factory.py
llm/mock_provider.py
llm/openai_provider.py
llm/provider.py
llm/response_parser.py
man1lab/__init__.py
man1lab/__main__.py
man1lab.egg-info/PKG-INFO
man1lab.egg-info/SOURCES.txt
man1lab.egg-info/dependency_links.txt
man1lab.egg-info/entry_points.txt
man1lab.egg-info/requires.txt
man1lab.egg-info/top_level.txt
models/__init__.py
models/execution.py
models/execution_plan.py
models/execution_planning_runtime.py
models/execution_strategy.py
models/paper.py
models/paper_reproduction_analysis.py
models/report.py
models/research_resource_discovery.py
models/review.py
models/review_report.py
models/routing.py
models/task.py
models/verification.py
models/workspace.py
planning/__init__.py
planning/patch_planner.py
ports/__init__.py
ports/adaptation_provider.py
ports/collection_provider.py
ports/document_parser.py
ports/evidence_provider.py
ports/generation_provider.py
ports/output_format.py
ports/parsed_document.py
ports/parser_settings.py
ports/ranking_provider.py
ports/resource_binding_provider.py
ports/reuse_provider.py
ports/risk_provider.py
ports/strategy_provider.py
ports/verification_provider.py
prompt/__init__.py
prompt/builder.py
prompt/exceptions.py
prompt/loader.py
prompts/coder/config.md
prompts/coder/dependencies.md
prompts/coder/script.md
prompts/coder/source.md
prompts/coder/system.md
prompts/patch_planner/examples.md
prompts/patch_planner/extraction.md
prompts/patch_planner/schema.md
prompts/patch_planner/system.md
prompts/planner/examples.md
prompts/planner/extraction.md
prompts/planner/schema.md
prompts/planner/system.md
prompts/reader/examples.md
prompts/reader/extraction.md
prompts/reader/output.md
prompts/reader/schema.md
prompts/reader/system.md
prompts/reviewer/examples.md
prompts/reviewer/extraction.md
prompts/reviewer/schema.md
prompts/reviewer/system.md
providers/__init__.py
providers/embedded/__init__.py
providers/embedded/adaptation.py
providers/embedded/embedded_evidence_provider.py
providers/embedded/embedded_ranking_provider.py
providers/embedded/embedded_resource_provider.py
providers/embedded/embedded_verification_provider.py
providers/embedded/generation.py
providers/embedded/resource_binding.py
providers/embedded/reuse.py
providers/embedded/risk.py
providers/embedded/strategy.py
providers/embedded/decision_foundation/__init__.py
providers/embedded/decision_foundation/adaptation_decision.py
providers/embedded/decision_foundation/binding_decision.py
providers/embedded/decision_foundation/common.py
providers/embedded/decision_foundation/dimensions.py
providers/embedded/decision_foundation/facts.py
providers/embedded/decision_foundation/generation_decision.py
providers/embedded/decision_foundation/reuse_decision.py
providers/embedded/decision_foundation/risk_decision.py
providers/embedded/decision_foundation/strategy_decision.py
providers/github/__init__.py
providers/github/auth.py
providers/github/client.py
providers/github/collection.py
providers/github/evidence.py
providers/github/exceptions.py
providers/github/mapper.py
providers/github/models.py
providers/github/ranking.py
providers/github/verification.py
providers/llm/__init__.py
providers/llm/anthropic_provider.py
providers/llm/base.py
providers/llm/deepseek_provider.py
providers/llm/errors.py
providers/llm/manager.py
providers/llm/model_management.py
providers/llm/models.py
providers/llm/openai_provider.py
providers/llm/persistence.py
providers/llm/profiles.py
providers/llm/provider_registry.py
providers/llm/registry.py
providers/noop/__init__.py
providers/noop/adaptation.py
providers/noop/collection.py
providers/noop/evidence.py
providers/noop/generation.py
providers/noop/noop_evidence_provider.py
providers/noop/noop_ranking_provider.py
providers/noop/noop_verification_provider.py
providers/noop/ranking.py
providers/noop/resource_binding.py
providers/noop/reuse.py
providers/noop/risk.py
providers/noop/strategy.py
providers/noop/verification.py
routing/__init__.py
routing/task_router.py
services/__init__.py
services/environment_service.py
services/exceptions.py
services/execution_service.py
services/pdf_service.py
services/verification_service.py
services/discovery/__init__.py
services/discovery/candidate_merge.py
services/discovery/collection_service.py
services/discovery/evidence_merge.py
services/discovery/evidence_service.py
services/discovery/ranking_merge.py
services/discovery/ranking_service.py
services/discovery/verification_merge.py
services/discovery/verification_service.py
services/execution_planning/__init__.py
services/execution_planning/adaptation_merge.py
services/execution_planning/adaptation_service.py
services/execution_planning/generation_merge.py
services/execution_planning/generation_service.py
services/execution_planning/protocols.py
services/execution_planning/resource_binding_merge.py
services/execution_planning/resource_binding_service.py
services/execution_planning/reuse_merge.py
services/execution_planning/reuse_service.py
services/execution_planning/risk_merge.py
services/execution_planning/risk_service.py
services/execution_planning/strategy_merge.py
services/execution_planning/strategy_service.py
tests/test_anthropic_provider.py
tests/test_cleanup.py
tests/test_cli.py
tests/test_coder.py
tests/test_coder_acceptance.py
tests/test_coder_contract.py
tests/test_coder_population.py
tests/test_coder_quality.py
tests/test_configuration.py
tests/test_discovery_collection.py
tests/test_discovery_evidence.py
tests/test_discovery_ranking.py
tests/test_discovery_verification.py
tests/test_document_parser.py
tests/test_environment_service.py
tests/test_execution_planning_adaptation_provider.py
tests/test_execution_planning_binding_provider.py
tests/test_execution_planning_generation_provider.py
tests/test_execution_planning_reuse_provider.py
tests/test_execution_planning_risk_provider.py
tests/test_execution_planning_runtime.py
tests/test_execution_planning_services.py
tests/test_execution_planning_strategy_provider.py
tests/test_execution_planning_workflow.py
tests/test_execution_strategy_builder.py
tests/test_execution_strategy_model.py
tests/test_execution_strategy_validation.py
tests/test_experiment_tracking.py
tests/test_github_client.py
tests/test_github_collection_provider.py
tests/test_github_evidence_provider.py
tests/test_github_mapper.py
tests/test_github_models.py
tests/test_github_ranking_provider.py
tests/test_github_verification_provider.py
tests/test_init_wizard.py
tests/test_llm_provider.py
tests/test_model_cli.py
tests/test_model_registry.py
tests/test_package_distribution.py
tests/test_paper_reproduction_analysis.py
tests/test_paper_validation.py
tests/test_patch_plan.py
tests/test_pdf_service.py
tests/test_pipeline_integration.py
tests/test_planner.py
tests/test_platform_facade.py
tests/test_platform_integration.py
tests/test_prompt.py
tests/test_reader.py
tests/test_reader_prompt_integration.py
tests/test_research_resource_discovery.py
tests/test_response_parser.py
tests/test_review.py
tests/test_script_execution.py
tests/test_sdk.py
tests/test_smoke.py
tests/test_task_routing.py
tests/test_task_validation.py
tests/test_verification.py
tracking/__init__.py
tracking/bootstrap.py
tracking/mlflow_tracker.py
tracking/noop_tracker.py
tracking/protocol.py
tracking/provider.py
tracking/workflow.py
validation/__init__.py
validation/analysis_builder.py
validation/exceptions.py
validation/execution_strategy.py
validation/paper.py
validation/paper_reproduction_analysis.py
validation/patch.py
validation/research_resource_discovery.py
validation/review.py
validation/task.py
workflow/__init__.py
workflow/orchestrator.py
workflow/pipeline.py
workspace/__init__.py
workspace/manager.py