LICENSE
README.md
pyproject.toml
src/workflow_clinic/__init__.py
src/workflow_clinic/cli.py
src/workflow_clinic/exceptions.py
src/workflow_clinic/main.py
src/workflow_clinic.egg-info/PKG-INFO
src/workflow_clinic.egg-info/SOURCES.txt
src/workflow_clinic.egg-info/dependency_links.txt
src/workflow_clinic.egg-info/entry_points.txt
src/workflow_clinic.egg-info/requires.txt
src/workflow_clinic.egg-info/top_level.txt
src/workflow_clinic/advisor/__init__.py
src/workflow_clinic/advisor/retriever.py
src/workflow_clinic/critic/__init__.py
src/workflow_clinic/critic/agent.py
src/workflow_clinic/kb/rules_knowledge.toml
src/workflow_clinic/models/__init__.py
src/workflow_clinic/models/diagnosis.py
src/workflow_clinic/models/metadata.py
src/workflow_clinic/models/task.py
src/workflow_clinic/models/workflow_bundle.py
src/workflow_clinic/parsers/__init__.py
src/workflow_clinic/parsers/base.py
src/workflow_clinic/parsers/nextflow.py
src/workflow_clinic/parsers/registry.py
src/workflow_clinic/reporting/__init__.py
src/workflow_clinic/reporting/fingerprint.py
src/workflow_clinic/reporting/github_publisher.py
src/workflow_clinic/reporting/issue_generator.py
src/workflow_clinic/rules/__init__.py
src/workflow_clinic/rules/base.py
src/workflow_clinic/rules/container.py
src/workflow_clinic/rules/credentials.py
src/workflow_clinic/rules/paths.py
src/workflow_clinic/rules/registry.py
src/workflow_clinic/rules/resources.py
src/workflow_clinic/rules/runner.py
src/workflow_clinic/utils/__init__.py
src/workflow_clinic/utils/git.py
tests/test_cli.py
tests/test_cli_create_issue.py
tests/test_critic.py
tests/test_diagnosis_schema.py
tests/test_fingerprint.py
tests/test_github_publisher.py
tests/test_issue_generator.py
tests/test_knowledge_store.py
tests/test_logging.py
tests/test_nextflow_parser.py
tests/test_optional_deps.py
tests/test_parser.py
tests/test_remote_examine.py
tests/test_rules.py
tests/test_smoke.py
tests/test_workflow_bundle.py