LICENSE
README.md
pyproject.toml
src/agent_skill/AGENTS.md
src/agent_skill/CLAUDE.md
src/agent_skill/README.md
src/agent_skill/SKILL.md
src/agent_skill/api_registry.md
src/agent_skill/baseline_and_current_range.md
src/agent_skill/event_detection_policy.md
src/agent_skill/output_contract.md
src/agent_skill/poremind_encoder_policy.md
src/agent_skill/workflow_state_machine.md
src/agent_skill/examples/minimal_user_prompt.md
src/agent_skill/platform_adapters/README.md
src/agent_skill/platform_adapters/aider_CONVENTIONS.md
src/agent_skill/platform_adapters/claude_CLAUDE.md
src/agent_skill/platform_adapters/codex_AGENTS.md
src/agent_skill/platform_adapters/continue_prompt.md
src/agent_skill/platform_adapters/cursor_rule.mdc
src/agent_skill/recipes/frac_pp0_pp1_pp2.md
src/agent_skill/recipes/mspa_amino_acid.md
src/agent_skill/recipes/mspa_polydA_polydC.md
src/agent_skill/recipes/rna_conformation_timecourse.md
src/agent_skill/recipes/solid_state_protein.md
src/agent_skill/recipes/unknown_prediction.md
src/agent_skill/schemas/params.lock.schema.json
src/agent_skill/templates/analysis_run.py
src/agent_skill/templates/custom_features.py
src/agent_skill/templates/encoder_features.py
src/agent_skill/templates/reproduce_analysis.py
src/agent_skill/templates/save_outputs.py
src/poremind/__init__.py
src/poremind/baseline.py
src/poremind/events.py
src/poremind/features.py
src/poremind/io.py
src/poremind/magjam.py
src/poremind/ml.py
src/poremind/pipeline.py
src/poremind/pl.py
src/poremind/preprocess.py
src/poremind/workflow.py
src/poremind.egg-info/PKG-INFO
src/poremind.egg-info/SOURCES.txt
src/poremind.egg-info/dependency_links.txt
src/poremind.egg-info/entry_points.txt
src/poremind.egg-info/requires.txt
src/poremind.egg-info/top_level.txt
src/ui/__init__.py
src/ui/app.py
src/ui/controller.py
src/ui/session.py
src/ui/assets/poremind_logo.png
src/ui/assets/poremind_science_background.png
tests/test_magjam_integration.py
tests/test_pipeline_and_ml.py
tests/test_ui_controller.py