What problem does it solve? Decisions made in chat sessions and exploratory probes disappear when the session ends, leaving no reproducible record of why a method, parameter, or phase boundary was chosen. This Skill enforces a discipline of writing durable, git-tracked reasoning notes so every non-trivial choice in a computational analysis project survives handoffs and future sessions. ## Core Features & Use Cases - Structured decision notes: A fixed note format captures scope, sources, evidence, the decision made, and rejected alternatives for each choice. - Scope-based placement: Notes land in docs/_internal/<stage-stem>/ for stage-scoped work or docs/_internal/_project/ for cross-stage and research topics, with session.md as the live work-state record. - No-ephemeral discipline: Throwaway probes stay in _scratch/ or $TMPDIR; only the extracted answer is committed, and every 03_results/ artifact must trace back to a committed analysis stage. - Use Case: After choosing a clustering resolution in a single-cell RNA-seq analysis, write a trace note recording the evidence, the chosen resolution, and why alternatives were rejected before moving to annotation. ## Quick Start Write a reasoning trace note for the normalization method decision we just made, including the evidence and the alternatives we rejected.
