Dated markdown files, one per work session where you thought about something. Not "what I did" (commits cover that) but "what I was thinking about and why" — half-formed ideas, observations, the concrete failing example that forced a redesign. This reasoning evaporates fast and is exactly what the paper's motivation section will need.
Filename: YYYY-MM-DD.md (multiple entries per day → append, or -2 suffix).
Keep it informal. Link to decisions (../decisions/NNNN-*.md), examples, and
dead ends (../antipatterns.md) liberally.