[{"type":"thinking","thinking":"Now the stray duplicate in research/paper/. It's an older draft of the compendium (54,034 vs 54,367 bytes, missing the intro paragraph). It's untracked. Deleting is destructive — but it's clearly superseded. I'll ask the user in the summary rather than delete; or since the user's intent is cleanup/referencing, I could ask via AskUserQuestion. Minor — I'll flag it in the final summary and let them decide. Actually, simpler: just flag it.\n\nNow commit. Then deliver the regroup analysis.","signature":""},{"type":"text","text":"Now commit the registration."},{"type":"tool_use","id":"Bash_19","name":"Bash","input":{"command":"cd /d/Python/Quantum && git add research/resources/index.md NGUYEN.md research/derivations/D-001-quantum-formalism-index.md && git -c user.name=\"NGUYEN-RH-1\" -c user.email=\"research@local\" commit -m \"$(cat <<'EOF'\nSession 008: register R7 resources atlas (43-note RH-equivalence reference) — index.md + manifest + D-001 pointer\nEOF\n)\" && git status --short","description":"Commit R7 atlas registration"},"extra_content":null}]