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Claude Code writes one transcript JSONL line per content block, so a single API response (one message.id) spans multiple assistant lines that each repeat the same message.usage. sumUsageFromTranscript summed every line, inflating token totals and estimated_cost_usd roughly 2.5-3x. Verified on a real session: 704 assistant lines but only 286 unique message.ids (2.46 lines/response on average); line-summing reported $866.52 while the deduped total is $332.62. Usage payloads are identical across lines of the same id (0/286 varied), so counting once per id is equivalent to taking the last line per id. Fix: collect usage into a Map keyed by message.id (last line wins) and sum unique entries. Lines without a message.id (older transcript shapes) keep the previous per-line behavior via a synthetic key, so existing tests and old transcripts are unaffected. Adds a regression test: a response split into 3 content-block lines with the same message.id is counted exactly once. Note: rows already written to ~/.claude/metrics/costs.jsonl by the old code carry inflated token counts and estimates (except rows whose cost came from the harness-cost cache, where cost is authoritative but token counts are still inflated). Downstream consumers may want to annotate history; this change intentionally does not rewrite the raw log. Co-authored-by: Claude Fable 5 <noreply@anthropic.com>