docs(FN-4166): cross-reference persistAgentThinkingLog in agents.md
Fusion-Task-Id: FN-4166 Fusion-Task-Lineage: 8c491fd0-2390-4501-9b80-8c45c9ebf6b5
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@@ -1271,6 +1271,10 @@ Run records are stored in structured JSON files at `.fusion/agents/{agentId}-run
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Heartbeat events are also appended to `.fusion/agents/{agentId}-heartbeats.jsonl` for legacy compatibility. The structured storage is the source of truth; heartbeat events provide a fallback for older run data.
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### Thinking/Reasoning Log Persistence
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By default, `thinking`/reasoning agent log entries are discarded after each run. The `persistAgentThinkingLogPermanent` and `persistAgentThinkingLogEphemeral` project settings (both `boolean`, default `false`) control whether these entries are persisted for permanent and ephemeral agents respectively. A legacy `persistAgentThinkingLog` fallback is also supported. When disabled, only thinking rows are suppressed; normal assistant text and tool rows are unchanged. See the [settings reference](./settings-reference.md) for full configuration details.
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### Stopping Runs
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Use `POST /api/agents/:id/runs/stop` to terminate an active run:
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