Upgrade the Atomic harness to 0.9.32

apps/server/src/harness/atomic/adapter.ts

@@ -195,7 +195,17 @@ export function atomicTurnExtension(policy: TurnPolicy): ExtensionFactory {
 				};
 			},
 		});
+		let stage = false;
+		atomic.on("session_start", (_event, ctx) => {
+			stage = ctx.subagentPolicy !== undefined;
+		});
 		atomic.on("before_agent_start", event => {
+			if (stage) {
+				atomic.setActiveTools(
+					atomic.getActiveTools().filter(name => name !== ATOMIC_RESULT_TOOL_NAME),
+				);
+				return;
+			}
 			if (!policy.full) atomic.setActiveTools(activeNames(policy));
 			return {
 				systemPrompt: policy.full
@@ -204,6 +214,10 @@ export function atomicTurnExtension(policy: TurnPolicy): ExtensionFactory {
 			};
 		});
 		atomic.on("tool_call", event => {
+			if (stage) {
+				if (event.toolName !== ATOMIC_RESULT_TOOL_NAME) return;
+				return { block: true, reason: `${event.toolName} is not available in a workflow stage.` };
+			}
 			if (policy.full && event.toolName !== ATOMIC_RESULT_TOOL_NAME) return;
 			if (activeNames(policy).includes(event.toolName)) return;
 			return { block: true, reason: `${event.toolName} is not available in this turn.` };

apps/server/src/harness/atomic/full.test.ts

@@ -517,6 +517,8 @@ test(
 			)!;
 			expect(stage.toolNames).toContain("bash");
 			expect(stage.toolNames).toContain("write");
+			expect(stage.toolNames).not.toContain(ATOMIC_RESULT_TOOL_NAME);
+			expect(stage.system).not.toContain("CHOPIN-INSTRUCTIONS-MARKER");
 		} finally {
 			if (environment !== undefined) process.env.NODE_ENV = environment;
 			await room.close();

apps/server/src/harness/atomic/full.ts

@@ -251,10 +251,10 @@ export function workflowRuns(planner: FullPlanner): ExtensionFactory {
 		let names = new Map<string, string>();
 		let parents = new Map<string, string>();
 		let seen = new Set<string>();
-		planner.rootOf = runId => parents.get(runId) ?? runId;
+		let stage = true;
 		let ready = false;
 		let publish = () => {
-			if (!ready) return;
+			if (stage || !ready) return;
 			for (let [id, card] of cards) {
 				if (seen.has(id) && !roots.has(id) && card.ended === undefined) {
 					card.status = "finished";
@@ -270,6 +270,9 @@ export function workflowRuns(planner: FullPlanner): ExtensionFactory {
 			for (let wake of planner.waiters ?? []) wake();
 		};
 		atomic.on("session_start", (_event, ctx) => {
+			stage = ctx.subagentPolicy !== undefined;
+			if (stage) return;
+			planner.rootOf = runId => parents.get(runId) ?? runId;
 			lease?.dispose();
 			lease = ctx.observeWorkflowActivity(frame => {
 				if (frame.kind === "snapshot") {
@@ -283,7 +286,7 @@ export function workflowRuns(planner: FullPlanner): ExtensionFactory {
 			});
 		});
 		atomic.on("tool_result", event => {
-			if (event.toolName !== "workflow" || event.input.action !== "run") return;
+			if (stage || event.toolName !== "workflow" || event.input.action !== "run") return;
 			let runId = launchedRunId(event.content);
 			let name = typeof event.input.workflow === "string" ? event.input.workflow : undefined;
 			if (!runId || !name) return;
@@ -295,6 +298,7 @@ export function workflowRuns(planner: FullPlanner): ExtensionFactory {
 			}
 		});
 		atomic.on("workflow_lifecycle", event => {
+			if (stage) return;
 			if (event.target.kind !== "prompt") parents.set(event.target.runId, event.rootRunId);
 			foldLifecycle(cards, event, names.get(event.rootRunId));
 			publish();

docs/self-hosting.md

@@ -115,7 +115,7 @@ it. The Pi contract suite (`apps/server/src/harness/pi.contract.test.ts`)
 covers this against the real Pi agent loop; run it before bumping
 `@ai-sdk/harness-pi` or `@earendil-works/pi-coding-agent`.
 
-`HARNESS=atomic` runs Atomic 0.9.31 in the Chopin server process through its
+`HARNESS=atomic` runs Atomic 0.9.32 in the Chopin server process through its
 headless SDK (`createAgentSession()`). It does not spawn the `atomic` CLI, use
 RPC mode, or substitute Atomic for Pi's runtime.
 

package.json

@@ -67,7 +67,7 @@
 				"@ai-sdk/harness-pi": "1.0.148",
 				"@ai-sdk/mcp": "2.0.72",
 				"@ai-sdk/sandbox-just-bash": "1.0.146",
-				"@bastani/atomic": "0.9.31",
+				"@bastani/atomic": "0.9.32",
 				"@earendil-works/pi-coding-agent": "0.85.1",
 				"ai": "7.0.135",
 				"typebox": "1.3.7",