Upgrade Atomic to the stable 0.9.39 release

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

@@ -156,9 +156,9 @@ export type AtomicSettings = {
 	extensions?: readonly string[];
 	/**
 	 * The SQLite file the workflows of Planner sessions are journaled in, in place
-	 * of Atomic's default beside its agent directory. Atomic reads the journal
-	 * location only from `ATOMIC_WORKFLOW_JOURNAL_PATH` and the on-disk settings,
-	 * so the adapter sets that variable until it shuts down.
+	 * of Atomic's default beside its agent directory. Each Planner session is given
+	 * it through `createAgentSession({ journal })`, which takes precedence over
+	 * `ATOMIC_WORKFLOW_JOURNAL_PATH`; the process environment is left unchanged.
 	 */
 	journal?: string;
 };
@@ -472,8 +472,6 @@ export function createAtomicAdapter(
 	}
 	let runtime: Promise<ModelRuntime> | undefined;
 	let open = new Set<HarnessV1Session>();
-	let journal = process.env.ATOMIC_WORKFLOW_JOURNAL_PATH;
-	if (settings.journal) process.env.ATOMIC_WORKFLOW_JOURNAL_PATH = settings.journal;
 
 	return {
 		specificationVersion: "harness-v1",
@@ -660,6 +658,7 @@ export function createAtomicAdapter(
 						builtins: full ? undefined : BUILTINS_OFF,
 						tools: full ? undefined : [...hostNames, ATOMIC_RESULT_TOOL_NAME],
 						extensionBindings: full ? { humanInput: full.humanInput } : undefined,
+						journal: full && settings.journal ? { path: settings.journal } : undefined,
 						customTools: turn.tools.map(hostTool),
 					});
 					let session = created.session;
@@ -838,9 +837,6 @@ export function createAtomicAdapter(
 
 		async shutdown() {
 			await Promise.allSettled([...open].map(session => session.doDestroy()));
-			if (!settings.journal) return;
-			if (journal === undefined) delete process.env.ATOMIC_WORKFLOW_JOURNAL_PATH;
-			else process.env.ATOMIC_WORKFLOW_JOURNAL_PATH = journal;
 		},
 	};
 }

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

@@ -320,6 +320,7 @@ export default workflow({
 					operator: await Bun.file(join(agentDir, "settings.json")).exists(),
 					journal: await Bun.file(journal).exists(),
 					defaultJournal: await Bun.file(join(root, "workflows", "journal.sqlite")).exists(),
+					environment: process.env.ATOMIC_WORKFLOW_JOURNAL_PATH,
 					project: projectPackage
 						? await Bun.file(join(cwd, ".atomic", "settings.json")).text()
 						: undefined,
@@ -531,8 +532,10 @@ test(
 			expect(stage.toolNames).toContain("write");
 			expect(stage.toolNames).not.toContain(ATOMIC_RESULT_TOOL_NAME);
 			expect(stage.system).not.toContain("CHOPIN-INSTRUCTIONS-MARKER");
-			// The run is journaled where Chopin chose, not in Atomic's default beside its agent directory.
+			// The run is journaled where Chopin chose, not in Atomic's default beside its agent directory,
+			// and through the session rather than the process-wide environment variable.
 			expect(result.files).toMatchObject({ journal: true, defaultJournal: false });
+			expect(result.files?.environment).toBeUndefined();
 		} finally {
 			if (environment !== undefined) process.env.NODE_ENV = environment;
 			await room.close();

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

@@ -53,10 +53,12 @@ export function stateDirectory(): string {
 /**
  * Where Planner sessions journal their workflow runs. A run resumes only with
  * the journal and working directory it started with, so the journal lives
- * beside the channel directories rather than in Atomic's own home.
+ * beside the channel directories rather than in Atomic's own home. An
+ * operator's non-empty `ATOMIC_WORKFLOW_JOURNAL_PATH` still names the file.
  */
 export function workflowJournal(): string {
-	return join(stateDirectory(), "atomic", "workflows.sqlite");
+	return process.env.ATOMIC_WORKFLOW_JOURNAL_PATH
+		|| join(stateDirectory(), "atomic", "workflows.sqlite");
 }
 
 /**

apps/server/src/harness/harnesses.test.ts

@@ -2,6 +2,7 @@ import { afterEach, expect, it } from "bun:test";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 
+import { workflowJournal } from "./atomic/workspace";
 import { harnesses, harnessFor, registerCredential, shutdownHarnesses } from "./harnesses";
 
 afterEach(shutdownHarnesses);
@@ -60,20 +61,22 @@ it("journals Atomic workflow runs in Chopin's state directory unless the operato
 	let state = join(tmpdir(), `chopin-state-${crypto.randomUUID()}`);
 	let restore = (name: string, value: string | undefined) =>
 		value === undefined ? delete process.env[name] : process.env[name] = value;
-	let journal = (): string | undefined => process.env.ATOMIC_WORKFLOW_JOURNAL_PATH;
 	try {
 		process.env.XDG_STATE_HOME = state;
 		delete process.env.ATOMIC_WORKFLOW_JOURNAL_PATH;
-		harnessFor({ harness: "atomic", harnessAuth: "ai-gateway", host: "0.0.0.0" });
 		if (process.platform === "linux") {
-			expect(journal()).toBe(join(state, "chopin", "atomic", "workflows.sqlite"));
+			expect(workflowJournal()).toBe(join(state, "chopin", "atomic", "workflows.sqlite"));
 		}
+		// Each Planner session is given its journal; the process environment is left alone.
+		harnessFor({ harness: "atomic", harnessAuth: "ai-gateway", host: "0.0.0.0" });
+		expect(process.env.ATOMIC_WORKFLOW_JOURNAL_PATH).toBeUndefined();
 		await shutdownHarnesses();
-		expect(journal()).toBeUndefined();
 
 		process.env.ATOMIC_WORKFLOW_JOURNAL_PATH = "/srv/atomic/runs.sqlite";
+		expect(workflowJournal()).toBe("/srv/atomic/runs.sqlite");
 		harnessFor({ harness: "atomic", harnessAuth: "ai-gateway", host: "0.0.0.0" });
-		expect(journal()).toBe("/srv/atomic/runs.sqlite");
+		await shutdownHarnesses();
+		expect(process.env.ATOMIC_WORKFLOW_JOURNAL_PATH).toBe("/srv/atomic/runs.sqlite");
 	} finally {
 		await shutdownHarnesses();
 		restore("XDG_STATE_HOME", previous.state);

apps/server/src/harness/harnesses.ts

@@ -22,7 +22,7 @@ function createAtomicHarness(
 	return createAtomicAdapter({
 		auth: settings.auth as AtomicAuthMode,
 		extensions: settings.extensions,
-		journal: process.env.ATOMIC_WORKFLOW_JOURNAL_PATH || workflowJournal(),
+		journal: workflowJournal(),
 	});
 }
 

docs/hosted-agent.md

@@ -612,7 +612,9 @@ workflow journal, so runs interrupted that way can be resumed from a later
 session. Chopin keeps that journal at
 `$XDG_STATE_HOME/chopin/atomic/workflows.sqlite` under the same per-user state
 directory as the documents' own directories, because a run resumes only with
-the journal and working directory it started in. A non-empty
+the journal and working directory it started in. Each Planner session is
+given that file through Atomic's `createAgentSession({ journal })`, so the
+server's process environment is left unchanged. An operator's non-empty
 `ATOMIC_WORKFLOW_JOURNAL_PATH` names another file instead; Atomic's
 `workflows.journal` setting is not used for Planner sessions. A Build is not a workflow run and has no card in Chat: its tasks, their
 state and pull requests show under **Build**, whichever machine runs it. The

docs/self-hosting.md

@@ -75,7 +75,7 @@ each owner's GitHub App user token and does not consume `HARNESS_AUTH`;
 setting `auto` on loopback passes the startup guard but does not enable host
 login in that adapter.
 
-`HARNESS=atomic` runs Atomic 0.9.38-alpha.9 in the Chopin server process through its
+`HARNESS=atomic` runs Atomic 0.9.39 in the Chopin server process through its
 headless SDK (`createAgentSession()`). It does not spawn the `atomic` CLI or use
 RPC mode.
 
@@ -152,7 +152,8 @@ Atomic caveats:
   x64, including glibc and musl native modules. Expect a larger image.
 - Atomic workflows need no database server. Their runs are journaled in a
   SQLite file, `$XDG_STATE_HOME/chopin/atomic/workflows.sqlite`, beside the
-  documents' Planner directories (see
+  documents' Planner directories, which Chopin passes to each Planner session
+  as its `journal` rather than through the process environment (see
   [Full Atomic Planner](hosted-agent.md#full-atomic-planner)). The Docker image
   sets `XDG_STATE_HOME=/var/lib/chopin`; mount a volume there to keep runs
   and those directories when the container is replaced.

package.json

@@ -66,7 +66,7 @@
 				"@ai-sdk/harness": "1.0.146",
 				"@ai-sdk/mcp": "2.0.72",
 				"@ai-sdk/sandbox-just-bash": "1.0.146",
-				"@bastani/atomic": "0.9.38-alpha.9",
+				"@bastani/atomic": "0.9.39",
 				"ai": "7.0.135",
 				"typebox": "1.3.7",
 				"zod": "4.4.3"