From 2d0d546734a4a56e9497be96524529efc504a93a Mon Sep 17 00:00:00 2001
From: Dotta <bippadotta@protonmail.com>
Date: Mon, 20 Jul 2026 14:06:30 +0000
Subject: [PATCH] fix(cli): stamp quarantined runs with seed epoch

Co-Authored-By: Paperclip <noreply@paperclip.ing>
---
 cli/src/__tests__/worktree.test.ts |  8 ++++++++
 cli/src/commands/worktree.ts       | 22 ++++++++++++++++++++++
 2 files changed, 30 insertions(+)

diff --git a/cli/src/__tests__/worktree.test.ts b/cli/src/__tests__/worktree.test.ts
index a67dffe5d16..7330ec785cc 100644
--- a/cli/src/__tests__/worktree.test.ts
+++ b/cli/src/__tests__/worktree.test.ts
@@ -1410,11 +1410,19 @@ describe("worktree helpers", () => {
       for (const run of quarantinedRuns) {
         expect(run.status).toBe("cancelled");
         expect(run.errorCode).toBe("worktree_seed_quarantine");
+        expect(run.seedEpoch).toEqual(expect.any(String));
         expect(run.processPid).toBeNull();
         expect(run.processGroupId).toBeNull();
         expect(run.finishedAt).toBeInstanceOf(Date);
       }
 
+      const [seededSettings] = await db.select().from(instanceSettings);
+      const seededExperimental = seededSettings?.experimental as Record<string, unknown>;
+      expect(quarantinedRuns.map((run) => run.seedEpoch)).toEqual([
+        seededExperimental.worktreeRunExecutionSeedEpoch,
+        seededExperimental.worktreeRunExecutionSeedEpoch,
+      ]);
+
       const [succeededRun] = await db.select().from(heartbeatRuns).where(eq(heartbeatRuns.id, succeededRunId));
       expect(succeededRun?.status).toBe("succeeded");
       expect(succeededRun?.wakeupRequestId).toBe(completedWakeupId);
diff --git a/cli/src/commands/worktree.ts b/cli/src/commands/worktree.ts
index 5efcea5db2c..529f7be44d0 100644
--- a/cli/src/commands/worktree.ts
+++ b/cli/src/commands/worktree.ts
@@ -1336,6 +1336,27 @@ export async function quarantineSeededWorktreeExecutionState(
   try {
     await db.transaction(async (tx) => {
       const now = new Date();
+      const [settingsRow] = await tx
+        .select({ id: instanceSettings.id, experimental: instanceSettings.experimental })
+        .from(instanceSettings)
+        .where(eq(instanceSettings.singletonKey, "default"))
+        .limit(1);
+      const experimental = isRecord(settingsRow?.experimental) ? settingsRow.experimental : {};
+      const existingSeedEpoch = experimental.worktreeRunExecutionSeedEpoch;
+      const seedEpoch = typeof existingSeedEpoch === "string" && existingSeedEpoch.length > 0
+        ? existingSeedEpoch
+        : randomUUID();
+
+      if (settingsRow && seedEpoch !== existingSeedEpoch) {
+        await tx
+          .update(instanceSettings)
+          .set({
+            experimental: { ...experimental, worktreeRunExecutionSeedEpoch: seedEpoch },
+            updatedAt: now,
+          })
+          .where(eq(instanceSettings.id, settingsRow.id));
+      }
+
       const pendingWakeups = await tx
         .select({ id: agentWakeupRequests.id })
         .from(agentWakeupRequests)
@@ -1354,6 +1375,7 @@ export async function quarantineSeededWorktreeExecutionState(
         .set({
           status: "cancelled",
           errorCode: WORKTREE_SEED_QUARANTINE_ERROR_CODE,
+          seedEpoch,
           processPid: null,
           processGroupId: null,
           scheduledRetryAt: null,