fix: reconcile run provenance with current master

Co-Authored-By: Paperclip <noreply@paperclip.ing>

cli/src/__tests__/worktree.test.ts

@@ -85,6 +85,9 @@ function mockVerifiedSeedResult() {
     migrationRevision: "0142_test.sql",
     pausedScheduledRoutines: 0,
     executionQuarantine: {
+      cancelledHeartbeatRuns: 0,
+      deletedPendingWakeups: 0,
+      clearedIssueMonitors: 0,
       disabledTimerHeartbeats: 0,
       resetRunningAgents: 0,
       quarantinedInProgressIssues: 0,
@@ -662,6 +665,9 @@ describe("worktree helpers", () => {
         ...mockVerifiedSeedResult(),
         pausedScheduledRoutines: 2,
         executionQuarantine: {
+          cancelledHeartbeatRuns: 1,
+          deletedPendingWakeups: 1,
+          clearedIssueMonitors: 1,
           disabledTimerHeartbeats: 1,
           resetRunningAgents: 1,
           quarantinedInProgressIssues: 1,
@@ -1490,6 +1496,7 @@ describe("worktree helpers", () => {
           experimental: {
             enableWorktreeRunExecution: true,
             worktreeRunExecutionInstanceNonce: "9ed115ac-9e93-4fe9-a4f1-eb4ea2b0fb24",
+            worktreeRunExecutionSeedEpoch: "cb1137c7-5630-44b9-a213-762203cc4a38",
             worktreeRunExecutionActivatedAt: "2026-07-16T12:00:00.000Z",
             worktreeRunExecutionActivationInstanceId: "source-instance",
             enableSmokeLab: true,
@@ -1503,6 +1510,7 @@ describe("worktree helpers", () => {
       expect(settings?.experimental).toMatchObject({
         enableWorktreeRunExecution: false,
         worktreeRunExecutionInstanceNonce: null,
+        worktreeRunExecutionSeedEpoch: expect.any(String),
         worktreeRunExecutionActivatedAt: null,
         worktreeRunExecutionActivationInstanceId: null,
         enableSmokeLab: true,

cli/src/commands/worktree.ts

@@ -18,7 +18,6 @@ import path from "node:path";
 import { execFileSync } from "node:child_process";
 import { randomUUID } from "node:crypto";
 import { createServer } from "node:net";
-import { randomUUID } from "node:crypto";
 import { Readable } from "node:stream";
 import * as p from "@clack/prompts";
 import pc from "picocolors";
@@ -1494,7 +1493,6 @@ export async function quarantineSeededWorktreeExecutionState(
         summary.stoppedExecutionWorkspaceRuntimes += 1;
       }
 
-      const now = new Date();
       const stoppedRuntimeServices = await tx
         .update(workspaceRuntimeServices)
         .set({
@@ -4370,7 +4368,7 @@ async function backupWorktreeReseedTarget(input: {
 }
 
 async function runWorktreeReseed(opts: WorktreeReseedOptions): Promise<void> {
-  const seedMode = opts.seedMode ?? "minimal";
+  const seedMode = opts.seedMode ?? "full";
   if (!isWorktreeSeedMode(seedMode)) {
     throw new Error(`Unsupported seed mode "${seedMode}". Expected one of: minimal, full.`);
   }

server/src/__tests__/instance-settings-service.test.ts

@@ -7,6 +7,7 @@ import {
 } from "../services/instance-settings.js";
 
 const INSTANCE_NONCE = "9ed115ac-9e93-4fe9-a4f1-eb4ea2b0fb24";
+const SEED_EPOCH = "4dcd3d50-ff32-4a71-aee6-69aac032e1e6";
 
 describe("instance settings service", () => {
   it("ignores retired experimental flags without resetting current settings", () => {
@@ -57,6 +58,7 @@ describe("instance settings service", () => {
       enableSandboxDuplexBridge: false,
       enableWorktreeRunExecution: false,
       worktreeRunExecutionInstanceNonce: null,
+      worktreeRunExecutionSeedEpoch: null,
       worktreeRunExecutionActivatedAt: null,
       worktreeRunExecutionActivationInstanceId: null,
       issueGraphLivenessAutoRecoveryLookbackHours: 48,
@@ -198,6 +200,7 @@ describe("instance settings service", () => {
       {
         enableWorktreeRunExecution: false,
         worktreeRunExecutionInstanceNonce: INSTANCE_NONCE,
+        worktreeRunExecutionSeedEpoch: SEED_EPOCH,
       },
       { enableWorktreeRunExecution: true },
       {
@@ -219,6 +222,7 @@ describe("instance settings service", () => {
       {
         enableWorktreeRunExecution: true,
         worktreeRunExecutionInstanceNonce: INSTANCE_NONCE,
+        worktreeRunExecutionSeedEpoch: SEED_EPOCH,
         worktreeRunExecutionActivatedAt: "2026-07-10T12:00:00.000Z",
         worktreeRunExecutionActivationInstanceId: INSTANCE_NONCE,
       },
@@ -241,6 +245,7 @@ describe("instance settings service", () => {
       {
         enableWorktreeRunExecution: false,
         worktreeRunExecutionInstanceNonce: INSTANCE_NONCE,
+        worktreeRunExecutionSeedEpoch: SEED_EPOCH,
       },
       { enableWorktreeRunExecution: true },
       {
@@ -286,6 +291,7 @@ describe("instance settings service", () => {
       {
         enableWorktreeRunExecution: false,
         worktreeRunExecutionInstanceNonce: "e7904e84-5d6a-44af-bd5f-1c93d9636bc3",
+        worktreeRunExecutionSeedEpoch: "cb1137c7-5630-44b9-a213-762203cc4a38",
         worktreeRunExecutionActivatedAt: "2026-07-10T12:00:00.000Z",
         worktreeRunExecutionActivationInstanceId: "copied-instance",
       },
@@ -300,12 +306,14 @@ describe("instance settings service", () => {
     expect(next.worktreeRunExecutionActivatedAt).toBeNull();
     expect(next.worktreeRunExecutionActivationInstanceId).toBeNull();
     expect(next.worktreeRunExecutionInstanceNonce).toBeNull();
+    expect(next.worktreeRunExecutionSeedEpoch).toBeNull();
   });
 
   it("resolves worktree run execution as armed only when the cutoff matches the current instance", async () => {
     const experimental = normalizeExperimentalSettings({
       enableWorktreeRunExecution: true,
       worktreeRunExecutionInstanceNonce: INSTANCE_NONCE,
+      worktreeRunExecutionSeedEpoch: SEED_EPOCH,
       worktreeRunExecutionActivatedAt: "2026-07-10T12:00:00.000Z",
       worktreeRunExecutionActivationInstanceId: INSTANCE_NONCE,
     });
@@ -322,6 +330,8 @@ describe("instance settings service", () => {
       armed: true,
       cutoff: "2026-07-10T12:00:00.000Z",
       activationInstanceId: INSTANCE_NONCE,
+      instanceNonce: INSTANCE_NONCE,
+      seedEpoch: SEED_EPOCH,
       reason: null,
     });
   });
@@ -330,6 +340,7 @@ describe("instance settings service", () => {
     const experimental = normalizeExperimentalSettings({
       enableWorktreeRunExecution: true,
       worktreeRunExecutionInstanceNonce: INSTANCE_NONCE,
+      worktreeRunExecutionSeedEpoch: SEED_EPOCH,
       worktreeRunExecutionActivationInstanceId: INSTANCE_NONCE,
     });
 
@@ -352,6 +363,7 @@ describe("instance settings service", () => {
     const experimental = normalizeExperimentalSettings({
       enableWorktreeRunExecution: true,
       worktreeRunExecutionInstanceNonce: INSTANCE_NONCE,
+      worktreeRunExecutionSeedEpoch: SEED_EPOCH,
       worktreeRunExecutionActivatedAt: "2026-07-10T12:00:00.000Z",
       worktreeRunExecutionActivationInstanceId: "f6690751-2ed0-4113-9403-241c2cc3ace9",
     });

server/src/__tests__/routines-service.test.ts

@@ -214,6 +214,7 @@ describeEmbeddedPostgres("routine service live-execution coalescing", () => {
     const experimental = {
       enableWorktreeRunExecution: true,
       worktreeRunExecutionInstanceNonce: instanceId,
+      worktreeRunExecutionSeedEpoch: "00000000-0000-4000-8000-000000000002",
       worktreeRunExecutionActivatedAt: cutoff.toISOString(),
       worktreeRunExecutionActivationInstanceId: instanceId,
     };

server/src/__tests__/workspace-runtime.test.ts

@@ -4619,7 +4619,7 @@ describe("ensureRuntimeServicesForRun", () => {
     // A Paperclip dev runtime must answer `/api/health` semantically before it may
     // be published, so the fake serves the same shape a real one does.
     const serviceCommand =
-      "node -e \"require('node:http').createServer((req,res)=>{if(req.url==='/api/health'){res.setHeader('content-type','application/json');res.end(JSON.stringify({status:'ok'}));return;}res.end(process.env.PAPERCLIP_HOME)}).listen(Number(process.env.PORT), '127.0.0.1')\"";
+      "node -e \"require('node:http').createServer((req,res)=>{if(req.url==='/api/health'){res.setHeader('content-type','application/json');res.end(JSON.stringify({status:'ok'}));return;}res.end(process.env.WORKSPACE_MARKER)}).listen(Number(process.env.PORT), '127.0.0.1')\"";
     const config = {
       workspaceRuntime: {
         services: [