FN-5794: run worktree init for fresh merge workspaces

Run merge worktree initialization automatically when a merge workspace is newly created.

- detect when integration worktree creation is fresh and invoke the configured init command
- preserve existing behavior for already-initialized worktrees while improving setup reliability
- add integration tests covering init command execution paths for merge worktree setup

Files changed:
 .changeset/fn-5794-merge-worktree-init.md          |  5 +++
 .../__tests__/merger-integration-worktree.test.ts  | 16 +++++++++
 packages/engine/src/merger.ts                      | 39 +++++++++++++++++++++-
 3 files changed, 59 insertions(+), 1 deletion(-)

Fusion-Task-Id: FN-5794

Fusion-Task-Lineage: f368099f-a179-466e-b994-2a503167112c

.changeset/fn-5794-merge-worktree-init.md

@@ -0,0 +1,5 @@
+---
+"@runfusion/fusion": patch
+---
+
+Run the configured `worktreeInitCommand` when the merger has to create a fresh merge worktree during reuse-worktree reacquisition. This bootstraps newly created merge workspaces before merge verification/workflow steps run, while leaving pooled/reused existing worktrees unchanged.

packages/engine/src/__tests__/merger-integration-worktree.test.ts

@@ -1,4 +1,5 @@
 import { beforeEach, describe, expect, it, vi } from "vitest";
+import { readFileSync } from "node:fs";
 
 import {
   createMockStore,
@@ -222,6 +223,21 @@ describe("probeIntegrationWorktreeState", () => {
   });
 });
 
+describe("merger fresh reacquire init wiring", () => {
+  it("wires fresh acquireTaskWorktree calls with init command execution", () => {
+    const mergerSource = readFileSync(new URL("../merger.ts", import.meta.url), "utf-8");
+    const freshAcquireBlock = mergerSource.match(/const acquisition = await acquireTaskWorktree\(\{[\s\S]*?\n\s*\}\);/);
+    expect(freshAcquireBlock?.[0]).toContain("runInitCommand: true");
+    expect(freshAcquireBlock?.[0]).toContain("runConfiguredCommand:");
+    expect(freshAcquireBlock?.[0]).toContain("runConfiguredMergeWorktreeCommand");
+  });
+
+  it("keeps direct-reuse shortcut on existing registrations", () => {
+    const mergerSource = readFileSync(new URL("../merger.ts", import.meta.url), "utf-8");
+    expect(mergerSource).toContain("Skip acquireTaskWorktree's");
+  });
+});
+
 describe("acquireReuseHandoff", () => {
   beforeEach(() => {
     vi.clearAllMocks();

packages/engine/src/merger.ts

@@ -7781,7 +7781,9 @@ export async function aiMergeTask(
       logger: mergerLog,
       audit,
       runContext: engineRunContext,
-      runInitCommand: false,
+      runInitCommand: true,
+      runConfiguredCommand: async (command, cwd, timeoutMs, env) =>
+        runConfiguredMergeWorktreeCommand(command, cwd, timeoutMs, env, audit),
       createWorktree: async (branch, path, _taskId, _startPoint, _allowSiblingBranchRename) => {
         await execAsync(`git worktree add -f ${quoteArg(path)} ${quoteArg(branch)}`, {
           cwd: projectRootDir,
@@ -11929,6 +11931,41 @@ function getPostMergeScriptSandboxBackend(auditor?: RunAuditor): SandboxBackend
   return resolveSandboxBackend({ auditor });
 }
 
+async function runConfiguredMergeWorktreeCommand(
+  command: string,
+  cwd: string,
+  timeoutMs: number,
+  extraEnv?: NodeJS.ProcessEnv,
+  auditor?: RunAuditor,
+): Promise<{
+  stdout?: string;
+  stderr?: string;
+  exitCode?: number | null;
+  signal?: NodeJS.Signals | null;
+  timedOut?: boolean;
+  bufferExceeded?: boolean;
+  spawnError?: Error;
+}> {
+  const backend = getPostMergeScriptSandboxBackend(auditor);
+  const result = await backend.run(command, {
+    cwd,
+    encoding: "utf-8",
+    timeoutMs,
+    maxBuffer: 10 * 1024 * 1024,
+    ...(extraEnv !== undefined && { env: extraEnv }),
+  });
+
+  return {
+    stdout: result.stdout,
+    stderr: result.stderr,
+    exitCode: result.exitCode,
+    signal: result.signal,
+    timedOut: result.timedOut,
+    bufferExceeded: result.bufferExceeded,
+    spawnError: result.spawnError,
+  };
+}
+
 /** Execute a script-mode post-merge workflow step in the provided execution directory. */
 async function executePostMergeScriptStep(
   store: TaskStore,