fix(migration): respect existing pnpm config location in package.json

When a project already has a "pnpm" field in package.json (e.g., with
overrides, ignoredBuiltDependencies), keep using package.json for pnpm
config instead of creating a new pnpm-workspace.yaml. Only use
pnpm-workspace.yaml for projects without existing pnpm config.

This fixes ecosystem CI failures where projects with existing
pnpm.overrides in package.json (like dify) broke when overrides were
moved to pnpm-workspace.yaml, since pnpm doesn't properly apply file:
overrides from workspace yaml to transitive dependencies.

Author: fengmk2

packages/cli/src/migration/__tests__/__snapshots__/migrator.spec.ts.snap

@@ -28,7 +28,7 @@ exports[`rewritePackageJson > should rewrite devDependencies and dependencies on
     "foo": "1.0.0",
   },
   "devDependencies": {
-    "vite-plus": "catalog:",
+    "vite-plus": "latest",
   },
 }
 `;

packages/cli/src/migration/migrator.ts

@@ -696,7 +696,11 @@ export function rewriteStandaloneProject(
   }
 
   const packageManager = workspaceInfo.packageManager;
-  if (packageManager === PackageManager.pnpm) {
+  // Respect the project's existing pnpm config location: if package.json already
+  // has a "pnpm" field, keep using package.json; otherwise use pnpm-workspace.yaml.
+  const existingPkg = readJsonFile(packageJsonPath);
+  const usePnpmWorkspaceYaml = packageManager === PackageManager.pnpm && !existingPkg.pnpm;
+  if (usePnpmWorkspaceYaml) {
     rewritePnpmWorkspaceYaml(projectPath);
   }
   let extractedStagedConfig: Record<string, string | string[]> | null = null;
@@ -727,16 +731,23 @@ export function rewriteStandaloneProject(
       };
     } else if (packageManager === PackageManager.pnpm) {
       const overrideKeys = Object.keys(VITE_PLUS_OVERRIDE_PACKAGES);
-      if (isForceOverrideMode()) {
-        // In force-override mode, keep overrides in package.json pnpm.overrides
-        // because pnpm ignores pnpm-workspace.yaml overrides when pnpm.overrides
-        // exists in package.json (even with unrelated entries like rollup).
+      if (!usePnpmWorkspaceYaml) {
+        // Project already has pnpm config in package.json — keep using it.
         pkg.pnpm = {
           ...pkg.pnpm,
           overrides: {
             ...pkg.pnpm?.overrides,
             ...VITE_PLUS_OVERRIDE_PACKAGES,
-            [VITE_PLUS_NAME]: VITE_PLUS_VERSION,
+            ...(isForceOverrideMode() ? { [VITE_PLUS_NAME]: VITE_PLUS_VERSION } : {}),
+          },
+          peerDependencyRules: {
+            allowAny: [
+              ...new Set([...(pkg.pnpm?.peerDependencyRules?.allowAny ?? []), ...overrideKeys]),
+            ],
+            allowedVersions: {
+              ...pkg.pnpm?.peerDependencyRules?.allowedVersions,
+              ...Object.fromEntries(overrideKeys.map((key) => [key, '*'])),
+            },
           },
         };
       } else {
@@ -791,12 +802,17 @@ export function rewriteStandaloneProject(
       }
     }
 
-    extractedStagedConfig = rewritePackageJson(pkg, packageManager, false, skipStagedMigration);
+    extractedStagedConfig = rewritePackageJson(
+      pkg,
+      packageManager,
+      usePnpmWorkspaceYaml,
+      skipStagedMigration,
+    );
 
     // ensure vite-plus is in devDependencies
     if (!pkg.devDependencies?.[VITE_PLUS_NAME] || isForceOverrideMode()) {
       const version =
-        packageManager === PackageManager.pnpm && !VITE_PLUS_VERSION.startsWith('file:')
+        usePnpmWorkspaceYaml && !VITE_PLUS_VERSION.startsWith('file:')
           ? 'catalog:'
           : VITE_PLUS_VERSION;
       pkg.devDependencies = {
@@ -1329,8 +1345,7 @@ export function rewritePackageJson(
     const updated = rewriteScripts(JSON.stringify(config), readRulesYaml());
     extractedStagedConfig = updated ? JSON.parse(updated) : config;
   }
-  const supportCatalog =
-    packageManager === PackageManager.pnpm || (isMonorepo && packageManager !== PackageManager.npm);
+  const supportCatalog = isMonorepo && packageManager !== PackageManager.npm;
   let needVitePlus = false;
   for (const [key, version] of Object.entries(VITE_PLUS_OVERRIDE_PACKAGES)) {
     const value = supportCatalog && !version.startsWith('file:') ? 'catalog:' : version;