fix(migration): preserve custom pnpm overrides and peerDependencyRules

Move any remaining non-Vite pnpm.overrides from package.json to
pnpm-workspace.yaml instead of leaving them behind. pnpm ignores
workspace-level overrides when pnpm.overrides exists in package.json,
even with unrelated entries, so all overrides must live in the
workspace yaml.

Also surgically remove only Vite-managed entries from
pnpm.peerDependencyRules instead of deleting the entire object,
preserving any custom rules the project already had.

Author: fengmk2

packages/cli/snap-tests-global/migration-monorepo-pnpm-overrides-dependency-selector/snap.txt

@@ -31,13 +31,7 @@ export default defineConfig({
     "vite": "catalog:",
     "vite-plus": "catalog:"
   },
-  "packageManager": "pnpm@<semver>+sha512.cf9998222162dd85864d0a8102e7892e7ba4ceadebbf5a31f9c2fce48dfce317a9c53b9f6464d1ef9042cba2e02ae02a9f7c143a2b438cd93c91840f0192b9dd",
-  "pnpm": {
-    "overrides": {
-      "react-click-away-listener>react": "0.0.0-experimental-7dc903cd-20251203",
-      "supertest>superagent": "9.0.2"
-    }
-  }
+  "packageManager": "pnpm@<semver>+sha512.cf9998222162dd85864d0a8102e7892e7ba4ceadebbf5a31f9c2fce48dfce317a9c53b9f6464d1ef9042cba2e02ae02a9f7c143a2b438cd93c91840f0192b9dd"
 }
 
 > cat pnpm-workspace.yaml # check pnpm-workspace.yaml
@@ -54,6 +48,7 @@ overrides:
   'supertest>superagent': '9.0.2'
   vite: 'catalog:'
   vitest: 'catalog:'
+  react-click-away-listener>react: <semver>
 peerDependencyRules:
   allowAny:
     - vite

packages/cli/src/migration/migrator.ts

@@ -700,6 +700,7 @@ export function rewriteStandaloneProject(
     rewritePnpmWorkspaceYaml(projectPath);
   }
   let extractedStagedConfig: Record<string, string | string[]> | null = null;
+  let remainingPnpmOverrides: Record<string, string> | undefined;
   editJsonFile<{
     overrides?: Record<string, string>;
     resolutions?: Record<string, string>;
@@ -739,22 +740,40 @@ export function rewriteStandaloneProject(
           },
         };
       } else {
-        // pnpm uses overrides/peerDependencyRules from pnpm-workspace.yaml
-        // clean up any existing entries from package.json
+        // Remove Vite-managed keys from pnpm.overrides
         for (const key of [...overrideKeys, ...REMOVE_PACKAGES]) {
           if (pkg.pnpm?.overrides?.[key]) {
             delete pkg.pnpm.overrides[key];
           }
         }
-        delete pkg.pnpm?.peerDependencyRules;
-        if (pkg.pnpm?.overrides && Object.keys(pkg.pnpm.overrides).length === 0) {
-          delete pkg.pnpm.overrides;
+        // Remove dependency selectors targeting vite
+        for (const key in pkg.pnpm?.overrides) {
+          if (key.includes('>')) {
+            const splits = key.split('>');
+            if (splits[splits.length - 1].trim() === 'vite') {
+              delete pkg.pnpm.overrides[key];
+            }
+          }
+        }
+        // Move any remaining overrides to pnpm-workspace.yaml then delete all
+        // (pnpm ignores workspace-level overrides when pnpm.overrides exists in package.json)
+        if (pkg.pnpm?.overrides && Object.keys(pkg.pnpm.overrides).length > 0) {
+          remainingPnpmOverrides = { ...pkg.pnpm.overrides };
+        }
+        delete pkg.pnpm?.overrides;
+        // Only remove Vite-managed peerDependencyRules entries, preserve custom ones
+        cleanupPeerDependencyRules(pkg.pnpm?.peerDependencyRules, overrideKeys);
+        if (
+          pkg.pnpm?.peerDependencyRules &&
+          Object.keys(pkg.pnpm.peerDependencyRules).length === 0
+        ) {
+          delete pkg.pnpm.peerDependencyRules;
         }
         if (pkg.pnpm && Object.keys(pkg.pnpm).length === 0) {
           delete pkg.pnpm;
         }
       }
-      // remove dependency selector from vite, e.g. "vite-plugin-svgr>vite"
+      // remove dependency selector from vite in force-override mode
       for (const key in pkg.pnpm?.overrides) {
         if (key.includes('>')) {
           const splits = key.split('>');
@@ -784,6 +803,11 @@ export function rewriteStandaloneProject(
     return pkg;
   });
 
+  // Move remaining non-Vite pnpm.overrides to pnpm-workspace.yaml
+  if (remainingPnpmOverrides) {
+    migratePnpmOverridesToWorkspaceYaml(projectPath, remainingPnpmOverrides);
+  }
+
   // Merge extracted staged config into vite.config.ts, then remove lint-staged from package.json
   if (extractedStagedConfig) {
     if (mergeStagedConfigToViteConfig(projectPath, extractedStagedConfig, silent, report)) {
@@ -983,6 +1007,55 @@ function rewritePnpmWorkspaceYaml(projectPath: string): void {
   });
 }
 
+/**
+ * Move remaining non-Vite pnpm.overrides from package.json to pnpm-workspace.yaml.
+ * pnpm ignores workspace-level overrides when pnpm.overrides exists in package.json,
+ * so all overrides must live in pnpm-workspace.yaml.
+ */
+function migratePnpmOverridesToWorkspaceYaml(
+  projectPath: string,
+  overrides: Record<string, string>,
+): void {
+  const pnpmWorkspaceYamlPath = path.join(projectPath, 'pnpm-workspace.yaml');
+  editYamlFile(pnpmWorkspaceYamlPath, (doc) => {
+    for (const [key, value] of Object.entries(overrides)) {
+      if (!doc.hasIn(['overrides', key])) {
+        doc.setIn(['overrides', scalarString(key)], scalarString(value));
+      }
+    }
+  });
+}
+
+/**
+ * Remove only Vite-managed entries from peerDependencyRules, preserving custom ones.
+ */
+function cleanupPeerDependencyRules(
+  peerDependencyRules:
+    | { allowAny?: string[]; allowedVersions?: Record<string, string> }
+    | undefined,
+  overrideKeys: string[],
+): void {
+  if (!peerDependencyRules) {
+    return;
+  }
+  if (Array.isArray(peerDependencyRules.allowAny)) {
+    peerDependencyRules.allowAny = peerDependencyRules.allowAny.filter(
+      (key) => !overrideKeys.includes(key),
+    );
+    if (peerDependencyRules.allowAny.length === 0) {
+      delete peerDependencyRules.allowAny;
+    }
+  }
+  if (peerDependencyRules.allowedVersions) {
+    for (const key of overrideKeys) {
+      delete peerDependencyRules.allowedVersions[key];
+    }
+    if (Object.keys(peerDependencyRules.allowedVersions).length === 0) {
+      delete peerDependencyRules.allowedVersions;
+    }
+  }
+}
+
 /**
  * Rewrite .yarnrc.yml to add vite-plus dependencies
  * @param projectPath - The path to the project
@@ -1085,13 +1158,17 @@ function rewriteRootWorkspacePackageJson(
     return;
   }
 
+  let remainingPnpmOverrides: Record<string, string> | undefined;
   editJsonFile<{
     resolutions?: Record<string, string>;
     overrides?: Record<string, string>;
     devDependencies?: Record<string, string>;
     pnpm?: {
       overrides?: Record<string, string>;
-      peerDependencyRules?: Record<string, unknown>;
+      peerDependencyRules?: {
+        allowAny?: string[];
+        allowedVersions?: Record<string, string>;
+      };
     };
   }>(packageJsonPath, (pkg) => {
     if (packageManager === PackageManager.yarn) {
@@ -1109,6 +1186,7 @@ function rewriteRootWorkspacePackageJson(
     } else if (packageManager === PackageManager.bun) {
       // bun overrides are handled in rewriteBunCatalog() with catalog: references
     } 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
@@ -1122,27 +1200,43 @@ function rewriteRootWorkspacePackageJson(
           },
         };
       } else {
-        // pnpm use overrides field at pnpm-workspace.yaml
-        // so we don't need to set overrides field at package.json
-        // remove packages from `resolutions` field and `pnpm.overrides` field if they exist
-        // https://pnpm.io/9.x/package_json#resolutions
-        for (const key of [...Object.keys(VITE_PLUS_OVERRIDE_PACKAGES), ...REMOVE_PACKAGES]) {
+        // Remove Vite-managed keys from pnpm.overrides
+        for (const key of [...overrideKeys, ...REMOVE_PACKAGES]) {
           if (pkg.pnpm?.overrides?.[key]) {
             delete pkg.pnpm.overrides[key];
           }
           if (pkg.resolutions?.[key]) {
             delete pkg.resolutions[key];
           }
         }
-        delete pkg.pnpm?.peerDependencyRules;
-        if (pkg.pnpm?.overrides && Object.keys(pkg.pnpm.overrides).length === 0) {
-          delete pkg.pnpm.overrides;
+        // Remove dependency selectors targeting vite
+        for (const key in pkg.pnpm?.overrides) {
+          if (key.includes('>')) {
+            const splits = key.split('>');
+            if (splits[splits.length - 1].trim() === 'vite') {
+              delete pkg.pnpm.overrides[key];
+            }
+          }
+        }
+        // Move any remaining overrides to pnpm-workspace.yaml then delete all
+        // (pnpm ignores workspace-level overrides when pnpm.overrides exists in package.json)
+        if (pkg.pnpm?.overrides && Object.keys(pkg.pnpm.overrides).length > 0) {
+          remainingPnpmOverrides = { ...pkg.pnpm.overrides };
+        }
+        delete pkg.pnpm?.overrides;
+        // Only remove Vite-managed peerDependencyRules entries, preserve custom ones
+        cleanupPeerDependencyRules(pkg.pnpm?.peerDependencyRules, overrideKeys);
+        if (
+          pkg.pnpm?.peerDependencyRules &&
+          Object.keys(pkg.pnpm.peerDependencyRules).length === 0
+        ) {
+          delete pkg.pnpm.peerDependencyRules;
         }
         if (pkg.pnpm && Object.keys(pkg.pnpm).length === 0) {
           delete pkg.pnpm;
         }
       }
-      // remove dependency selector from vite, e.g. "vite-plugin-svgr>vite": "npm:vite@7.0.12"
+      // remove dependency selector from vite in force-override mode
       for (const key in pkg.pnpm?.overrides) {
         if (key.includes('>')) {
           const splits = key.split('>');
@@ -1166,6 +1260,11 @@ function rewriteRootWorkspacePackageJson(
     return pkg;
   });
 
+  // Move remaining non-Vite pnpm.overrides to pnpm-workspace.yaml
+  if (remainingPnpmOverrides) {
+    migratePnpmOverridesToWorkspaceYaml(projectPath, remainingPnpmOverrides);
+  }
+
   // rewrite package.json
   rewriteMonorepoProject(projectPath, packageManager, skipStagedMigration);
 }