Copy PNPM patches to isolated directory

.claude/CLAUDE.md

@@ -89,3 +89,7 @@ The codebase uses `~/` as path alias for `src/` (configured in tsconfig.json).
 ## Testing
 
 Tests use Vitest and are co-located with source files (`*.test.ts`).
+
+## Code Style
+
+- Use JSDoc style comments (`/** ... */`) for all comments, including single-line comments

package.json

@@ -1,6 +1,6 @@
 {
   "name": "isolate-package",
-  "version": "1.26.1",
+  "version": "1.27.0-0",
   "description": "Isolate a monorepo package with its shared dependencies to form a self-contained directory, compatible with Firebase deploy",
   "author": "Thijs Koerselman",
   "license": "MIT",

src/isolate.ts

@@ -22,6 +22,7 @@ import {
 } from "./lib/output";
 import { detectPackageManager, shouldUsePnpmPack } from "./lib/package-manager";
 import { getVersion } from "./lib/package-manager/helpers/infer-from-files";
+import { copyPatches } from "./lib/patches/copy-patches";
 import { createPackagesRegistry, listInternalPackages } from "./lib/registry";
 import type { PackageManifest } from "./lib/types";
 import {
@@ -211,15 +212,39 @@ export function createIsolator(config?: IsolateConfig) {
       config,
     });
 
-    if (usedFallbackToNpm) {
-      /**
-       * When we fall back to NPM, we set the manifest package manager to the
-       * available NPM version.
-       */
+    /** Copy patch files if includePatchedDependencies is enabled */
+    const copiedPatches = await copyPatches({
+      workspaceRootDir,
+      targetPackageManifest: outputManifest,
+      isolateDir,
+      includePatchedDependencies: config.includePatchedDependencies,
+      includeDevDependencies: config.includeDevDependencies,
+    });
+
+    const hasCopiedPatches = Object.keys(copiedPatches).length > 0;
+
+    /** Update manifest if patches were copied or npm fallback is needed */
+    if (hasCopiedPatches || usedFallbackToNpm) {
       const manifest = await readManifest(isolateDir);
 
-      const npmVersion = getVersion("npm");
-      manifest.packageManager = `npm@${npmVersion}`;
+      if (hasCopiedPatches) {
+        if (!manifest.pnpm) {
+          manifest.pnpm = {};
+        }
+        manifest.pnpm.patchedDependencies = copiedPatches;
+        log.debug(
+          `Added ${Object.keys(copiedPatches).length} patches to isolated package.json`
+        );
+      }
+
+      if (usedFallbackToNpm) {
+        /**
+         * When we fall back to NPM, we set the manifest package manager to the
+         * available NPM version.
+         */
+        const npmVersion = getVersion("npm");
+        manifest.packageManager = `npm@${npmVersion}`;
+      }
 
       await writeManifest(isolateDir, manifest);
     }
@@ -286,7 +311,7 @@ export function createIsolator(config?: IsolateConfig) {
   };
 }
 
-// Keep the original function for backward compatibility
+/** Keep the original function for backward compatibility */
 export async function isolate(config?: IsolateConfig): Promise<string> {
   return createIsolator(config)();
 }

src/lib/lockfile/helpers/generate-pnpm-lockfile.ts

@@ -15,7 +15,11 @@ import { pruneLockfile as pruneLockfile_v9 } from "pnpm_prune_lockfile_v9";
 import { pick } from "remeda";
 import { useLogger } from "~/lib/logger";
 import type { PackageManifest, PackagesRegistry } from "~/lib/types";
-import { getErrorMessage, isRushWorkspace } from "~/lib/utils";
+import {
+  filterPatchedDependencies,
+  getErrorMessage,
+  isRushWorkspace,
+} from "~/lib/utils";
 import { pnpmMapImporter } from "./pnpm-map-importer";
 
 export async function generatePnpmLockfile({
@@ -163,13 +167,18 @@ export async function generatePnpmLockfile({
     }
 
     /**
-     * Don't know how to map the patched dependencies yet, so we just include
-     * them but I don't think it would work like this. The important thing for
-     * now is that they are omitted by default, because that is the most common
-     * use case.
+     * Filter patched dependencies to only include patches for packages that
+     * will actually be present in the isolated lockfile based on dependency
+     * type. We read patchedDependencies from workspace root lockfile, but
+     * filter based on target package dependencies.
      */
     const patchedDependencies = includePatchedDependencies
-      ? lockfile.patchedDependencies
+      ? filterPatchedDependencies(
+          lockfile.patchedDependencies,
+          targetPackageManifest,
+          includeDevDependencies,
+          log
+        )
       : undefined;
 
     if (useVersion9) {

src/lib/lockfile/helpers/pnpm-map-importer.ts

@@ -50,7 +50,7 @@ function pnpmMapDependenciesLinks(
       return value;
     }
 
-    // Replace backslashes with forward slashes to support Windows Git Bash
+    /** Replace backslashes with forward slashes to support Windows Git Bash */
     const relativePath = path
       .relative(importerPath, got(directoryByPackageName, key))
       .replace(path.sep, path.posix.sep);