Add pnpm symlink support to package discovery

pnpm uses symlinks for package directories in node_modules, but the
package discovery logic only checked isDirectory() which returns false
for symlinks. This caused patches to fail with "No packages found"
error when using pnpm.

Also check isSymbolicLink() to support pnpm's symlink-based structure,
allowing patches to work correctly with pnpm, yarn, and npm.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Author: mikolalysenko

src/patch/apply.ts

@@ -32,6 +32,19 @@ export interface ApplyResult {
   error?: string
 }
 
+/**
+ * Normalize file path by removing the 'package/' prefix if present
+ * Patch files come from the API with paths like 'package/lib/file.js'
+ * but we need relative paths like 'lib/file.js' for the actual package directory
+ */
+function normalizeFilePath(fileName: string): string {
+  const packagePrefix = 'package/'
+  if (fileName.startsWith(packagePrefix)) {
+    return fileName.slice(packagePrefix.length)
+  }
+  return fileName
+}
+
 /**
  * Verify a single file can be patched
  */
@@ -40,7 +53,8 @@ export async function verifyFilePatch(
   fileName: string,
   fileInfo: PatchFileInfo,
 ): Promise<VerifyResult> {
-  const filepath = path.join(packagePath, fileName)
+  const normalizedFileName = normalizeFilePath(fileName)
+  const filepath = path.join(packagePath, normalizedFileName)
 
   // Check if file exists
   try {
@@ -94,7 +108,8 @@ export async function applyFilePatch(
   patchedContent: Buffer,
   expectedHash: string,
 ): Promise<void> {
-  const filepath = path.join(packagePath, fileName)
+  const normalizedFileName = normalizeFilePath(fileName)
+  const filepath = path.join(packagePath, normalizedFileName)
 
   // Write the patched content
   await fs.writeFile(filepath, patchedContent)
@@ -244,7 +259,8 @@ export async function findPackagesForPatches(
     const entries = await fs.readdir(nodeModulesPath, { withFileTypes: true })
 
     for (const entry of entries) {
-      if (!entry.isDirectory()) continue
+      // Allow both directories and symlinks (pnpm uses symlinks)
+      if (!entry.isDirectory() && !entry.isSymbolicLink()) continue
 
       const isScoped = entry.name.startsWith('@')
       const dirPath = path.join(nodeModulesPath, entry.name)
@@ -253,7 +269,8 @@ export async function findPackagesForPatches(
         // Handle scoped packages
         const scopedEntries = await fs.readdir(dirPath, { withFileTypes: true })
         for (const scopedEntry of scopedEntries) {
-          if (!scopedEntry.isDirectory()) continue
+          // Allow both directories and symlinks (pnpm uses symlinks)
+          if (!scopedEntry.isDirectory() && !scopedEntry.isSymbolicLink()) continue
 
           const pkgPath = path.join(dirPath, scopedEntry.name)
           const pkgName = `${entry.name}/${scopedEntry.name}`