Fix: Bun bytecode extraction — fall back to npm source for patchable JS

src/installationDetection.ts

@@ -380,7 +380,7 @@ async function extractVersionFromJsFile(cliPath: string): Promise<string> {
 async function extractVersionFromNativeBinary(
   binaryPath: string
 ): Promise<string> {
-  const claudeJsBuffer =
+  const { data: claudeJsBuffer } =
     await extractClaudeJsFromNativeInstallation(binaryPath);
 
   if (!claudeJsBuffer) {

src/lib/content.ts

@@ -29,7 +29,7 @@ import { Installation } from './types';
  */
 export async function readContent(installation: Installation): Promise<string> {
   if (installation.kind === 'native') {
-    const buffer = await extractClaudeJsFromNativeInstallation(
+    const { data: buffer } = await extractClaudeJsFromNativeInstallation(
       installation.path
     );
     if (!buffer) {
@@ -61,7 +61,8 @@ export async function writeContent(
     await repackNativeInstallation(
       installation.path,
       modifiedBuffer,
-      installation.path
+      installation.path,
+      false
     );
   } else {
     await replaceFileBreakingHardLinks(installation.path, content, 'patch');

src/nativeInstallation.ts

@@ -3,7 +3,9 @@
  */
 
 import fs from 'node:fs';
-import { execSync } from 'node:child_process';
+import path from 'node:path';
+import os from 'node:os';
+import { execSync, execFileSync } from 'node:child_process';
 import LIEF from 'node-lief';
 import { isDebug, debug } from './utils';
 
@@ -151,6 +153,7 @@ export function resolveNixBinaryWrapper(binaryPath: string): string | null {
  * - flags: u32
  */
 const BUN_TRAILER = Buffer.from('\n---- Bun! ----\n');
+const BUN_BYTECODE_PREFIX = '// @bun @bytecode';
 
 // Size constants for binary structures
 const SIZEOF_OFFSETS = 32;
@@ -701,9 +704,59 @@ function getBunData(
  * real binary path here. This is handled at detection time in
  * `installationDetection.ts`.
  */
+function fetchNpmSource(version: string): Buffer | null {
+  const tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'tweakcc-npm-'));
+  try {
+    debug(`fetchNpmSource: Downloading @anthropic-ai/claude-code@${version}`);
+    execFileSync(
+      'npm',
+      [
+        'pack',
+        `@anthropic-ai/claude-code@${version}`,
+        '--pack-destination',
+        tmpDir,
+      ],
+      { stdio: 'pipe', timeout: 30_000, cwd: tmpDir }
+    );
+
+    const files = fs.readdirSync(tmpDir);
+    const tgz = files.find(f => f.endsWith('.tgz'));
+    if (!tgz) {
+      debug('fetchNpmSource: No .tgz file found after npm pack');
+      return null;
+    }
+
+    execFileSync('tar', ['xzf', path.join(tmpDir, tgz), 'package/cli.js'], {
+      stdio: 'pipe',
+      timeout: 30_000,
+      cwd: tmpDir,
+    });
+
+    const cliJsPath = path.join(tmpDir, 'package', 'cli.js');
+    if (!fs.existsSync(cliJsPath)) {
+      debug('fetchNpmSource: cli.js not found in extracted package');
+      return null;
+    }
+
+    const content = fs.readFileSync(cliJsPath);
+    debug(`fetchNpmSource: Got cli.js, ${content.length} bytes`);
+    return content;
+  } catch (error) {
+    debug('fetchNpmSource: Failed to fetch npm source:', error);
+    return null;
+  } finally {
+    try {
+      fs.rmSync(tmpDir, { recursive: true, force: true });
+    } catch {
+      // Ignore cleanup errors
+    }
+  }
+}
+
 export function extractClaudeJsFromNativeInstallation(
-  nativeInstallationPath: string
-): Buffer | null {
+  nativeInstallationPath: string,
+  version?: string
+): { data: Buffer | null; clearBytecode: boolean } {
   try {
     LIEF.logging.disable();
     const binary = LIEF.parse(nativeInstallationPath);
@@ -722,9 +775,6 @@ export function extractClaudeJsFromNativeInstallation(
           `extractClaudeJsFromNativeInstallation: Module ${index}: ${moduleName}`
         );
 
-        // Module name is typically:
-        // - Unix/macOS: /$bunfs/root/claude
-        // - Windows:    B:/~BUN/root/claude.exe
         if (!isClaudeModule(moduleName)) return undefined;
 
         const moduleContents = getStringPointerContent(
@@ -741,29 +791,54 @@ export function extractClaudeJsFromNativeInstallation(
     );
 
     if (result) {
-      return result;
+      const head = result.subarray(0, 30).toString('utf8');
+      if (head.startsWith(BUN_BYTECODE_PREFIX)) {
+        debug(
+          'extractClaudeJsFromNativeInstallation: Extracted content is Bun bytecode — falling back to npm source'
+        );
+
+        if (version) {
+          const npmSource = fetchNpmSource(version);
+          if (npmSource) {
+            debug(
+              `extractClaudeJsFromNativeInstallation: Using npm source (${npmSource.length} bytes) instead of bytecode`
+            );
+            return { data: npmSource, clearBytecode: true };
+          }
+          debug(
+            'extractClaudeJsFromNativeInstallation: npm source fetch failed, returning bytecode content as-is'
+          );
+        } else {
+          debug(
+            'extractClaudeJsFromNativeInstallation: No version provided, cannot fetch npm source'
+          );
+        }
+      }
+
+      return { data: result, clearBytecode: false };
     }
 
     debug(
       'extractClaudeJsFromNativeInstallation: claude module not found in any module'
     );
 
-    return null;
+    return { data: null, clearBytecode: false };
   } catch (error) {
     debug(
       'extractClaudeJsFromNativeInstallation: Error during extraction:',
       error
     );
 
-    return null;
+    return { data: null, clearBytecode: false };
   }
 }
 
 function rebuildBunData(
   bunData: Buffer,
   bunOffsets: BunOffsets,
   modifiedClaudeJs: Buffer | null,
-  moduleStructSize: number
+  moduleStructSize: number,
+  clearBytecode: boolean
 ): Buffer {
   // Phase 1: Collect all string data
   const stringsData: Buffer[] = [];
@@ -786,14 +861,18 @@ function rebuildBunData(
 
     // Check if this is claude.js and we have modified contents
     let contentsBytes: Buffer;
+    let bytecodeBytes: Buffer;
     if (modifiedClaudeJs && isClaudeModule(moduleName)) {
       contentsBytes = modifiedClaudeJs;
+      bytecodeBytes = clearBytecode
+        ? Buffer.alloc(0)
+        : getStringPointerContent(bunData, module.bytecode);
     } else {
       contentsBytes = getStringPointerContent(bunData, module.contents);
+      bytecodeBytes = getStringPointerContent(bunData, module.bytecode);
     }
 
     const sourcemapBytes = getStringPointerContent(bunData, module.sourcemap);
-    const bytecodeBytes = getStringPointerContent(bunData, module.bytecode);
     const moduleInfoBytes = getStringPointerContent(bunData, module.moduleInfo);
     const bytecodeOriginPathBytes = getStringPointerContent(
       bunData,
@@ -1392,19 +1471,20 @@ function repackELFOverlay(
 export function repackNativeInstallation(
   binPath: string,
   modifiedClaudeJs: Buffer,
-  outputPath: string
+  outputPath: string,
+  clearBytecode: boolean
 ): void {
   LIEF.logging.disable();
   const binary = LIEF.parse(binPath);
 
-  // Extract Bun data and rebuild with modified claude.js
   const { bunOffsets, bunData, sectionHeaderSize, moduleStructSize } =
     getBunData(binary);
   const newBuffer = rebuildBunData(
     bunData,
     bunOffsets,
     modifiedClaudeJs,
-    moduleStructSize
+    moduleStructSize,
+    clearBytecode
   );
 
   switch (binary.format) {

src/nativeInstallationLoader.ts

@@ -54,13 +54,17 @@ async function tryLoadNativeInstallationModule(): Promise<NativeInstallationModu
  * Returns null if node-lief is not available or extraction fails.
  */
 export async function extractClaudeJsFromNativeInstallation(
-  nativeInstallationPath: string
-): Promise<Buffer | null> {
+  nativeInstallationPath: string,
+  version?: string
+): Promise<{ data: Buffer | null; clearBytecode: boolean }> {
   const mod = await tryLoadNativeInstallationModule();
   if (!mod) {
-    return null;
+    return { data: null, clearBytecode: false };
   }
-  return mod.extractClaudeJsFromNativeInstallation(nativeInstallationPath);
+  return mod.extractClaudeJsFromNativeInstallation(
+    nativeInstallationPath,
+    version
+  );
 }
 
 /**
@@ -71,17 +75,22 @@ export async function extractClaudeJsFromNativeInstallation(
 export async function repackNativeInstallation(
   binPath: string,
   modifiedClaudeJs: Buffer,
-  outputPath: string
+  outputPath: string,
+  clearBytecode: boolean
 ): Promise<void> {
-  // The module should already be cached from a prior extractClaudeJsFromNativeInstallation() call
   const mod = await tryLoadNativeInstallationModule();
   if (!mod) {
     throw new Error(
       '`repackNativeInstallation()` called but `node-lief` is not available. ' +
         'This is unexpected - `extractClaudeJsFromNativeInstallation()` should have been called first.'
     );
   }
-  mod.repackNativeInstallation(binPath, modifiedClaudeJs, outputPath);
+  mod.repackNativeInstallation(
+    binPath,
+    modifiedClaudeJs,
+    outputPath,
+    clearBytecode
+  );
 }
 
 /**

src/patches/index.ts

@@ -539,6 +539,7 @@ export const applyCustomization = async (
   patchFilter?: string[] | null
 ): Promise<ApplyCustomizationResult> => {
   let content: string;
+  let clearBytecode = false;
 
   if (ccInstInfo.nativeInstallationPath) {
     // For native installations: restore the binary, then extract to memory
@@ -561,14 +562,18 @@ export const applyCustomization = async (
       `Extracting claude.js from ${backupExists ? 'backup' : 'native installation'}: ${pathToExtractFrom}`
     );
 
-    const claudeJsBuffer =
-      await extractClaudeJsFromNativeInstallation(pathToExtractFrom);
+    const { data: claudeJsBuffer, clearBytecode: needsClearBytecode } =
+      await extractClaudeJsFromNativeInstallation(
+        pathToExtractFrom,
+        ccInstInfo.version
+      );
 
     if (!claudeJsBuffer) {
       throw new Error('Failed to extract claude.js from native installation');
     }
 
-    // Save original extracted JS for debugging
+    clearBytecode = needsClearBytecode;
+
     const origPath = path.join(CONFIG_DIR, 'native-claudejs-orig.js');
     fsSync.writeFileSync(origPath, claudeJsBuffer);
     debug(`Saved original extracted JS from native to: ${origPath}`);
@@ -904,7 +909,8 @@ export const applyCustomization = async (
     await repackNativeInstallation(
       ccInstInfo.nativeInstallationPath,
       modifiedBuffer,
-      ccInstInfo.nativeInstallationPath
+      ccInstInfo.nativeInstallationPath,
+      clearBytecode
     );
   } else {
     // For NPM installations: replace the cli.js file

src/tests/config.test.ts

@@ -429,7 +429,7 @@ describe('config.ts', () => {
       vi.spyOn(
         nativeInstallation,
         'extractClaudeJsFromNativeInstallation'
-      ).mockResolvedValue(mockJsBuffer);
+      ).mockResolvedValue({ data: mockJsBuffer, clearBytecode: false });
 
       const result = await findClaudeCodeInstallation(mockConfig, {
         interactive: true,
@@ -569,7 +569,7 @@ describe('config.ts', () => {
       vi.spyOn(
         nativeInstallation,
         'extractClaudeJsFromNativeInstallation'
-      ).mockResolvedValue(mockJsBuffer);
+      ).mockResolvedValue({ data: mockJsBuffer, clearBytecode: false });
 
       const result = await findClaudeCodeInstallation(mockConfig, {
         interactive: true,
@@ -693,7 +693,7 @@ describe('config.ts', () => {
       vi.spyOn(
         nativeInstallation,
         'extractClaudeJsFromNativeInstallation'
-      ).mockResolvedValue(mockJsBuffer);
+      ).mockResolvedValue({ data: mockJsBuffer, clearBytecode: false });
 
       const result = await findClaudeCodeInstallation(mockConfig, {
         interactive: true,
@@ -758,7 +758,7 @@ describe('config.ts', () => {
       vi.spyOn(
         nativeInstallation,
         'extractClaudeJsFromNativeInstallation'
-      ).mockResolvedValue(mockJsBuffer);
+      ).mockResolvedValue({ data: mockJsBuffer, clearBytecode: false });
 
       const result = await findClaudeCodeInstallation(mockConfig, {
         interactive: true,
@@ -1131,7 +1131,7 @@ describe('config.ts', () => {
       vi.spyOn(
         nativeInstallation,
         'extractClaudeJsFromNativeInstallation'
-      ).mockResolvedValue(mockJsBuffer);
+      ).mockResolvedValue({ data: mockJsBuffer, clearBytecode: false });
 
       const result = await findClaudeCodeInstallation(mockConfig, {
         interactive: true,
@@ -1323,11 +1323,10 @@ describe('config.ts', () => {
       // WASMagic reports binary
       mockMagicInstance.detect.mockReturnValue('application/octet-stream');
 
-      // Mock native extraction to return null (extraction failed)
       vi.spyOn(
         nativeInstallation,
         'extractClaudeJsFromNativeInstallation'
-      ).mockResolvedValue(null);
+      ).mockResolvedValue({ data: null, clearBytecode: false });
 
       vi.spyOn(fs, 'readFile').mockRejectedValue(createEnoent());
 
@@ -1461,10 +1460,12 @@ describe('config.ts', () => {
 
       mockMagicInstance.detect.mockReturnValue('application/octet-stream');
 
-      // Mock extractClaudeJsFromNativeInstallation to return content without VERSION
       vi.mocked(
         nativeInstallation.extractClaudeJsFromNativeInstallation
-      ).mockResolvedValue(Buffer.from('no version here'));
+      ).mockResolvedValue({
+        data: Buffer.from('no version here'),
+        clearBytecode: false,
+      });
 
       // Should throw error since no VERSION found
       await expect(
@@ -1513,10 +1514,9 @@ describe('config.ts', () => {
 
       mockMagicInstance.detect.mockReturnValue('application/octet-stream');
 
-      // Mock extractClaudeJsFromNativeInstallation to return null (extraction failed)
       vi.mocked(
         nativeInstallation.extractClaudeJsFromNativeInstallation
-      ).mockResolvedValue(null);
+      ).mockResolvedValue({ data: null, clearBytecode: false });
 
       // Should throw error since extraction failed
       await expect(