fix: Windows CRLF crash + npm shim / native binary detection

src/installationDetection.ts

@@ -334,6 +334,51 @@ async function getClaudeFromPath(): Promise<string | null> {
   }
 }
 
+/**
+ * On Windows, npm creates lightweight shim scripts (a `#!/bin/sh` shell script
+ * and a `.cmd` batch file) that exec the real binary.  When `which` returns one
+ * of these shims, `resolvePathToInstallationType` sees an unrecognized text
+ * file instead of the actual executable.
+ *
+ * This function reads the shim content and extracts the target path.
+ * Returns null if the file is not a recognized npm shim.
+ */
+async function resolveNpmShimTarget(shimPath: string): Promise<string | null> {
+  try {
+    const content = await fs.readFile(shimPath, 'utf8');
+
+    // npm sh shim: exec "$basedir/node_modules/.../claude.exe"  "$@"
+    // Multiple "$basedir/..." references can appear (e.g. the "$basedir/node"
+    // probe at the top of npm-cli-shim sh scripts); enumerate all and pick
+    // the first node_modules path that exists on disk.
+    for (const m of content.matchAll(/"\$basedir\/([^"]+)"/g)) {
+      if (!m[1].includes('node_modules')) continue;
+      const target = path.resolve(path.dirname(shimPath), m[1]);
+      if (await doesFileExist(target)) {
+        debug(`resolveNpmShimTarget: resolved sh shim -> ${target}`);
+        return target;
+      }
+    }
+
+    // npm .cmd shim: "%dp0%\node_modules\...\claude.exe"  %*
+    for (const m of content.matchAll(/"%dp0%\\([^"]+)"/g)) {
+      if (!m[1].includes('node_modules')) continue;
+      const target = path.resolve(
+        path.dirname(shimPath),
+        m[1].replace(/\\/g, '/')
+      );
+      if (await doesFileExist(target)) {
+        debug(`resolveNpmShimTarget: resolved cmd shim -> ${target}`);
+        return target;
+      }
+    }
+
+    return null;
+  } catch {
+    return null;
+  }
+}
+
 // ============================================================================
 // Version extraction
 // ============================================================================
@@ -682,7 +727,29 @@ export async function findClaudeCodeInstallation(
   if (pathClaudeExe) {
     debug(`Checking claude on PATH: ${pathClaudeExe}`);
 
-    const resolved = await resolvePathToInstallationType(pathClaudeExe);
+    let resolved = await resolvePathToInstallationType(pathClaudeExe);
+
+    // On Windows, `which` may find an npm shim (sh/cmd wrapper) instead of the
+    // actual binary.  Try to follow the shim to the real executable.
+    if (!resolved) {
+      const shimTarget = await resolveNpmShimTarget(pathClaudeExe);
+      if (shimTarget) {
+        debug(`Resolved npm shim -> ${shimTarget}`);
+        resolved = await resolvePathToInstallationType(shimTarget);
+      }
+      // Also try the .cmd variant alongside the bare shim
+      if (!resolved) {
+        const cmdPath = pathClaudeExe + '.cmd';
+        if (await doesFileExist(cmdPath)) {
+          const cmdTarget = await resolveNpmShimTarget(cmdPath);
+          if (cmdTarget) {
+            debug(`Resolved npm .cmd shim -> ${cmdTarget}`);
+            resolved = await resolvePathToInstallationType(cmdTarget);
+          }
+        }
+      }
+    }
+
     if (!resolved) {
       debug(
         `Unable to detect installation type from 'claude' on PATH (${pathClaudeExe}). ` +

src/installationPaths.ts

@@ -251,6 +251,84 @@ const getNativeSearchPathsWithInfo = (): SearchPathInfo[] => {
   // Versioned binaries (filenames are versions like 2.0.65)
   addPath(`${home}/.local/share/claude/versions/*`, true);
 
+  // CC 2.1.116+ ships as a native binary (bin/claude.exe on Windows, bin/claude elsewhere)
+  // inside the npm package — no cli.js. Add native binary search paths that mirror CLIJS
+  // search locations so the binary is discovered even when cli.js is absent.
+  const bin = process.platform === 'win32' ? 'bin/claude.exe' : 'bin/claude';
+  const nativeMod = `node_modules/@anthropic-ai/claude-code/${bin}`;
+
+  if (process.platform === 'win32') {
+    addPath(
+      `${home}/AppData/Local/Volta/tools/image/packages/@anthropic-ai/claude-code/${nativeMod}`
+    );
+    addPath(`${home}/AppData/Roaming/npm/${nativeMod}`);
+    addPath(`${home}/AppData/Roaming/nvm/*/${nativeMod}`, true);
+    addPath(`${home}/AppData/Local/Yarn/config/global/${nativeMod}`);
+    addPath(`${home}/AppData/Local/pnpm/global/*/${nativeMod}`, true);
+    addPath(`${home}/AppData/Roaming/Yarn/config/global/${nativeMod}`);
+    addPath(`${home}/AppData/Roaming/pnpm-global/${nativeMod}`);
+    addPath(`${home}/AppData/Roaming/pnpm-global/*/${nativeMod}`, true);
+    addPath(`${home}/.bun/install/global/${nativeMod}`);
+    addPath(`${home}/AppData/Local/fnm_multishells/*/${nativeMod}`, true);
+    addPath(`${home}/AppData/Local/mise/installs/node/*/${nativeMod}`, true);
+    addPath(
+      `${home}/AppData/Local/mise/installs/npm-anthropic-ai-claude-code/*/${nativeMod}`,
+      true
+    );
+    addPath(`C:/nvm4w/nodejs/${nativeMod}`);
+    addPath(`${home}/n/versions/node/*/lib/${nativeMod}`, true);
+  } else {
+    if (process.platform === 'darwin') {
+      addPath(`${home}/Library/${nativeMod}`);
+      addPath(`/opt/local/lib/${nativeMod}`);
+    }
+    addPath(`${home}/.local/lib/${nativeMod}`);
+    addPath(`${home}/.local/share/${nativeMod}`);
+    addPath(`${home}/.npm-global/lib/${nativeMod}`);
+    addPath(`${home}/.npm-packages/lib/${nativeMod}`);
+    addPath(`${home}/.npm/lib/${nativeMod}`);
+    addPath(`${home}/npm/lib/${nativeMod}`);
+    addPath(`/usr/lib/${nativeMod}`);
+    addPath(`/usr/local/lib/${nativeMod}`);
+    addPath(`/opt/homebrew/lib/${nativeMod}`);
+    addPath(`${home}/.linuxbrew/lib/${nativeMod}`);
+    addPath(`${home}/.config/yarn/global/${nativeMod}`);
+    addPath(`${home}/.yarn/global/${nativeMod}`);
+    addPath(`${home}/.bun/install/global/${nativeMod}`);
+    addPath(`${home}/.pnpm-global/${nativeMod}`);
+    addPath(`${home}/.pnpm-global/*/${nativeMod}`, true);
+    addPath(`${home}/.local/share/pnpm/global/${nativeMod}`);
+    addPath(`${home}/.local/share/pnpm/global/*/${nativeMod}`, true);
+    addPath(`${home}/.volta/tools/image/node/*/lib/${nativeMod}`, true);
+    addPath(`${home}/.fnm/node-versions/*/installation/lib/${nativeMod}`, true);
+    addPath(`${home}/.nvm/versions/node/*/lib/${nativeMod}`, true);
+    addPath(`/usr/local/nvm/versions/node/*/lib/${nativeMod}`, true);
+    addPath(`${home}/.nodenv/versions/*/lib/${nativeMod}`, true);
+    addPath(`${home}/.asdf/installs/nodejs/*/lib/${nativeMod}`, true);
+    addPath(`${home}/.local/share/mise/installs/node/*/lib/${nativeMod}`, true);
+    addPath(
+      `${home}/.local/share/mise/installs/npm-anthropic-ai-claude-code/*/lib/${nativeMod}`,
+      true
+    );
+    if (process.env.NPM_PREFIX)
+      addPath(`${process.env.NPM_PREFIX}/lib/${nativeMod}`);
+    if (process.env.N_PREFIX)
+      addPath(`${process.env.N_PREFIX}/lib/${nativeMod}`);
+    if (process.env.VOLTA_HOME)
+      addPath(`${process.env.VOLTA_HOME}/lib/${nativeMod}`);
+    if (process.env.NVM_DIR) addPath(`${process.env.NVM_DIR}/lib/${nativeMod}`);
+    if (process.env.MISE_DATA_DIR)
+      addPath(
+        `${process.env.MISE_DATA_DIR}/installs/node/*/lib/${nativeMod}`,
+        true
+      );
+    if (process.env.MISE_DATA_DIR)
+      addPath(
+        `${process.env.MISE_DATA_DIR}/installs/npm-anthropic-ai-claude-code/*/lib/${nativeMod}`,
+        true
+      );
+  }
+
   // Convert to backslashes on Windows
   if (process.platform === 'win32') {
     pathInfos.forEach(info => {

src/patches/systemPrompts.test.ts

@@ -166,6 +166,60 @@ describe('systemPrompts.ts', () => {
       expect(result.newContent).toBe('description:"Hello\\nWorld"');
     });
 
+    it('should convert CRLF line endings to \\n for double-quoted string literals (Windows)', async () => {
+      const mockPromptData = buildMockPromptData({
+        prompt: { content: 'Hello\r\nWorld' },
+        regex: 'Hello(?:\n|\\\\n)World',
+        getInterpolatedContent: () => 'Hello\r\nWorld',
+        pieces: ['Hello\r\nWorld'],
+      });
+
+      setupMocks(mockPromptData);
+
+      const cliContent = 'description:"Hello\\nWorld"';
+
+      const result = await applySystemPrompts(cliContent, '1.0.0', false);
+
+      expect(result.newContent).toBe('description:"Hello\\nWorld"');
+      expect(result.newContent).not.toMatch(/\r/);
+    });
+
+    it('should convert CRLF line endings to \\n for single-quoted string literals (Windows)', async () => {
+      const mockPromptData = buildMockPromptData({
+        prompt: { content: 'Hello\r\nWorld' },
+        regex: 'Hello(?:\n|\\\\n)World',
+        getInterpolatedContent: () => 'Hello\r\nWorld',
+        pieces: ['Hello\r\nWorld'],
+      });
+
+      setupMocks(mockPromptData);
+
+      const cliContent = "msg:'Hello\\nWorld'";
+
+      const result = await applySystemPrompts(cliContent, '1.0.0', false);
+
+      expect(result.newContent).toBe("msg:'Hello\\nWorld'");
+      expect(result.newContent).not.toMatch(/\r/);
+    });
+
+    it('should normalize CRLF to LF for backtick template literals (Windows)', async () => {
+      const mockPromptData = buildMockPromptData({
+        prompt: { content: 'Hello\r\nWorld' },
+        regex: 'Hello(?:\n|\\\\n)World',
+        getInterpolatedContent: () => 'Hello\r\nWorld',
+        pieces: ['Hello\r\nWorld'],
+      });
+
+      setupMocks(mockPromptData);
+
+      const cliContent = 'description:`Hello\nWorld`';
+
+      const result = await applySystemPrompts(cliContent, '1.0.0', false);
+
+      expect(result.newContent).toBe('description:`Hello\nWorld`');
+      expect(result.newContent).not.toMatch(/\r/);
+    });
+
     it('should keep actual newlines for backtick template literals', async () => {
       const mockPromptData = buildMockPromptData({
         prompt: { content: 'Hello\nWorld' },

src/patches/systemPrompts.ts

@@ -161,12 +161,15 @@ export const applySystemPrompts = async (
       }
 
       if (delimiter === '"') {
-        replacementContent = replacementContent.replace(/\n/g, '\\n');
+        replacementContent = replacementContent.replace(/\r\n|\r|\n/g, '\\n');
         replacementContent = escapeUnescapedChar(replacementContent, '"');
       } else if (delimiter === "'") {
-        replacementContent = replacementContent.replace(/\n/g, '\\n');
+        replacementContent = replacementContent.replace(/\r\n|\r|\n/g, '\\n');
         replacementContent = escapeUnescapedChar(replacementContent, "'");
       } else if (delimiter === '`') {
+        replacementContent = replacementContent
+          .replace(/\r\n/g, '\n')
+          .replace(/\r/g, '\n');
         const { content: escaped, incomplete } =
           escapeDepthZeroBackticks(replacementContent);
         if (incomplete) {