diff --git a/tools/flattener/main.js b/tools/flattener/main.js
index 50a831bf..665d79e4 100644
--- a/tools/flattener/main.js
+++ b/tools/flattener/main.js
@@ -70,7 +70,7 @@ program
   .name('bmad-flatten')
   .description('BMAD-METHOD™ codebase flattener tool')
   .version('1.0.0')
-  .option('-i, --input <path>', 'Input directory to flatten', process.cwd())
+  .option('-i, --input <path>', 'Input directory to flatten', process.env.INIT_CWD || process.cwd())
   .option('-o, --output <path>', 'Output file path', 'flattened-codebase.xml')
   .action(async (options) => {
     let inputDir = path.resolve(options.input);
@@ -87,7 +87,7 @@ program
     const noPathArguments = !userSpecifiedInput && !userSpecifiedOutput;
 
     if (noPathArguments) {
-      const detectedRoot = await findProjectRoot(process.cwd());
+      const detectedRoot = await findProjectRoot(process.env.INIT_CWD || process.cwd());
       const suggestedOutput = detectedRoot
         ? path.join(detectedRoot, 'flattened-codebase.xml')
         : path.resolve('flattened-codebase.xml');
@@ -101,7 +101,10 @@ program
           inputDir = detectedRoot;
           outputPath = suggestedOutput;
         } else {
-          inputDir = await promptPath('Enter input directory path', process.cwd());
+          inputDir = await promptPath(
+            'Enter input directory path',
+            process.env.INIT_CWD || process.cwd(),
+          );
           outputPath = await promptPath(
             'Enter output file path',
             path.join(inputDir, 'flattened-codebase.xml'),
@@ -109,7 +112,10 @@ program
         }
       } else {
         console.log('Could not auto-detect a project root.');
-        inputDir = await promptPath('Enter input directory path', process.cwd());
+        inputDir = await promptPath(
+          'Enter input directory path',
+          process.env.INIT_CWD || process.cwd(),
+        );
         outputPath = await promptPath(
           'Enter output file path',
           path.join(inputDir, 'flattened-codebase.xml'),