eat: enhance flattener tool with improved CLI integration and custom directory support (#372)

* feat(cli): move flatten command to installer and update docs

Refactor the flatten command from tools/cli.js to tools/installer/bin/bmad.js for better integration. Add support for custom input directory and improve error handling. Update documentation in README.md and working-in-the-brownfield.md to reflect new command usage. Also clean up package-lock.json and add it to .gitignore.

* chore: update gitignore and add package-lock.json for installer tool

Remove package-lock.json from root gitignore since it's now needed for the installer tool
Add package-lock.json with dependencies for the bmad-method installer

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Co-authored-by: Devin Stagner <devin@blackstag.family>

tools/installer/bin/bmad.js

@@ -110,6 +110,20 @@ program
     }
   });
 
+program
+  .command('flatten')
+  .description('Flatten codebase to XML format')
+  .option('-i, --input <path>', 'Input directory to flatten', process.cwd())
+  .option('-o, --output <path>', 'Output file path', 'flattened-codebase.xml')
+  .action(async (options) => {
+    try {
+      await installer.flatten(options);
+    } catch (error) {
+      console.error(chalk.red('Flatten failed:'), error.message);
+      process.exit(1);
+    }
+  });
+
 async function promptInstallation() {
   
   // Display ASCII logo