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/cli.js

@@ -149,13 +149,4 @@ program
     });
   });
 
-program
-  .command('flatten')
-  .description('Flatten codebase to XML format')
-  .option('-o, --output <path>', 'Output file path', 'flattened-codebase.xml')
-  .action(async (options) => {
-    const flattener = require('./flattener/main');
-    await flattener.parseAsync(['flatten', '--output', options.output], { from: 'user' });
-  });
-
 program.parse();