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>

bmad-core/working-in-the-brownfield.md

@@ -5,7 +5,7 @@
 > Gemini Web's 1M+ token context window or Gemini CLI (when it's working) can analyze your ENTIRE codebase, or critical sections of it, all at once (obviously within reason):
 >
 > - Upload via GitHub URL or use gemini cli in the project folder
-> - If working in the web: use the flattener-tool to flatten your project into a single file, then upload that file to your web agent.
+> - If working in the web: use `npx bmad-method flatten` to flatten your project into a single file, then upload that file to your web agent.
 
 ## What is Brownfield Development?
 
@@ -27,7 +27,7 @@ If you have just completed an MVP with BMad, and you want to continue with post-
 ## The Complete Brownfield Workflow
 
 1. **Follow the [<ins>User Guide - Installation</ins>](user-guide.md#installation) steps to setup your agent in the web.**
-2. **Generate a 'flattened' single file of your entire codebase** run: ```npm run flatten```
+2. **Generate a 'flattened' single file of your entire codebase** run: ```npx bmad-method flatten```
 
 ### Choose Your Approach