Bug Report Checklist
Overview
The MCP scaffolding CLI prompt should also include an option to include MCP servers plus also the package.json direct dependencies for API documentation.
When that option is chosen (with the package.json direct deps for documentation APIs) then the CLI should use the automcp npm package which does exactly that - scaffolds MCP config based on the package.json. It should of course do this in addition to scaffolding the template MCP config from the template directory.
Additional Info
About automcp: https://github.com/lirantal/automcp/