Commands
The framework installs the command vendor/bin/wp-app-framework into your project. It runs in the project whose vendor/autoload.php it loads, which is the project you call it in.
Options take their value with =: --output=dist/theme.zip. meta-fields and table-fields replace an existing file only with --force; they are the only commands that write source code.
Your project usually runs them through Composer scripts, for example "build-manifest": "wp-app-framework build" and "release": "wp-app-framework release" (see Getting started).