Config.xml is located in a different location in PGB vs. the local CLI. When converting from PGB to local CLI, do something like the following:
1. Create a project using the CLI with the same name & ID:
phonegap create test com.example.test test
2. Copy your PGB files to the new project's www directory:
cp -r /path/to/PGB/files/*.* .
2. Move config.xml from www to the parent directory:
mv config.xml ../config.xml
3. Move any splash/icon resources to the parent directory:
mv res ../res
4. Edit config.xml so that any path references (icons/splashes) are correct.
5. Build the app and test, test, test!
Hope that helps.