You work on separate pieces at a time and upload each version to a gallery. It is a sort of tag-team.
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Let's say I create a project base for a platformer and upload it. Then, you would add the scrolling environment and upload it. Then I add more characters and upload it, etc. until the entire project is finished. More than two people can do this, and this is how Scratch collaborations work, doing bits and pieces of projects separately.
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Your brother uploads the project to the Scratch website, then you view the project, download it from the top right corner of the page, make your edits, and reupload it to the website. To upload it, press "share to website" from the "share" button in the project editor menu.
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ohh so THATS how you do it
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