“You made these from scratch?”
Your coworker brought muffins to work today to share. They look great. You're amazed that she made them herself.
You made these from scratch?
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In very casual spoken English, people sometimes start questions with "You" instead of "Do you" or "Are you". For example:
You want something from the grocery store?
You sent it already?
Doing something "from scratch" means that you do it from the very beginning, without having some parts of it done for you.
For example, baking cookies "from scratch" means combining flour, eggs, sugar, etc. to make the cookies (instead of buying pre-made cookies or frozen cookie dough):
Want a cookie? I made it from scratch!
"Starting over from scratch" means doing something again from the beginning. You can use this phrase if you did some work but now you have to do it over again because you lost it or because there was a problem with the first version.