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I started with cs50 web earlier this year, completed the first 3 assignments and then submitted by pushing them to the relevant branch of the submit50/USERNAME.git repository, and got a grading email for each submission.

In the 4th assignment I read that I should push to me50/USERNAME.git. When I check cs50.me it says that I have not submitted any assignment. Do I have to resubmit the previous assignments to the "new" repository, for them to count ?

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You're correct that the submission process changed in late July. All of your old submissions can be seen here: http://legacy.cs50.me and new submissions here: http://submit.cs50.io

Both groups of submissions are used for grading, so you should see the progress here: http://cs50.me/cs50w

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