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I'm just wondering why check50 has an upload stage to begin with? What is it uploading?

$ check50 cs50/2018/ap/pennies
Connecting.........
Authenticating......
Preparing................
Uploading...............
Checking........

Even if it has to connect and authenticate to download the tests, why is it uploading and what is it uploading?

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As part of check50, the file as-is is pushed up to your github. you can see this with check50 -v

Uploading...
git commit --allow-empty --message='20190126T233954Z'
[cs50/2018/ap/pennies 94de8a6] 20190126T233954Z
git rev-parse HEAD
94de8a67ef1f942fb8ab89ee80b572ce69a33924
git push origin 'refs/heads/cs50/2018/ap/pennies'
Password for 'https://EvanCarroll@github.com': 
Counting objects: 1, done.
Writing objects: 100% (1/1), 200 bytes | 200.00 KiB/s, done.
Total 1 (delta 0), reused 0 (delta 0)
To https://github.com/check50/EvanCarroll
   b2f2637..94de8a6  cs50/2018/ap/pennies -> cs50/2018/ap/pennies

This can be disabled with -l

-l, --local          run checks locally instead of uploading to cs50

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