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I hate magic numbers in grading. I always try to show students how they get the score they do and give them feedback on exactly what went wrong if I do remove points. I've had classes where I just get a "-5" on something and I'm like "WHAT DOES THAT EVEN MEAN?!" https://t.co/Zv4OXet6Cn
You can perhaps attach a document explaining what is wrong. If the submission is one or many plain text files, you can also make diff recursively compare an empty file or folder against the submission.

That will add line prefixes which you can use to separate their changes, from your non-prefixed comments.
I do that. It's in the screenshot of the original tweet.

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