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Why is Merge Deleting Files? Edited

I'm working on a group project with some students.

We're using gitlab but I believe we are all using sourcetree as the GUI.

Now we have dev as our main branch that we branch out from and then merge back into.

One of the contributors, tried to merge into dev, and I think because she didn't fetch first, it caused some files to be deleted, since she was merging into an older commit(was odd it even let her push considering that). So then she used the reverse commit feature(where new commit but reverses the old one). And then correctly merged afterwards.

But for some reason, now when I try to merge with dev from my branch, it deletes a lot of files.

The weirder thing is, when I merged, the files weren't even in the staging list. They only appeared after I actually commited.

Only thing I could think of, was that the system wasn't designed to take into consideration reverse commits?

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