Let's say your course lasts 10 weeks.
1) You can have one assignment per week, then download 10 zip files, unzip them, and combine all files into one folder. With the correct Assignment naming, the files could be sorted by student and by assignment.
2) If you decide to have only one Assignment, then allow students to upload up to 10 files. Some student file naming would have to be used to keep the 10 files chronologic, but then you would end up with only one big zip file.
Of these two approaches, I prefer #1. This puts the file naming much more under your control (student-assignment-filename.)
1) You can have one assignment per week, then download 10 zip files, unzip them, and combine all files into one folder. With the correct Assignment naming, the files could be sorted by student and by assignment.
2) If you decide to have only one Assignment, then allow students to upload up to 10 files. Some student file naming would have to be used to keep the 10 files chronologic, but then you would end up with only one big zip file.
Of these two approaches, I prefer #1. This puts the file naming much more under your control (student-assignment-filename.)
As another alternative, you could have one assignment link, and tell students to maintain only one file, but have them on a weekly basic append more information to their re-submitted file. This relies on students having more computer-savvy than the examinators, however.