Sorry for responding so late, I moved to another department at our university so I don't spend almost any time with Moodle now. In the current version of Echo-assignment, there is only one database entry for each student's submission, so you would need to rewrite uploading code and change the database schema to make it work.
Unfortunately I'll most likely don't have time to do the things you mentioned, but it should not be a big problem for an experienced Moodle developer. However, I could offer a little help
Have you tried setting groups to "separate groups" and allowing students to view each others submissions? That could solve part of your collaboration problem.
Good luck with Moodle,
Echo-assignment and 1.5?
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