I would build up a hierarchy system very much based on the standard files and folders system that people are used to. Use the standard naming, New Folder,delete etc. This should make everyone no matter their OS feel at home.
For multiple files in a project, I would see this going out like a treeview with expansion
–Project 1
----File 1
----File 2
I personally don’t really care about having offline access, and would prefer the time and energy be put elsewhere. As a Dir of Engineering in the medical field, I look at every single feature, and although it may look simple today, it has to be tested, documented and maintained for it’s life when it is released. Nothing is simple or free.