Thanks for the link.
1) The setup I'm looking for has a file server that is different from the web server that will host the web interface. Is that something that own cloud supports? The files in the file server might be stored in a hierarchy of folders that might be totally distinct from the way the user sees the files on the web client end.
2) How hard would it be to modify the core of own cloud to deal with differential uploads?
3) How hard would it be to keep the back bone of owncloud and re-design a different user interface?
4) I don't want to just do file sync. Basically, I have are many people that need to access upload/download files from a file server, comment on files, etc.. I want to make this task as easy as possible so that even a high school kid can do it. I need a web interface like drop box. But I also want all the files to reside on my own file server, not someone else computer. And I want to be able to control the GUI and add features as needed.
For example, I might want to incorporate some data visualization tools into it. Or allow to user to run some simple scripts on some data files online.
5) Would git-annex or btsync be usable in the back end with a web interface on top?
Sorry for so many questions. I'm just trying to navigate through the range of options that there are out there.
Thanks very much for your answer.