Import Filesystem in menu

Hello all.

I am building a university students' community-site, and as concerning the subjects' part I have the following situation:
I already have a folder hierarchy under sites/default/files such as:

root: 6 Departure folders
depth-1: 10 semester folders ---- (same for every departure folder)
depth-2: 1 - 6 subject folders ---- (different for every semester folder)
depth-3: 5 material folders(categories) ---- (same for every subject folder)
depth-4: Files contained in each folder(docs, jpg, etc.) ---- (different for every material folder obviously)

What I want to achieve is: To have an exact representation of the above structure in a menu. And I am wondering if there is a
module or sth to help me import the filesystem structure. Also I would like when the administrator (or a user) uploads a file, the file
to be saved in the same folder which corresponds in the specific sub-menu.

Example: I upload a project for CS lesson Programming of the Semester 1. I want it to be saved in
sites/default/files/CS/1st/Programming/projects instead of sites/default/files
that is usually done with other modules.

A secondary wish of mine would be the ability to transform the attached files(final depth: pdf, jpgs, etc) to node, so that I could built
a custom node type to implement some features for the single files such us rating, commenting etc... I could make sth classic with CCK but remember that there is already 2GB to be attached in each node. Anyway this one is not yet clear to my mind...

I understand that what I ask is not simple so I don't except a specific module or guide to solve my hands immediately(although I hope so :)). I have already started reading about module development and I am willing to get deep into it, but I am still newbie enough and I get a bit out of time here, therefore every suggestion or idea could be helpful. For example what to focus while reading module development. Combination of existing modules which could help me and so. Besides I think that file management is a bigger and more general topic concerning the drupal users, and a relative module would be a good idea for someone looking to write some code ;)

Thank you all for your time.