Using Arduino libraries for adding more functionalities to a bootloader
@Majenko: I think, that the task IS possible, but it is really hard (and Leonardo may need more memory for that eventually and some shields too and so ...) but if I understand the problem, than the Leonardo should pretends to be mass storage device for that application, and pretend it have some folders and files on it, depending which RFID is used to activate it.

The application probabelly is NOT going to format the MSD because it would lose all the user data on it.

So Leonardo can do following:


pretend it is already formatted and have some known filesystem on it (vfat is easy enought and probabelly usable as many USB flash sticks came with it)
when the machine detects inserted USB, it ask for type - so it get MSD
then it will read partition table - Leonardo can emulate it easily, having "just one partition of given size and type" the partition can even be stored as a file on that fileserver to save Leonardo's memory.
next goes reading FAT table and root directory

knowing  the user from RFID it is possible to select the right directory on file server, 
then enumerate lengths of all files inside (and directories) 
make table with the names and "offset"
send back the FAT as if those files were ordered on the "disk" so each entry points to the following sector, until the last marks EOF
root directory begins after FAT and contains names of the files, their lenghts, dates and starting sectors (and some very basic right like read-only, system and such)
then follows files and directories

each time the machine asks for a "sector", it is possible to compute, in which file the sector is placed, read the portion of a file (potentially fill it with zeroes to "sector lenght" and return it as requested "sector"
if the sector is in directory instead, return the part of directory (that means filenames and such)
if the sector is outside it all (should not happen), return just zeroes.


On the other direction:


if you get something outside structure, put it to temp. file along with address of such stray "sector" 
if you get something in a file, just replace the file content on given offset
if you get something in directory, you need to compare it with previous version and "rename file", "create file" or "delete file" acordingly.
it would probabely need two directories on the server for each user - one for actual files, other for "lost sectors" and "deleted files" which could be "reconected", "undeleted" or "attached later" to the files/directories. The second directory can be emptied after "removing USB MSD" when user with given RFID logouts.


It is lot of work, but basically it could be done. It also needs a lot of accounting on the Leonardo and lot of communication with the fileserver, but it is possible to do.

It suppose, that the files on fileserver would not be modified by somebody else while "mounted" and that the Windows machine would not "format" the USB to some kind of filesystem, the Leonardo does not understand (how to translate to the real files on server).

But for the supposed use I think those two conditions could be reasonable. The MSD probabelly just holds the "user profile" so the machine can put in records of hir/her activiti, some stats and so on, probabely it would be just a few growing files maybe even just in root directory.

Anyway I would not like to write such system, as it is terrifying lot of work and a lot of things could go wrong, if there is a bug (or bad connection). 

Also the size of required memory for Leonardo is large - probabelly larger, than the Leonardo actually have, but it could be offloaded to the filesystem too (in "hidden directory" not shown to the machine) - which would be slow and hard to manage - or expanded by HW RAM, which would be a lot faster, but needs nontrivial settings.

(Remebers me, how I wrote resident program for DOS, which had just 130 bytes, which swaped in two 16KB widows of EMS where the rest of program (actually interpret of some pseudocode) was placed (it was like 4 or 6 such 16KB pages, but was able to swap itself acordingly) while the remaining two EMS pages was reserverd for data (like 300-400KB total of pseudocode and data) which was also swapped as needed to access everything. From DOS point of view it was just the 130B resident API, from the view of program, which was using it, it was 400KB engine running FORTH-like program and containing database. The result was like 3x faster processing of 2.000+ employes wages.) 

Here are the memory restrictions even more tight, but I thing, that it is possible to do such thing, only it is extremely hard to make it work reliably.