Basic file uploading

Basic file upload (path stored in the DB), email registration confirmation, and some template modifications.
We're putting all the files in one directory, which makes me a little uncomfortable. What do you think of importing them the files into tables like:

variants: 
   patient_id : int
   chrom : str 
   pos : int
   ref : str 
   alt : str 

hla_types: 
  patient_id : int
  allele : str 
  mhc_class : int (1 or 2)

Or, alternatively, how about at least making a subdirectory for each user?