Directories with huge number of files are slower to access. You could look at extended attributes (xattr) feature of most *NIX's. This is user defined informat

Directories with huge number of files are slower to access. You could look at extended attributes (xattr) feature of most *NIX's. This is user defined information which could easily be used in the manner that you suggest. A modified file manager would be able to handle the additional capabilities. Some music and photo management programs implement something similar so perhaps that could be used as a strarting point.