Today all TokuDB files are located in the datadir. What with file-per-index, multiple tables and partitions, one can easily end up with 20,000 files in the datadir directory.
This is problematic in multiple senses:
Not all file systems are easy on large amounts of files in one directory
For all the trees one cannot see the wood, so to speak. One has to "ls -l | grep -v tokudb" to take a look at the binary logs, directories etc.