However, the author is onto something: storing functions in a database. Using the file system results in exclusive containment (file can't be in two different directories - link don't count) that a database can avoid.
If you are lost, think of Gmail's tags with nesting. You can still have the hierarchy but data can be "located" under different tags. A lot of times the problem is using the file system as the back end. Python's modules, for instance, do not inherently enforce exclusive containment; the file system imposes this constraint.
I had a chat with Jeff Bone a year ago after I read his partially-related rant here: http://www.xent.com/pipermail/fork/Week-of-Mon-20091109/0545...
I wish I could paste everything he said to me in here; he pointed me to a lot of examples of good file system / graph database examples that get a lot of these things right. Quick further reading list: Original ReiserFS design, BeFS design, FluidDB, LUFS, and Tannenbaum's design for the directory services and file system of Ameoba.