How do Minecraft save files work? Is there a Python interface?
You're looking for mclevel.py. This (as the name hints at) allows python to manipulate Minecraft levels. I don't know if it also does minecarts, but I suppose so.
An example of what you can do with it: http://www.minecraftforum.net/viewtopic.php?f=25&t=52183
This Minepedia page has some documentation; here's a simple overview.
The folder hashing has been added because some systems had trouble handling folders with huge amounts of files.
Each chunk is as large as this hole: