Doing some reading on Stack Overflow, I've found a lot of information suggesting that proper organization of a file system is crucial to a well-written web app. One of the key pieces of evidence is high-frequency references to "separation of concerns" in questions related to keeping programs organized.
Now, I've found some information on organizing file systems (Filesystem Hierarchy Standard) from 2004. It raises only two concerns: first, the standard's a bit dated, so I believe it may be possible to do better given the changes in technology over the past 8 years; second, and most important, my application is very small compared to an entire Linux distro. I think that the file system should be organized very differently because of that.
Here's what I'm looking at, currently:
/scripts, /databases, /www -> /dev, /production -> login, router, admin pages, /sites
-> content types, static pages /modules, /includes, /css, /media
-> /module-specific-media
