I'm a php/Mysql developer and I recently signed on to rework an exisitng site that was having a lot of performance issues. Some of the problem is stuff I see all the time in the form of non normalized data base tables and poorly optimized queries and code.

But... the tricky part for me is that they are creating a directory for every user on their server (they should have used mod_rewrite to simulate directories and use the db to store the relevant info by user id. This seems to be bogging the system down as there are over 9000 subdirectories in the main directory now and it is growing. I'm not really sure if this is a server question or a webserver question because truthfully I usually leave this kind of stuff to the server admins and I try and stay only at the application level as much as possible but I need to figure out how this config could be impacting the server.

to give an example:
if the server was for avon ladies you might have code like this:
http://www.avon.com/index.php?id=nancyjones or
http://www.avon.com/index.php?id=12345 and mod_rewrite would accept this
http://avon.com/12345 or
http://avon.com/nancyjones
you can have millions of id's in your db but I don't think the server is going to be very happy with even 50,000 directories.

anyone have any ideas about the limits or the issues I might expect to see? Should I be having this discussion on an apache forum?

Mmm gross. Depends a lot on the filesystem etc but in any case, it's the wrong way to go about it and IMO they should look at someone like yourself perhaps to fix it. The mod_rewrite suggestion is good, does the guy admining the server have a clue? If so pitch it to them and see what sort of response you get and if it's a yes, up your fee