I have multisite installation running successfully on my site with one main site and two subdirectory sites. I'm using nginx, so I've had to make myself pretty familiar with the necessary rewriting rules to get things up and running. I even have W3TC running to my satisfaction on all three sites.
I remain puzzled about one thing: why do the subdirectory blogs insist on accessing wp-content/, wp-includes/, etc. through their subdirectories? In other words, why does my home site access it as /wp-content/ and my "cvx" site access it as /cvx/wp-content/, when it's the same data? Why force the web server to strip out the subdirectory? Why not just construct WP_CONTENT_URI to point to "/wp-content" in the first place?
I guess it's not that big of a deal in a vanilla WordPress installation, but it does mean I have duplicate copies of WP's static content out there on my CDN, and under certain circumstances visitors to my sites will grab duplicate copies of that content.
It seems like it would be relatively easy to override the code that constructs WP_CONTENT_URI, etc. to eliminate the "unnecessary" subdirectories. But that's just it, I can't read the minds of the WordPress developers, and there may be some logic behind this design choice that I'm missing. Can anyone illuminate that for me?