I just perused the userguide, nice to see some docs backing this otherwise I probably would have shyed away.
I noticed on the to do list was something for js minification (you have something implemented for css already looks like). At any rate, it was posted elsewhere in the forums here, but just in case you didn’t come across it:
http://farhadi.ir/works/smartoptimizer
That is php based apparently, for more general considerations you might be interested in this thread:
http://extjs.com/forum/showthread.php?t=34354
I glanced through a few pages of this thread, but the downside for the popular threads is they get so long. Anyway, a couple of questions/thoughts:
1. Your userguide is good an gives a good lay of the land. Something you might touch on briefly is the folder structure and use of matchbox. I was a little aware of it, and I saw the earlier posts this thread, but a little blurb on it would probably benefit people less informed than me.
2. I think I like your directory setup for the most part. I’m curious why you didn’t pull the application folder outside of it’s default location, perhaps on the same level with system and modules. Any downside to pulling it out on the same level that you know of?