What are your (web) server setup conventions?
delano: 1. /usr/local is where you install custom compiled binaries (which answers #4). /usr should contain only standard binaries, libraries, headers, etc...2. Some people use /usr/local, others use generic home directories (/home/PROJECT), and still others use /PROJECT. This is somewhat of a personal choice.3. If user content is uploaded directly to the filesystem, create a separate file system for it (if your root or project filesystems fill up, you're hooped). You could also consider uploading to S3 or a similar service.4. See #15. Be consistent and make notes about where things go (to remind yourself in 6 months and to make it easier to hand off). Also, be mindful of the filesystem permissions.