IMPORTANT: The accepted answer was accepted post-bounty, not necessarily because I felt it was the best answer.
I find myself doing things over an
I think what you have here is great.... What you've listed is of course all about the public front end of your app. My only addition to this, is to keep all your backend code and source out of the public web space if possible, as the less things you have in the public space, the more secure your app is.
So I'd suggest you take your entire tree, and put it in:
httpdocs/(all you had in your project template folder)
then put all your backend code (e.g. php libraries, sql files, etc) in adjacent subdirectories:
httpdocs/(all you had in your project template folder)
phplibs/
sql/
etc.
And, even for your front end stuff, make sure you don't copy in any example files that may come with your front end libraries, as the examples themselves may have security problems that would allow people to XSS or otherwise compromise your site.