You may find yourself interested in this topic -- I think the question you're asking is about the same as what I've asked here.
Also, let me use my situation to see if this is answerable:
WordPress is in /wp/
My layout is in /
I wanted my entries to be visible from a page in /
While leaving wordpress in /wp/
I've got this mostly working at the moment. However, I just need to find a way to rewrite the archives links (this might require some modification to the source sitting somewhere inside), and it may be the answer you're looking for.
What I've done:
Moved the page I wanted my entries to show up on to the directory I wanted it in;
Edited this line:
require_once('blog.header.php'); to look like this:
Saved and placed it where I wanted it, then viewed the page.
Why is it this simple?
Take a look at the next line:
$abspath variable gets its absolute path from the initial 'require_once' statement, so if you wanted to add things like plugins within the WordPress directory, instead of writing out the full path to it, copy the idea used with the above piece of code. You might end up with something like this:
Hopefully this is of use to you.