This looks like a much more formalized structure than what we do. Do you use it in production currently or is this a prototype?

This is my primary new WP project approach (which isn't perfect):

    mkdir Example-Project
    cd Example-Project

    # Grab the latest wordpress, www is our DocumentRoot
    curl wordpress.org/latest.tar.gz | tar -xvz --
    mv wordpress www
    cd www

    # Drop the default wp-content and symlink so we dont need to
    # keep all of wp in Git
    mv wp-content ..
    ln -s ../wp-content
    echo 'www/' >> .gitignore

    # Make the repo
    git init
    git add . && git commit -m 'First!'

The main problem I run into is with the symlink'd wp-content directory. WP seems to not interpret it well and I have to set up Alias directives in the virtualhost configuration to compensate. Are you doing anything similar with the app/ directory?