When upgrading an existing site, there should be at least one directory

("uploaded") that is writable by the web server. We can use this as a

reference point for all other directories that need to be made writable.
We now stat that directory and change ownership of all the other

directories.
I've also added uploaded/files as a generated directory. Technically,

this can be created on-the-fly, but since we know we want it, and make

the other directories, we may as well make this one up-front.

Created a site. Changed the ownership of a directory, and removed another.

Upgraded the site, and saw the expected permissions.