tree-wide: use path_join() instead of prefix_roota() in various cases

tree-wide: use path_join() instead of prefix_roota() in various cases

prefix_roota() is something we should stop using. It is bad for three
reasons:

1. As it names suggests it's supposed to be used when working relative
   to some root directory, but given it doesn't follow symlinks (and
   instead just stupidly joins paths) it is not a good choice for that.

2. More often than not it is currently used with inputs under control of
   the user, and that is icky given it typically allocates memory on the
   stack.

3. It's a redundant interface, where chase_symlinks() and path_join()
   already exist as better, safer interfaces.

Hence, let's start moving things from prefix_roota() to path_join() for
the cases where that's appropriate.