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.