This allows FullyQualifiedNameProvider to work with absolute paths,
rather than assuming all paths given will be relative to the current
directory. This enables tools like Fixit to provide a root path, and
have the FullyQualifiedNameProvider correctly scope the final results
relative to that root path.
This does require that both the root path and the given file paths
match the other as relative or absolute, due to the
`calculate_module_and_package` helper comparing file paths relative
to the root path, but this seems like a reasonable tradeoff, and
unlikely to cause a problem in normal use cases.