directoryPrefix and filenamePrefix support

Adds support for these new options, including mapping usage of the
old-style prefix option to the new option depending on what kind of
partial reference is encountered.

For bare filenames, prefix behaves like filenamePrefix. For paths
including a directory, prefix behaves like directoryPrefix (which
matches the current weird behavior).
Unit tests for new xxxPrefix options

Adds unit tests for filenamePrefix, directoryPrefix, and a combination
of the two. Reuses existing fixture data and expectation output, except
for the combination unit test which uses new expectation output.