This changeset attempts to reduce the number of places that behavior
substantively changes based on the presence of an external manifest or
not.  Key changes include

- Fetchers now take a manifest entry in their constructor.  The
  manifest has no knowledge of how the entry was created and doesn't
  care.

- Fetchers expect a fully resolved version in the manifest entry.
  Users can construct such a version using the
  #resolve_version(source, version) functions

- Omnibus::Project only interacts with the manifest in 2 ways: (1)
  passes it to the Software when constructing software objects, and
  (2) polling the software collection for their manifest entries to
  present it to the user.

- Omnibus::Software contains the main interaction with the manifest.
  When constructing a Fetcher, it passes its own manifest entry.
  Omnibus::Software#manifest_entry is now the only substantive place
  in the code where we do something different based on whether the
  user provided a manifest entry or not.