Use known locations for download only files when copying

An edge case bug existed where the file to be downloaded existed
in the search path, but not in the appropriate raw_data directory.
In this case the Retriever tried to copy the file from the
raw_data directory and threw an error. This situation could
occur if downloaded files are stored in version control, but
running the program calls the Retriever.

This is addressed by copying the file from the location where
find_file actually finds it. The details are reported so that
there is no confusion about where the files are coming from.
Allow explicitly listing files to be moved by the download engine

It is often desireable to download an archive with a number of
files to be extracted. The download_only engine would currently
only move those files if they were present in the raw_data
directory prior to running `retriever download DATASET` because
find_file didn't find them and therefore couldn't add them to
all_files.

This commit adds a register_files method that can be called from
a retriever script that processes an archive of files for download
to have the names of these files added to all_files following
the download.
Removing unused imports from bioclim script
Merge pull request #178 from ethanwhite/fix-download

Fixes to download only engine