Fixes to download only engine

1. Use known locations of download only files when copying. This fixes a bug that occurred if the file was present in the search path, but not in the raw_data directory, resulting in an error when the Retriever tried to copy it from the raw data directory.

2. Allow explicitly listing files to be moved by the download engine. This fixes an issue with the bioclim script that resulted in the files in the archive not being copied unless they were already present before running the Retriever, because they were not being added to all_files.