Update REAMDE file so that it has the most updated version of the instructions for using the command line interface.
Fix code block formatting in the README file
Replace pre and code tags with backticks in the README file so that it is formatted fully in markdown
Remove redundant line from README file
Replace additional code tag with backtick in README file
Merge pull request #169 from dmcglinn/master

Add a command line usage section to the  README file
Add a template for downloading a file directly and copying it to the desired directory
Add an engine for only downloading a file

At the moment this is just a dummy engine since it doesn't really
need to do anything.
Allow downloading of files without cleaning line endings

To allow us to use engine.download_file for directly downloading
non text files it is necessary to be able to override its line
ending cleanup.
Have the download only template bypass line ending cleanup
Report if a file is now downloaded because it is in the working directory

This is an edge case for the DownloadOnlyTemplate where the file
is in the current DATA_DIR, but not in the appropriate raw_data
directory.
Add a script to download the mammal super tree
Adding script for the Bioclim 2.5 square km data
Adding 'retriever download' alias to 'retriever install download' for simplicity.
Replace all non-downloading methods in download_only engine with a dummy method.
After running download_only script, copy all files into the home directory. Moving this step from bioclim script to the engine.
Overloading some more methods for download_only engine to correctly handle downloads.
Get rid of insert_data_from_file.
Refactoring try_install_all to take an optional list of engines to test.
This set reset isn't needed and might mess things up. Keep track of all found files until final_cleanup is called.