Clean up remote.py and misc.py changes.

Fixed method names to be non-redundant (remote_mktemp in remote is
now just mktemp, for example), and made some parameters be more
self descriptive.  Added some docstrings.  Fixed sudo setting in
get_file method.

Made chmod independent of the actual sftp file getting.
Do not do extra file copy if non-sudo read is needed.
Fixed some parameter names. Made sure temp files are removed.