Fixing issues with install's --target option.

 1. Check for the existence of a directory before copying from temporary directory to final target. If it exists, warn the user.
 2. If the user specifies the --upgrade option and the directory exists, delete it and continue with installation.
 3. Adding tests for above cases.

This resolves #1489, #1710 completely and parts of #1833.
Fixing pep8 errors
Covering case of single-module packages.

Behavior is now to overwrite files or folders if --upgrade is specified, however, links will not be overwritten.
Merge pull request #2007 from jonparrott/develop

Fixing issues with install's --target option.