Issue 2017189 by greg.1.anderson: Do not include options from alias records -unless- they are global options.
Remove unused variables.
Follow up to Issue #1936866 by jonhattan: Drush dl needs to put files in /modules or /themes, not /sites/all/whatever. Fix _pm_download_destination_lookup()
Issue #1295756 by moshe weitzman | Alan Evans: Drush ignores php item in site aliases which specifies the php binary to use.