[1110905] Agent auto update fails on windows
Add a longer pause on windows between stopping the legacy agent and
starting the update.  On Windows the wrapper must terminate and windows
must release file locks, this seems to account for some significant
extra time needed.
Add intentional API changes
Add intentional API changes (second try, fix cut+paste problem)
[BZ 961294] Expose config file option to the config mode for the wrapper script.
[BZ 961294] Move clean config option to the wrapper sh. The ec2 wrapper was using this option in an unreliable mode and could have resulted in errors in the wrapper or agent.
[BZ 961294] Add missing options to the help line.