Add items to the system path instead of the user path

[jrichter1]

Basically, whatever comes first takes precedence. And the newly installed stuff should be the higher priority, since system path always get read first.

[jrichter1]

this is actually the root cause for #1140

[jrichter1]

This also affects cygwin detection if multiple installations are present. A pre-existing cygwin may block the installer from detecting one it just installed.