Fix first run and upgrades on Windows

This release fixes several issues on Windows causing the first run ("install into PATH") to run on every invocation. Additionally, it fixes an issues with upgrades.

Note: if upgrading from 0.3.x on Windows, it may fail, in which case upgrade manually. It may also cause a Command prompt window to open (temporarily), and fail to run the requested command. If the command window persists, close it, and the upgrade will be finished successfully — just run the command again.