ensurepip forks a subprocess to run pip itself, but that subprocess only inherits a -I isolated mode flag (see _run_pip() in Lib/ensurepip/__init__.py), not the "-E -s" flags that the installer has been using. This means that parts of ensurepip don't actually run in an isolated environment and can make incorrect decisions based on packages installed in the user site-packages.
Rather than using Burn "Persisted" variables we now add registry keys for each added feature. These can be detected by the installer regardless of which version installed them, and we use this for Modify and Upgrade. In particular, Upgrades can't access the Persisted variables, but can find well-known registry keys.
There are also some changes to the bootstrap app to properly handle upgrades.
Finally, a few minor improvements to the Windows build to keep things tidier.
Michael Vincent
Steve Dower
Steve Dower