Remove "also uninstall prefs" setting.

Since the values are now stored in a file alongside the script, there's no practical place to keep them on uninstall anymore.  I.E. Always remove them on uninstall.

Refs #1798
Remove references to script.prefroot.

Except in one legacy migration codepath.  Values are now stored in per-script DBs instead.

Refs #1798
Migrate the stored values DB during script update/reinstall.

Refs #1798