Changes it does make aren't logged anywhere. Especially where users are requested for input via a popup window this would be very useful as it allows you to revisit the choices you made. I for example get a popup window for Spell Mastery, but I have no clue what it wants me to do and it accepts a blank input. Unless I remember that I need to look into that, I'm probably left with a broken Spell Mastery.
Decisions now get logged to the main log file as INFO lines. The log includes the request made, the options and the option selected/entered.