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I had to do the wizard three times before I figured out how the second page works. Very counter-intuitive.
Can you be more specific? - what did you find confusing (perhaps difficult to enumerate) - what you would expect as a solution (also perhaps difficult)
I found confusing the fact that all the files I want to change are listed in the table, but that I also have to select the checkbox in order for them to be changed. Why show me a list of things if they're not going to be used unless I select some other option? I think the default value of the checkbox is wrong for the common case, for starters. In general, I think the whole second page should go away, in favor of something like a button pair on the third page that says "Uncheck repository files" and "Check repository files", which is what you really want to do. The message on the second page is scary, and the list is purely informational (has no function other than to show me what might or might not be changed).
later
Reopening
The wizard has been redesigned in 3.1
