If you have a non-standard setup the Debian scripted install can make a mess and then bring up a text window saying things didn't go as planned.
They say things can't get lost "don't worry", but if you are running an 
ancient, a "Daily" build or non-Debian set-up worry. I'm sure it worked 
for them.
There is a Debian wiki about it but it didn't help my situation.

My advice: back-up everything related including hidden files in the users home directory, rename and hide them before pulling the trigger on the transition script.
--

Clarke



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