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Does it copy all files in ~/Library ? Including cache files and even things like Flash cookies? What about user created files/folders in / ?

etc etc

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Migration Assistant is fairly well documented in - basically if a newer or equivalent version of a file is not present, it gets moved by default.

In your case ~/Library is moved if you select that user - you can't deselect it like some other folders in the home folder.

Applications (which includes /Library/Application support as well as /Applications) move when that is selected.

Files in / only move if you choose other files. Everything goes AFAIK. Even ByHost preferences that no longer are used since the host has changed.

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The Migration Assistant will write to the logs, like every other application and service. Please see your logs for these details: /Library/Logs/SystemMigration.log

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nothing there for me, on Mountain Lion - I could find it under /private/var/log/system.log tho, marked with Sender as MigrateTool – cregox May 31 '13 at 13:03

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