Just uncheck them in the import window. You should still import the InvActionLists and MenuActionLists folders, though, as these may contain ActionLists used by your Menu Manager.
Unity 4.5 is a little better about selective updating luckily, you can collapse folders to have a better overview of all the files.
The one thing I noticed is that it now no longer singles out modified files at the bottom of the import window, so I'm glad I moved my modified scripts to a seperate folder otherwise I would have been sweating bullets trying to remember which ones to uncheck
I've found the best way to update AC (and other Unity assets for that matter) is to create a fresh branch in Git and import the asset there. That way I can see exactly what changed and then easily merge the changes with any customizations I may have made.
Takes 5-10 minutes for each update of AC but it's worth it in my experience. When I screw up the merge the worst thing that can happen is that I need to reset to my last known good configuration.
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Takes 5-10 minutes for each update of AC but it's worth it in my experience. When I screw up the merge the worst thing that can happen is that I need to reset to my last known good configuration.