this sounds like a possible duplicate of exclude packages from eclipse's organize imports.
basically, you want to change your type filters preference to exclude
java.awt.* packages. keep in mind that doing so will make things harder/confusing if you ever try to write awt/swing code.
one thing that pops into my mind is altering the class template in the preferences to include the line:
unless you are going to use the awt version of a list, or care about unused import statements, that should solve this annoying issue ..
manually invoke organize imports and it will ask you when an ambiguity is found.
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