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Unqualified class name in javadoc tags causes eclipse to include import when organizing imports. Enter the following class: -- public class JavaDocImport { /** * {@link IOException} */ public void foo() { } } -- and choose organize imports. The result (tested on Eclipse 3.1M4/M6) is -- import java.io.IOException; public class JavaDocImport { /** * {@link IOException} */ public void foo() { } } -- The same happens for other javadoc tags like @see and @throws. Solution is not to import but to automatically qualify class to {@link java.io.IOException} or to flag with a warning.
Move to JDT/UI
If you disable Javadoc processing in the compiler then organize import will not consider Javadoc statements. In this code assist in Javadoc statements will insert fully qualified names. Treating types during organize import differently than types in code requires an additional option (since I personally like the current behaviour). But this isn't on the radar for 3.1
As of now 'LATER' and 'REMIND' resolutions are no longer supported. Please reopen this bug if it is still valid for you.