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R2.0 When you save a file, it always uses the workbench encoding, which will be different than the encoding chosen by the user via Edit / Encoding. This can result in loss of data. It should save the file in the same encoding as shown in Edit / Encoding. Saving files using different encodings can result in problems for the Java builder, since it assumes all .java files use the same encoding (the workbench encoding). However, that is what the user asked for. The user may well use the workbench encoding for all .java files, but use different encodings for other files (e.g. UTF-8 for XML files). See also newsgroup thread "about Japanese Encode".
It's kind of ugly what you have to do to fix this in a subclass, too. All encoding-related behavior should be neatly broken out.
*** Bug 21167 has been marked as a duplicate of this bug. ***
This is in since M4.