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3.2 I have no idea how this happened but I was making a simple change in a Java file in 3.2 and checked it into a repository. Everything seemed okay until someone mailed me saying that the file was unreadable. Sure enough, the file had magically changed encodings from MacRoman (container default) to UTF-16. The properties dialog attributed this change to the content type of the file. Additionally, the "Other" combo did not contain MacRoman (but I could choose it by typing it). I could only revert the file by copying the text from Eclipse, pasting it into TextEdit, converting to plain text, and pasting back into Eclipse.
Have you seen this in 3.3
I'm going to close this bug based on its age and inability to reproduce.