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I had already reported this issue against Platform in bug 336734. I'm also asking JDT to consider this because almost every Java project contains some package.html or about.html files, which are often ISO-8859-1 encoded. When UTF is used on project level, these html files are also edited in UTF-8 and thus messed up. I think JDT should therefore derive the charset of html files from content if possible. As stated on bug 336734, such an extension already seems to exist in web tools. But installing web tools just to be able to edit html files in Java project properly seems a bit too much...
*** This bug has been marked as a duplicate of bug 336734 ***