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Having for example both Java and C++ sources in the same project is not well supported, except by manually modifying the .project file. See these threads: http://dev.eclipse.org/newslists/news.eclipse.tools.cdt/msg09365.html http://dev.eclipse.org/newslists/news.eclipse.newcomer/msg09941.html
*** This bug has been marked as a duplicate of 102527 ***