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The logic in NewClassCodeGenerator.getHeaderIncludeString method is based on projectLocation.isPrefixOf(headerLocation) condition that does not take linked folders into account. When the files for the new class are created under a linked folder, the include statement in the generated source file is created with angle brackets instead of quotes.
Created attachment 197212 [details] Fix To reduce risk associated with this change I didn't attempt to clean up the logic in NewClassCodeGenerator.getHeaderIncludeString, but instead added a simple additional condition to existing code that prevents creation of system includes for header files inside workspace.
Fixed in HEAD > 20110601.
*** cdt cvs genie on behalf of sprigogin *** Bug 348039 - When creating new class project header file is treated as system include. [*] NewClassCodeGenerator.java 1.34 http://dev.eclipse.org/viewcvs/index.cgi/org.eclipse.cdt/all/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/wizards/classwizard/NewClassCodeGenerator.java?root=Tools_Project&r1=1.33&r2=1.34