My jni folder in Eclipse looks like this:
It is grayed out and has a diagonal line across it. What does it mean? I can still edit my native C++ code in this folder and see the changes as I test the application.
It means the directory is being filtered from the source locations. It seems you can use this to exclude files that are not source from a source folder, although I've never used it.
I got rid of this irritation in Eclipse Indigo CDT by:
(Project) Properties ->C/C++ General ->Paths and Symbols ->Source Location Tab ->Edit Filter... ->Remove
You probably have something in the folder that is deprecated.
http://help.eclipse.org/indigo/index.jsp?topic=/org.eclipse.jdt.doc.user/reference/ref-icons.htm
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