Bug 11317 Won't export some files to .jar.
Create a new java project called "Foo". In the file system, create a folder named "Foo scripts", and in this folder create a file named "foo.txt". Drag this folder into the eclipse packages view and add it to the "Foo" project. Now try to export the project "Foo" to a .jar file. Only the manifest file shows up, even if the file "foo.txt" is checked!
org.eclipse.jdt.ui/ui/org/eclipse/jdt/internal/ui/jarpackager/JarFileExportOperation.java
/**
	 * Exports the resources as specified by the JAR package.
	 * 
	 * @param	progressMonitor	the progress monitor that displays the progress
	 * @see		#getStatus()
	 */
	public void run(IProgressMonitor progressMonitor) throws InvocationTargetException, InterruptedException {
		if (fJarPackage != null)
			singleRun(progressMonitor);
		else {
			int jarCount= fDescriptionFiles.length;
			progressMonitor.beginTask("", jarCount); 
			try {
				for (int i= 0; i < jarCount; i++) {
					SubProgressMonitor subProgressMonitor= new SubProgressMonitor(progressMonitor, 1);
					fJarPackage= readJarPackage(fDescriptionFiles[i]);
					if (fJarPackage != null)
						singleRun(subProgressMonitor);
				}
			} finally {
				progressMonitor.done();
			}
		}
	}
	public void singleRun(IProgressMonitor progressMonitor) throws InvocationTargetException, InterruptedException {
		try {
			if (!preconditionsOK())
				throw new InvocationTargetException(null, JarPackagerMessages.getString("JarFileExportOperation.jarCreationFailedSeeDetails")); 
			int totalWork= countSelectedElements();
			if (!isAutoBuilding() && fJarPackage.isBuildingIfNeeded()) {