Bug 63883 Cannot configure option for enabling/disabling exclusion filters or custom output folders on a per project basis
Build M9 JDT/Core supports setting enablement for exclusion patterns and custom output folders on a per project basis. This isn't surfaced in the UI. There is only a global flag in workspace preferences.
org.eclipse.jdt.ui/ui/org/eclipse/jdt/internal/ui/preferences/NewJavaProjectPreferencePage.java
import org.eclipse.jdt.internal.ui.dialogs.StatusUtil;
	
/*
 * The page for defaults for classpath entries in new java projects.
 * See PreferenceConstants to access or change these values through public API.
 */
public class NewJavaProjectPreferencePage extends PreferencePage implements IWorkbenchPreferencePage {
	public static final String ID= "org.eclipse.jdt.ui.preferences.NewJavaProjectPreferencePage"; 
	
	private static final String SRCBIN_FOLDERS_IN_NEWPROJ= PreferenceConstants.SRCBIN_FOLDERS_IN_NEWPROJ;
	private static final String SRCBIN_SRCNAME= PreferenceConstants.SRCBIN_SRCNAME;
	private static final String SRCBIN_BINNAME= PreferenceConstants.SRCBIN_BINNAME;
	private static final String CLASSPATH_JRELIBRARY_INDEX= PreferenceConstants.NEWPROJECT_JRELIBRARY_INDEX;
	private static final String CLASSPATH_JRELIBRARY_LIST= PreferenceConstants.NEWPROJECT_JRELIBRARY_LIST;
	
	private static String fgDefaultEncoding= System.getProperty("file.encoding"); 
	public static IClasspathEntry[] getDefaultJRELibrary() {
		IPreferenceStore store= JavaPlugin.getDefault().getPreferenceStore();
		
		String str= store.getString(CLASSPATH_JRELIBRARY_LIST);
		int index= store.getInt(CLASSPATH_JRELIBRARY_INDEX);
		
		StringTokenizer tok= new StringTokenizer(str, ";"); 
		while (tok.hasMoreTokens() && index > 0) {
			tok.nextToken();
			index--;
		}
		
		if (tok.hasMoreTokens()) {
			IClasspathEntry[] res= decodeJRELibraryClasspathEntries(tok.nextToken());