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
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 * Copyright (c) 2000, 2003 IBM Corporation and others.
 * All rights reserved. This program and the accompanying materials 
 * are made available under the terms of the Common Public License v1.0
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 * http://www.eclipse.org/legal/cpl-v10.html
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 * Contributors:
 *     IBM Corporation - initial API and implementation
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package org.eclipse.jdt.internal.ui.preferences;
import java.io.UnsupportedEncodingException;
import java.net.URLDecoder;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.NoSuchElementException;
import java.util.StringTokenizer;
import org.eclipse.core.resources.IProject;
import org.eclipse.core.resources.IResource;
import org.eclipse.core.resources.IWorkspace;
import org.eclipse.core.runtime.IPath;
import org.eclipse.core.runtime.IStatus;
import org.eclipse.core.runtime.Path;
import org.eclipse.core.runtime.Status;