### Eclipse Workspace Patch 1.0
#P org.eclipse.pde.api.tools
Index: plugin.xml
===================================================================
RCS file: /cvsroot/eclipse/pde/apitools/org.eclipse.pde.api.tools/plugin.xml,v
retrieving revision 1.38
diff -u -r1.38 plugin.xml
--- plugin.xml	14 Jan 2011 19:10:37 -0000	1.38
+++ plugin.xml	4 Mar 2011 15:29:48 -0000
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <?eclipse version="3.2"?>
 <!--
-    Copyright (c) 2009, 2010 IBM Corporation and others.
+    Copyright (c) 2009, 2011 IBM Corporation and others.
     All rights reserved. This program and the accompanying materials
     are made available under the terms of the Eclipse Public License v1.0
     which accompanies this distribution, and is available at
@@ -239,6 +239,16 @@
           library="lib/apitooling-ant.jar"
           name="apitooling.apiuse_reportconversion">
     </antTask>
+        <antTask
+          class="org.eclipse.pde.api.tools.internal.tasks.MissingRefProblemsTask"
+          library="lib/apitooling-ant.jar"
+          name="apitooling.apiusescanproblems">
+    </antTask>
+    <antTask
+          class="org.eclipse.pde.api.tools.internal.tasks.MissingRefProblemsReportConversionTask"
+          library="lib/apitooling-ant.jar"
+          name="apitooling.apiusescanproblem_reportconversion">
+    </antTask>
     <antTask
           class="org.eclipse.pde.api.tools.internal.tasks.ApiMigrationTask"
           library="lib/apitooling-ant.jar"
Index: src/org/eclipse/pde/api/tools/internal/builder/BaseApiAnalyzer.java
===================================================================
RCS file: /cvsroot/eclipse/pde/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/builder/BaseApiAnalyzer.java,v
retrieving revision 1.127
diff -u -r1.127 BaseApiAnalyzer.java
--- src/org/eclipse/pde/api/tools/internal/builder/BaseApiAnalyzer.java	28 Feb 2011 19:04:23 -0000	1.127
+++ src/org/eclipse/pde/api/tools/internal/builder/BaseApiAnalyzer.java	4 Mar 2011 15:29:50 -0000
@@ -280,7 +280,7 @@
 			Util.updateMonitor(localMonitor);
 			
 			if (component instanceof ProjectComponent) {
-				checkExternalDependencies(component, bcontext, localMonitor.newChild(1));
+				checkExternalDependencies(component, bcontext, null, localMonitor.newChild(1));
 			}
 		} catch(CoreException e) {
 			ApiPlugin.log(e);
@@ -305,8 +305,8 @@
 	 * @param monitor
 	 * @throws CoreException
 	 */
-	void checkExternalDependencies(IApiComponent apiComponent, IBuildContext bcontext, IProgressMonitor monitor) throws CoreException {
-		if (!isSeverityEnabled()) {
+	public void checkExternalDependencies(IApiComponent apiComponent, IBuildContext bcontext, Properties properties, IProgressMonitor monitor) throws CoreException {
+		if (!isSeverityEnabled(properties)) {
 			return;
 		}
 		String[] apiUseTypes = getApiUseTypes(bcontext);
@@ -367,19 +367,34 @@
 		}
 	}
 
-	public boolean isSeverityEnabled() {
+	public boolean isSeverityEnabled(Properties properties) {
 		IEclipsePreferences node = InstanceScope.INSTANCE.getNode(ApiPlugin.PLUGIN_ID);
-
-		if (!node.get(IApiProblemTypes.API_USE_SCAN_TYPE_SEVERITY, ApiPlugin.VALUE_IGNORE).equalsIgnoreCase(ApiPlugin.VALUE_IGNORE)) {
-			return true;
-		}
-		if (!node.get(IApiProblemTypes.API_USE_SCAN_METHOD_SEVERITY, ApiPlugin.VALUE_IGNORE).equalsIgnoreCase(ApiPlugin.VALUE_IGNORE)) {
-			return true;
+		if (properties == null) {
+			if (!isIgnore(node.get(IApiProblemTypes.API_USE_SCAN_TYPE_SEVERITY, ApiPlugin.VALUE_IGNORE)))
+				return true;
+			if (!isIgnore(node.get(IApiProblemTypes.API_USE_SCAN_METHOD_SEVERITY, ApiPlugin.VALUE_IGNORE)))
+				return true;
+			if (isIgnore(node.get(IApiProblemTypes.API_USE_SCAN_FIELD_SEVERITY, ApiPlugin.VALUE_IGNORE)))
+				return true;
+			return false;
+		} else {
+			if (properties.isEmpty())
+				return true; // preferences parameter not provided
+			if (!isIgnore(properties.get(IApiProblemTypes.API_USE_SCAN_TYPE_SEVERITY))) 
+				return true;
+			if (!isIgnore(properties.get(IApiProblemTypes.API_USE_SCAN_METHOD_SEVERITY))) 
+				return true;
+			if (!isIgnore(properties.get(IApiProblemTypes.API_USE_SCAN_FIELD_SEVERITY))) 
+				return true;
+			return false;
 		}
-		if (!node.get(IApiProblemTypes.API_USE_SCAN_FIELD_SEVERITY, ApiPlugin.VALUE_IGNORE).equalsIgnoreCase(ApiPlugin.VALUE_IGNORE)) {
-			return true;
+	}
+
+	private boolean isIgnore(Object value) {
+		if (value != null && (value.toString().equalsIgnoreCase(ApiPlugin.VALUE_ERROR) || value.toString().equalsIgnoreCase(ApiPlugin.VALUE_WARNING))) {
+			return false;
 		}
-		return false;
+		return true;
 	}
 	
 	/**
@@ -395,33 +410,36 @@
 	 */
 	protected IApiProblem createExternalDependenciesProblem(HashMap problems, IReferenceDescriptor dependency, String referenceTypeName, IMemberDescriptor referencedMember, int elementType, int flag) {	
 		String resource = referenceTypeName;
-		String primaryTypeName = referenceTypeName.replace('$', '.');
+		String primaryTypeName = referenceTypeName.replace('$', '.');		
 		int charStart = -1, charEnd = -1, lineNumber = -1; 
-		try {
-			IType type = fJavaProject.findType(primaryTypeName);
-			IResource res = Util.getResource(fJavaProject.getProject(), type);
-			if(res == null) {
-				return null;
-			}
-			if(!Util.isManifest(res.getProjectRelativePath())) {
-				resource = res.getProjectRelativePath().toString();
-			}
-			else {
-				resource = "."; //$NON-NLS-1$
-			}
-			if (type != null) {
-				ISourceRange range = type.getNameRange();
-				charStart = range.getOffset();
-				charEnd = charStart + range.getLength();
-				try {
-					IDocument document = Util.getDocument(type.getCompilationUnit());
-					lineNumber = document.getLineOfOffset(charStart);
-				} catch (BadLocationException e) {
-					// ignore
-				}			
-				catch (CoreException ce) {}
-			}
-		} catch (JavaModelException e) {}
+		if (fJavaProject != null) {
+			try {
+				
+				IType type = fJavaProject.findType(primaryTypeName);
+				IResource res = Util.getResource(fJavaProject.getProject(), type);
+				if(res == null) {
+					return null;
+				}
+				if(!Util.isManifest(res.getProjectRelativePath())) {
+					resource = res.getProjectRelativePath().toString();
+				}
+				else {
+					resource = "."; //$NON-NLS-1$
+				}
+				if (type != null) {
+					ISourceRange range = type.getNameRange();
+					charStart = range.getOffset();
+					charEnd = charStart + range.getLength();
+					try {
+						IDocument document = Util.getDocument(type.getCompilationUnit());
+						lineNumber = document.getLineOfOffset(charStart);
+					} catch (BadLocationException e) {
+						// ignore
+					}			
+					catch (CoreException ce) {}
+				}
+			} catch (JavaModelException e) {}
+		}
 		String[] msgArgs = new String[] {referenceTypeName, referencedMember.getName(), dependency.getComponent().getId()};
 		int kind = 0;
 		switch (elementType) {
@@ -441,7 +459,8 @@
 		}
 		
 		int dependencyNameIndex = 2;	// the comma separated list of dependent plugins 
-		String problemKey = referenceTypeName +  resource + dependency.getReferenceKind() + elementType + kind + flag;
+		int problemId = ApiProblemFactory.createProblemId(IApiProblem.CATEGORY_API_USE_SCAN_PROBLEM, elementType, kind, flag);
+		String problemKey = referenceTypeName +  problemId;
 		IApiProblem similarProblem =  (IApiProblem) problems.get(problemKey);
 		if (similarProblem != null) {
 			String[] existingMsgArgs = similarProblem.getMessageArguments()[dependencyNameIndex].split(", "); //$NON-NLS-1$
Index: src/org/eclipse/pde/api/tools/internal/search/MissingRefMetadata.java
===================================================================
RCS file: src/org/eclipse/pde/api/tools/internal/search/MissingRefMetadata.java
diff -N src/org/eclipse/pde/api/tools/internal/search/MissingRefMetadata.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/org/eclipse/pde/api/tools/internal/search/MissingRefMetadata.java	1 Jan 1970 00:00:00 -0000
@@ -0,0 +1,231 @@
+/*******************************************************************************
+ * Copyright (c) 2011 IBM Corporation and others.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *     IBM Corporation - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.pde.api.tools.internal.search;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.util.Calendar;
+
+import org.eclipse.core.runtime.CoreException;
+import org.eclipse.osgi.util.NLS;
+import org.eclipse.pde.api.tools.internal.IApiCoreConstants;
+import org.eclipse.pde.api.tools.internal.provisional.search.IMetadata;
+import org.eclipse.pde.api.tools.internal.util.Util;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.NodeList;
+
+import com.ibm.icu.text.DateFormat;
+
+/**
+ * Implementation of {@link IMetadata} for API Use Scan problem report
+ */
+public class MissingRefMetadata implements IMetadata {
+
+	/**
+	 * XML tag name for Profile
+	 */
+	public static final String PROFILE = "profile"; //$NON-NLS-1$
+	/**
+	 * XML tag name for the date the scan was run
+	 */
+	public static final String RUNATDATE = "runatdate"; //$NON-NLS-1$
+	/**
+	 * XML tag name for the report location
+	 */
+	public static final String REPORTLOCATION = "reportlocation"; //$NON-NLS-1$
+	/**
+	 * XML tag name for api use scan list
+	 */
+	public static final String APIUUSESCANS = "apiusescans"; //$NON-NLS-1$
+	/**
+	 * XML tag name for the value
+	 */
+	public static final String VALUE = "value"; //$NON-NLS-1$
+	/**
+	 * Root tag for the metadata file
+	 */
+	public static final String METADATA = "metadata"; //$NON-NLS-1$
+
+	private String profile = null;
+	private String runatdate = null;
+	private String reportlocation = null;
+	private String apiusescans = null;
+
+	/**
+	 * Constructor
+	 */
+	public MissingRefMetadata() {
+		//create an empty metadata object
+	}
+
+	/**
+	 * Constructor
+	 * @param profile
+	 * @param runatdate
+	 * @param reportlocation
+	 * @param scopepattern
+	 * @param refpattern
+	 * @param apiusescans
+	 */
+	public MissingRefMetadata(String profile, String reportlocation, String apiusescans) {
+		this.profile = profile;
+		this.runatdate = DateFormat.getDateTimeInstance().format(Calendar.getInstance().getTime());
+		this.reportlocation = reportlocation;
+		this.apiusescans = apiusescans;
+	}
+
+	/**
+	 * Returns the use metadata from meta.xml
+	 * @return
+	 * @throws Exception
+	 */
+	public static MissingRefMetadata getMetadata(File xmlFile) throws Exception {
+		MissingRefMetadata metadata = new MissingRefMetadata();
+		try {
+			if (xmlFile.exists()) {
+				String xmlstr = Util.getFileContentAsString(xmlFile);
+				Element doc = Util.parseDocument(xmlstr.trim());
+				Element element = null;
+				String value = null, name = null;
+				NodeList nodes = doc.getElementsByTagName("*"); //$NON-NLS-1$
+				for (int i = 0; i < nodes.getLength(); i++) {
+					element = (Element) nodes.item(i);
+					value = element.getAttribute(MissingRefMetadata.VALUE);
+					name = element.getNodeName();
+
+					if (PROFILE.equals(name)) {
+						metadata.setProfile(value);
+						continue;
+					}
+					if (RUNATDATE.equals(name)) {
+						metadata.setRunAtDate(value);
+						continue;
+					}
+					if (REPORTLOCATION.equals(name)) {
+						metadata.setReportLocation(value);
+						continue;
+					}
+					if (APIUUSESCANS.equals(name)) {
+						metadata.setApiUseScans(value);
+						continue;
+					}
+				}
+			}
+		} catch (CoreException e) {
+			throw new Exception(NLS.bind(SearchMessages.MissingRefMetadata_CoreExceptionInParsing, xmlFile.getAbsolutePath()));
+		}
+		return metadata;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.eclipse.pde.api.tools.internal.provisional.search.IMetadata#serializeToFile(java.io.File)
+	 */
+	public void serializeToFile(File file) throws IOException, CoreException {
+		BufferedWriter writer = null;
+		try {
+			Document doc = Util.newDocument();
+			Element root = doc.createElement(MissingRefMetadata.METADATA);
+			doc.appendChild(root);
+
+			Element child = doc.createElement(MissingRefMetadata.PROFILE);
+			root.appendChild(child);
+			child.setAttribute(MissingRefMetadata.VALUE, profile);
+
+			child = doc.createElement(MissingRefMetadata.RUNATDATE);
+			root.appendChild(child);
+			child.setAttribute(MissingRefMetadata.VALUE, runatdate);
+
+			child = doc.createElement(MissingRefMetadata.REPORTLOCATION);
+			root.appendChild(child);
+			child.setAttribute(MissingRefMetadata.VALUE, reportlocation);
+
+			child = doc.createElement(MissingRefMetadata.APIUUSESCANS);
+			root.appendChild(child);
+			child.setAttribute(MissingRefMetadata.VALUE, apiusescans);
+
+			writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(file), IApiCoreConstants.UTF_8));
+			writer.write(Util.serializeDocument(doc));
+			writer.flush();
+		} finally {
+			if (writer != null) {
+				writer.close();
+			}
+		}
+	}
+
+	/**
+	 * Allows the profile to be set. This method accepts <code>null</code>
+	 * @param profile the profile to set
+	 */
+	public void setProfile(String profile) {
+		this.profile = profile;
+	}
+
+	/**
+	 * Returns the profile set in this metadata or <code>null</code> if none.
+	 * @return the profile
+	 */
+	public String getProfile() {
+		return profile;
+	}
+
+	/**
+	 * Allows the run-at date to be set. This method accepts <code>null</code>
+	 * @param date the date to set
+	 */
+	public void setRunAtDate(String date) {
+		this.runatdate = date;
+	}
+
+	/**
+	 * Returns the run-at date set in this metadata or <code>null</code> if none.
+	 * @return the run-at date or <code>null</code>
+	 */
+	public String getRunAtDate() {
+		return this.runatdate;
+	}
+
+	/**
+	 * Returns the report location set in this metadata or <code>null</code> if none.
+	 * @return the report location or <code>null</code>
+	 */
+	public String getReportLocation() {
+		return this.reportlocation;
+	}
+
+	/**
+	 * Allows the report location to be set. This method accepts <code>null</code>.
+	 * @param location the new report location
+	 */
+	public void setReportLocation(String location) {
+		this.reportlocation = location;
+	}
+
+	/**
+	 * Returns the API Use Scans set in this metadata or <code>null</code> if none.
+	 * @return the apiusescans
+	 */
+	public String getApiUseScans() {
+		return apiusescans;
+	}
+
+	/**
+	 * Allows the API Use Scan to be set. This method accepts <code>null</code>
+	 * @param apiusescans the apiusescans to set
+	 */
+	public void setApiUseScans(String apiusescans) {
+		this.apiusescans = apiusescans;
+	}
+}
Index: src/org/eclipse/pde/api/tools/internal/search/MissingRefParser.java
===================================================================
RCS file: src/org/eclipse/pde/api/tools/internal/search/MissingRefParser.java
diff -N src/org/eclipse/pde/api/tools/internal/search/MissingRefParser.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/org/eclipse/pde/api/tools/internal/search/MissingRefParser.java	1 Jan 1970 00:00:00 -0000
@@ -0,0 +1,199 @@
+/*******************************************************************************
+ * Copyright (c) 2011 IBM Corporation and others.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *     IBM Corporation - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.pde.api.tools.internal.search;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.parsers.SAXParser;
+import javax.xml.parsers.SAXParserFactory;
+
+import org.eclipse.osgi.util.NLS;
+import org.eclipse.pde.api.tools.internal.IApiXmlConstants;
+import org.eclipse.pde.api.tools.internal.problems.ApiProblem;
+import org.eclipse.pde.api.tools.internal.provisional.Factory;
+import org.eclipse.pde.api.tools.internal.provisional.descriptors.IComponentDescriptor;
+import org.eclipse.pde.api.tools.internal.search.MissingRefReportConverter.MissingRefVisitor;
+import org.eclipse.pde.api.tools.internal.util.Util;
+import org.xml.sax.Attributes;
+import org.xml.sax.SAXException;
+import org.xml.sax.helpers.DefaultHandler;
+
+class MissingRefParser {
+
+	class MissingRefProblemHandler extends DefaultHandler {
+
+		List problems = new ArrayList();
+		private String typename;
+		private int linenumber;
+		private int charstart;
+		private int charend;
+		private int id;
+		private List messageargs = new ArrayList();
+		private Map extraargs = new HashMap();
+
+		public void startDocument() throws SAXException {
+
+		}
+
+		public void startElement(String uri, String localName, String qName, Attributes attributes) throws SAXException {
+			if (IApiXmlConstants.ELEMENT_API_PROBLEM.equalsIgnoreCase(qName)) {
+				typename = attributes.getValue(IApiXmlConstants.ATTR_TYPE_NAME);
+				linenumber = Integer.parseInt(attributes.getValue(IApiXmlConstants.ATTR_LINE_NUMBER));
+				charstart = Integer.parseInt(attributes.getValue(IApiXmlConstants.ATTR_CHAR_START));
+				charend = Integer.parseInt(attributes.getValue(IApiXmlConstants.ATTR_CHAR_END));
+				id = Integer.parseInt(attributes.getValue(IApiXmlConstants.ATTR_ID));
+			} else if (IApiXmlConstants.ELEMENT_PROBLEM_MESSAGE_ARGUMENTS.equalsIgnoreCase(qName)) {
+				messageargs.clear();
+			} else if (IApiXmlConstants.ELEMENT_PROBLEM_MESSAGE_ARGUMENT.equalsIgnoreCase(qName)) {
+				messageargs.add(attributes.getValue(IApiXmlConstants.ATTR_VALUE));
+			} else if (IApiXmlConstants.ELEMENT_PROBLEM_EXTRA_ARGUMENTS.equalsIgnoreCase(qName)) {
+				extraargs.clear();
+			} else if (IApiXmlConstants.ELEMENT_PROBLEM_EXTRA_ARGUMENT.equalsIgnoreCase(qName)) {
+				extraargs.put(attributes.getValue(IApiXmlConstants.ATTR_ID), attributes.getValue(IApiXmlConstants.ATTR_VALUE));
+			}
+		}
+
+		public void endElement(String uri, String localName, String qName) throws SAXException {
+			if (IApiXmlConstants.ELEMENT_API_PROBLEM.equalsIgnoreCase(qName)) {
+				String[] argumentids = new String[extraargs.size()];
+				Object[] arguments = new Object[extraargs.size()];
+				int i = 0;
+				for (Iterator iterator = extraargs.keySet().iterator(); iterator.hasNext(); i++) {
+					argumentids[i] = (String) iterator.next();
+					arguments[i] = extraargs.get(argumentids[i]);
+				}
+				ApiProblem problem = new ApiProblem(null, typename, (String[]) messageargs.toArray(new String[messageargs.size()]), argumentids, arguments, linenumber, charstart, charend, id);
+				problems.add(problem);
+			}
+		}
+
+		public void endDocument() throws SAXException {
+		}
+
+		public List getProblems() {
+			return problems;
+		}
+	}
+
+	public void parse(String xmlLocation, MissingRefVisitor visitor) throws Exception {
+		if (xmlLocation == null) {
+			throw new Exception(SearchMessages.missing_xml_files_location);
+		}
+		File reportsRoot = new File(xmlLocation);
+		if (!reportsRoot.exists() || !reportsRoot.isDirectory()) {
+			throw new Exception(NLS.bind(SearchMessages.invalid_directory_name, xmlLocation));
+		}
+		File[] components = getDirectories(reportsRoot);
+		components = sort(components);
+
+		visitor.visitScan();
+		SAXParser parser = getParser();
+		// Treat each top level directory as a producer component
+		for (int i = 0; i < components.length; i++) {
+			if (components[i].isDirectory()) {
+				String[] idv = getIdVersion(components[i].getName());
+				IComponentDescriptor targetComponent = Factory.componentDescriptor(idv[0], idv[1]);
+				if (visitor.visitComponent(targetComponent)) {
+					File[] xmlfiles = Util.getAllFiles(components[i], new FileFilter() {
+						public boolean accept(File pathname) {
+							return pathname.isFile() && pathname.getName().endsWith(".xml");  //$NON-NLS-1$
+						}
+					});
+					if (xmlfiles != null && xmlfiles.length > 0) {
+						xmlfiles = sort(xmlfiles); // sort to visit in determined order
+						for (int k = 0; k < xmlfiles.length; k++) {
+							try {
+								MissingRefProblemHandler handler = new MissingRefProblemHandler();
+								parser.parse(xmlfiles[k], handler);
+								List apiProblems = handler.getProblems();
+								visitor.addToCuurentReport(apiProblems);
+							} catch (SAXException e) {
+							} catch (IOException e) {
+							}
+						}
+					}
+					visitor.endVisitComponent();
+				}
+			}
+		}
+	}
+
+	/**
+	 * Sorts the given files by name (not path).
+	 * 
+	 * @param files
+	 * @return sorted files
+	 */
+	private File[] sort(File[] files) {
+		List sorted = new ArrayList(files.length + 2);
+		for (int i = 0; i < files.length; i++) {
+			sorted.add(files[i]);
+		}
+
+		Collections.sort(sorted, Util.filesorter);
+		return (File[]) sorted.toArray(new File[sorted.size()]);
+	}
+
+	private String[] getIdVersion(String value) {
+		int index = value.indexOf(' ');
+		if (index > 0) {
+			String id = value.substring(0, index);
+			String version = value.substring(index + 1);
+			if (version.startsWith("(")) {  //$NON-NLS-1$
+				version = version.substring(1);
+				if (version.endsWith(")")) {  //$NON-NLS-1$
+					version = version.substring(0, version.length() - 1);
+				}
+			}
+			return new String[] {id, version};
+		}
+		return new String[] {value, null};
+	}
+
+	/**
+	 * Returns a parser
+	 * @return default parser
+	 * @throws Exception forwarded general exception that can be trapped in Ant builds
+	 */
+	SAXParser getParser() throws Exception {
+		SAXParserFactory factory = SAXParserFactory.newInstance();
+		try {
+			return factory.newSAXParser();
+		} catch (ParserConfigurationException pce) {
+			throw new Exception(SearchMessages.UseReportConverter_pce_error_getting_parser, pce);
+		} catch (SAXException se) {
+			throw new Exception(SearchMessages.UseReportConverter_se_error_parser_handle, se);
+		}
+	}
+
+	/**
+	 * Returns all the child directories form the given directory
+	 * @param file
+	 * @return
+	 */
+	private File[] getDirectories(File file) {
+		File[] directories = file.listFiles(new FileFilter() {
+			public boolean accept(File pathname) {
+				return pathname.isDirectory() && !pathname.isHidden();
+			}
+		});
+		return directories;
+	}
+}
\ No newline at end of file
Index: src/org/eclipse/pde/api/tools/internal/search/MissingRefReportConverter.java
===================================================================
RCS file: src/org/eclipse/pde/api/tools/internal/search/MissingRefReportConverter.java
diff -N src/org/eclipse/pde/api/tools/internal/search/MissingRefReportConverter.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/org/eclipse/pde/api/tools/internal/search/MissingRefReportConverter.java	1 Jan 1970 00:00:00 -0000
@@ -0,0 +1,726 @@
+/*******************************************************************************
+ * Copyright (c) 2011 IBM Corporation and others.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *     IBM Corporation - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.pde.api.tools.internal.search;
+
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.xml.transform.Result;
+import javax.xml.transform.Source;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.transform.stream.StreamSource;
+
+import org.eclipse.core.runtime.CoreException;
+import org.eclipse.core.runtime.IPath;
+import org.eclipse.core.runtime.Path;
+import org.eclipse.osgi.util.NLS;
+import org.eclipse.pde.api.tools.internal.IApiCoreConstants;
+import org.eclipse.pde.api.tools.internal.problems.ApiProblem;
+import org.eclipse.pde.api.tools.internal.provisional.ApiPlugin;
+import org.eclipse.pde.api.tools.internal.provisional.descriptors.IComponentDescriptor;
+import org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblem;
+import org.eclipse.pde.api.tools.internal.util.Util;
+import org.osgi.framework.Version;
+
+public class MissingRefReportConverter extends HTMLConvertor {
+
+	/**
+	 * Constant used for controlling tracing in the report converter
+	 */
+	protected static boolean DEBUG = Util.DEBUG;
+
+	private String xmlLocation = null;
+	private String htmlLocation = null;
+	private File reportsRoot = null;
+	private File htmlIndex = null;
+	Report currentreport = null;
+
+	/**
+	 * Colour gold for the problems table header.
+	 */
+	public static final String PROBLEMS_TABLE_HEADER_COLOUR = "#E0C040"; //$NON-NLS-1$
+	/**
+	 * Style HTML bits for a page that shows references
+	 */
+	static final String REF_STYLE;
+	/**
+	 * The script block used to show an expanding table of references
+	 */
+	static final String REF_SCRIPT;
+
+	static {
+		StringBuffer buffer = new StringBuffer();
+		buffer.append("<style type=\"text/css\">\n"); //$NON-NLS-1$
+		buffer.append("\t.main {\t\tfont-family:Arial, Helvetica, sans-serif;\n\t}\n"); //$NON-NLS-1$
+		buffer.append("\t.main h3 {\n\t\tfont-family:Arial, Helvetica, sans-serif;\n\t\t\background-color:#FFFFFF;\n\t\tfont-size:14px;\n\t\tmargin:0.1em;\n\t}\n"); //$NON-NLS-1$
+		buffer.append("\t.main h4 {\n\t\tbackground-color:#CCCCCC;\n\t\tmargin:0.15em;\n\t}\n"); //$NON-NLS-1$
+		buffer.append("\ta.typeslnk {\n\t\tfont-family:Arial, Helvetica, sans-serif;\n\t\ttext-decoration:none;\n\t\tmargin-left:0.25em;\n\t}\n"); //$NON-NLS-1$
+		buffer.append("\ta.typeslnk:hover {\n\t\ttext-decoration:underline;\n\t}\n"); //$NON-NLS-1$
+		buffer.append("\ta.kindslnk {\n\t\tfont-family:Arial, Helvetica, sans-serif;\n\t\ttext-decoration:none;\n\t\tmargin-left:0.25em;\n\t}\n"); //$NON-NLS-1$
+		buffer.append("\t.types {\n\t\tdisplay:none;\n\t\tmargin-bottom:0.25em;\n\t\tmargin-top:0.25em;\n\t\tmargin-right:0.25em;\n\t\tmargin-left:0.75em;\n\t}\n"); //$NON-NLS-1$
+		buffer.append("</style>\n"); //$NON-NLS-1$
+		REF_STYLE = buffer.toString();
+
+		buffer = new StringBuffer();
+		buffer.append("<script type=\"text/javascript\">\n\tfunction expand(location) {\n\t\tif(document.getElementById) {\n\t\t\tvar childhtml = location.firstChild;\n\t\t\tif(!childhtml.innerHTML) {\n\t\t\t\tchildhtml = childhtml.nextSibling;\n\t\t\t}\n\t\t\tchildhtml.innerHTML = childhtml.innerHTML == '[+] ' ? '[-] ' : '[+] ';\n\t\t\tvar parent = location.parentNode;\n\t\t\tchildhtml = parent.nextSibling.style ? parent.nextSibling : parent.nextSibling.nextSibling;\n\t\t\tchildhtml.style.display = childhtml.style.display == 'block' ? 'none' : 'block';\n\t\t}\n\t}\n</script>\n"); //$NON-NLS-1$
+		buffer.append("<noscript>\n\t<style type=\"text/css\">\n\t\t.types {display:block;}\n\t\t.kinds{display:block;}\n\t</style>\n</noscript>\n"); //$NON-NLS-1$
+		REF_SCRIPT = buffer.toString();
+	}
+
+	/**
+	 * Root item describing the use of one component
+	 */
+	static class Report {
+		String name = null;
+		List apiProblems;
+		int typeProblems = 0;
+		int methodProblems = 0;
+		int fieldProblems = 0;
+
+		public void add(List apiProblems) {
+			this.apiProblems = apiProblems;
+			for (Iterator iterator = apiProblems.iterator(); iterator.hasNext();) {
+				ApiProblem apiProblem = (ApiProblem) iterator.next();
+				switch (apiProblem.getKind()) {
+					case 1 :
+						++typeProblems;
+						break;
+					case 2 :
+						++methodProblems;
+						break;
+					case 3 :
+						++fieldProblems;
+						break;
+				}
+			}
+		}
+
+		public int getTotal() {
+			return typeProblems + methodProblems + fieldProblems;
+		}
+
+	}
+
+	/**
+	 * Constructor
+	 * @param htmlroot the folder root where the HTML reports should be written
+	 * @param xmlroot the folder root where the current API use scan output is located
+	 */
+	public MissingRefReportConverter(String htmlroot, String xmlroot) {
+		this.xmlLocation = xmlroot;
+		this.htmlLocation = htmlroot;
+	}
+
+	/**
+	 * Method used for initializing tracing in the report converter
+	 */
+	public static void setDebug(boolean debugValue) {
+		DEBUG = debugValue || Util.DEBUG;
+	}
+
+	/**
+	 * Runs the converter on the given locations
+	 */
+	public void convert() throws Exception {
+		if (getHtmlLocation() == null) {
+			return;
+		}
+		File htmlRoot = new File(getHtmlLocation());
+		if (!htmlRoot.exists()) {
+			if (!htmlRoot.mkdirs()) {
+				throw new Exception(NLS.bind(SearchMessages.could_not_create_file, getHtmlLocation()));
+			}
+		} else {
+			htmlRoot.mkdirs();
+		}
+		if (getXmlLocation() == null) {
+			throw new Exception(SearchMessages.missing_xml_files_location);
+		}
+		File reportsRoot = getReportsRoot();
+		if (!reportsRoot.exists() || !reportsRoot.isDirectory()) {
+			throw new Exception(NLS.bind(SearchMessages.invalid_directory_name, getXmlLocation()));
+		}
+
+		long start = 0;
+		if (DEBUG) {
+			start = System.currentTimeMillis();
+		}
+		writeNotSearchedPage(htmlRoot);
+		writeMissingPage(htmlRoot);
+
+		if (DEBUG) {
+			System.out.println("done in: " + (System.currentTimeMillis() - start) + " ms"); //$NON-NLS-1$ //$NON-NLS-2$
+			System.out.println("Parsing use scan..."); //$NON-NLS-1$
+			start = System.currentTimeMillis();
+		}
+		List result = parse();
+		if (DEBUG) {
+			System.out.println("done in: " + (System.currentTimeMillis() - start) + " ms"); //$NON-NLS-1$ //$NON-NLS-2$
+			System.out.println("Sorting reports and writing index..."); //$NON-NLS-1$
+			start = System.currentTimeMillis();
+		}
+		writeIndexPage(result);
+	}
+
+	private void writeMissingPage(File htmlRoot) {
+		// TODO Auto-generated method stub
+		
+	}
+
+	/**
+	 * Writes out the file of components that were not searched: either because they appeared in an exclude list
+	 * or they have no .api_description file
+	 * 
+	 * @param htmlroot
+	 */
+	void writeNotSearchedPage(final File htmlroot) throws Exception {
+		File originhtml = null;
+		try {
+			String filename = "not_searched"; //$NON-NLS-1$
+			originhtml = new File(htmlroot, filename+HTML_EXTENSION); 
+			if(!originhtml.exists()) {
+				originhtml.createNewFile();
+			}
+			File xml = new File(getReportsRoot(), filename+XML_EXTENSION); 
+			if(!xml.exists()) {
+				//try <root>/xml in case a raw report root is specified
+				xml = new File(getReportsRoot()+File.separator+"xml", filename+XML_EXTENSION); //$NON-NLS-1$
+			}
+			InputStream defaultXsltInputStream = MissingRefReportConverter.class.getResourceAsStream(getNotSearchedXSLPath()); 
+			Source xslt = null;
+			if (defaultXsltInputStream != null) {
+				xslt = new StreamSource(new BufferedInputStream(defaultXsltInputStream));
+			}
+			if(xslt == null) {
+				throw new Exception(SearchMessages.UseReportConverter_no_xstl_specified);
+			}
+			if (xml.exists()) {
+				applyXSLT(xslt, xml, originhtml);
+			}
+		}
+		catch(IOException ioe) {
+			throw new Exception(NLS.bind(SearchMessages.ioexception_writing_html_file, originhtml.getAbsolutePath()));
+		}
+		catch (TransformerException te) {
+			throw new Exception(SearchMessages.UseReportConverter_te_applying_xslt_skipped, te);
+		}
+		catch (CoreException e) {
+			throw new Exception(NLS.bind(SearchMessages.UseReportConverter_coreexception_writing_html_file, originhtml.getAbsolutePath()));
+		}
+	}
+	
+	/**
+	 * Returns path of XSL file to use when generating "not searched" information.
+	 * 
+	 * @return path to the XSL file
+	 */
+	String getNotSearchedXSLPath() {
+		return "/notsearched.xsl"; //$NON-NLS-1$
+	}
+	
+	/**
+	 * Applies the given XSLT source to the given XML file outputting to the given HTML file
+	 * @param xslt
+	 * @param xmlfile
+	 * @param htmlfile
+	 * @throws TransformerException
+	 */
+	protected void applyXSLT(Source xslt, File xmlfile, File htmlfile) throws TransformerException {
+		Source xml = new StreamSource(xmlfile);
+		Result html = new StreamResult(htmlfile);
+		TransformerFactory factory = TransformerFactory.newInstance();
+		Transformer former = factory.newTransformer(xslt);
+		former.transform(xml, html);
+	}
+
+	/**
+	 * Gets the HTML path to write out the transformed XML file to
+	 * @param reportroot
+	 * @param xmlfile
+	 * @return
+	 */
+	protected String getHTMLFileLocation(File xmlfile) {
+		File reportRoot = new File(getXmlLocation());
+		IPath xml = new Path(xmlfile.getPath());
+		IPath report = new Path(reportRoot.getPath());
+		int segments = xml.matchingFirstSegments(report);
+		if (segments > 0) {
+			if (xml.getDevice() != null) {
+				xml = xml.setDevice(null);
+			}
+			IPath html = xml.removeFirstSegments(segments);
+			return html.removeLastSegments(1).toOSString();
+		}
+		return null;
+	}
+
+	class MissingRefVisitor {
+		public List reports;
+
+		public void visitScan() {
+			reports = new ArrayList();
+		}
+
+		public boolean visitComponent(IComponentDescriptor targetComponent) {
+			currentreport = new Report();
+			currentreport.name = composeName(targetComponent.getId(), targetComponent.getVersion());
+			reports.add(currentreport);
+			return true;
+		}
+
+		/**
+		 * Builds the name for the component
+		 * @param id id of the component
+		 * @param version version of the component, can be <code>null</code>
+		 * @return string name
+		 */
+		protected String composeName(String id, String version) {
+			String versionName = version;
+			if (version == null) {
+				versionName = Version.emptyVersion.toString();
+			}
+			StringBuffer buffer = new StringBuffer(3 + id.length() + versionName.length());
+			buffer.append(id).append(" (").append(versionName).append(")"); //$NON-NLS-1$ //$NON-NLS-2$
+			return buffer.toString();
+		}
+
+		public void endVisitComponent() {
+			try {
+				writeIndexFileForComponent(currentreport);
+			} catch (Exception e) {
+				ApiPlugin.log(e);
+			}
+		}
+
+		private void writeIndexFileForComponent(Report report) throws Exception {
+			PrintWriter writer = null;
+			File originhtml = null;
+			try {
+				File htmlroot = new File(getHtmlLocation(), report.name);
+				if (!htmlroot.exists()) {
+					htmlroot.mkdirs();
+				}
+				originhtml = new File(htmlroot, "index.html"); //$NON-NLS-1$
+				if (!originhtml.exists()) {
+					originhtml.createNewFile();
+				}
+				StringBuffer buffer = new StringBuffer();
+				buffer.append(HTML_HEADER);
+				buffer.append(OPEN_HTML).append(OPEN_HEAD).append(CONTENT_TYPE_META);
+				buffer.append(REF_STYLE);
+				buffer.append(REF_SCRIPT);
+				buffer.append(OPEN_TITLE).append(getProblemTitle(report.name)).append(CLOSE_TITLE);
+				buffer.append(CLOSE_HEAD);
+				buffer.append(OPEN_BODY);
+				buffer.append(OPEN_H3).append(getProblemTitle(report.name)).append(CLOSE_H3);
+				buffer.append(getProblemSummary(report));
+
+				StringBuffer typeProblems = new StringBuffer();
+				StringBuffer methodProblems = new StringBuffer();
+				StringBuffer fieldProblems = new StringBuffer();
+				for (Iterator iterator = report.apiProblems.iterator(); iterator.hasNext();) {
+					ApiProblem apiProblem = (ApiProblem) iterator.next();
+					switch (apiProblem.getKind()) {
+						case IApiProblem.API_USE_SCAN_TYPE_PROBLEM :
+							typeProblems.append(getProblemTable(apiProblem));
+							break;
+						case IApiProblem.API_USE_SCAN_METHOD_PROBLEM :
+							methodProblems.append(getProblemTable(apiProblem));
+							break;
+						case IApiProblem.API_USE_SCAN_FIELD_PROBLEM :
+							fieldProblems.append(getProblemTable(apiProblem));
+					}
+
+				}
+				buffer.append(getProblemsTableHeader(SearchMessages.MissingRefReportConverter_ProblemDetails, SearchMessages.MissingRefReportConverter_ProblemTypes)); 
+				if (typeProblems.length() > 0) {
+					buffer.append(getProblemRow(typeProblems, SearchMessages.MissingRefReportConverter_Type));
+				}
+				if (methodProblems.length() > 0) {
+					buffer.append(getProblemRow(methodProblems, SearchMessages.MissingRefReportConverter_Method));
+				}
+				if (fieldProblems.length() > 0) {
+					buffer.append(getProblemRow(fieldProblems, SearchMessages.MissingRefReportConverter_Field)); 
+				}
+				buffer.append(CLOSE_TABLE);
+
+				buffer.append(OPEN_P).append("<a href=\"../index.html\">").append(SearchMessages.MissingRefReportConverter_BackToIndex).append(CLOSE_A).append(CLOSE_P); //$NON-NLS-1$ 
+				buffer.append(W3C_FOOTER);
+				buffer.append(CLOSE_BODY);
+
+				writer = new PrintWriter(new OutputStreamWriter(new FileOutputStream(originhtml), IApiCoreConstants.UTF_8));;
+				writer.println(buffer.toString());
+				writer.flush();
+			} catch (IOException ioe) {
+				throw new Exception(NLS.bind(SearchMessages.ioexception_writing_html_file, originhtml.getAbsolutePath()));
+			} finally {
+				if (writer != null) {
+					writer.close();
+				}
+
+			}
+		}
+
+		private StringBuffer getProblemRow(StringBuffer type, String header) {
+			StringBuffer buffer = new StringBuffer();
+			buffer.append(OPEN_TR);
+			buffer.append("<td align=\"left\">\n"); //$NON-NLS-1$
+			buffer.append(OPEN_B);
+			buffer.append("<a href=\"javascript:void(0)\" class=\"typeslnk\" onclick=\"expand(this)\" title=\""); //$NON-NLS-1$
+			buffer.append(header).append("\">\n"); //$NON-NLS-1$
+			buffer.append("<span>[+] </span>").append(header).append("\n"); //$NON-NLS-1$//$NON-NLS-2$
+			buffer.append(CLOSE_A).append(CLOSE_B);
+			buffer.append("<div colspan=\"6\" class=\"types\">\n"); //$NON-NLS-1$
+			buffer.append(type).append("\n"); //$NON-NLS-1$
+			buffer.append(CLOSE_DIV);
+			buffer.append(CLOSE_TR);
+			return buffer;
+		}
+
+		private StringBuffer getProblemTable(ApiProblem apiProblem) {
+			StringBuffer buffer = new StringBuffer();
+			buffer.append("<table width=\"100%\" border=\"0\" cellspacing=\"1\" cellpadding=\"6\">\n"); //$NON-NLS-1$
+			buffer.append("<tr align=\"left\"> \n"); //$NON-NLS-1$
+			buffer.append("<td colspan=\"3\" bgcolor=\"#CCCCCC\">").append(OPEN_B).append(apiProblem.getTypeName()).append(CLOSE_B).append(CLOSE_TD); //$NON-NLS-1$
+			buffer.append(CLOSE_TR);
+
+			buffer.append("<tr bgcolor=\"").append(PROBLEMS_TABLE_HEADER_COLOUR).append("\">"); //$NON-NLS-1$ //$NON-NLS-2$
+			buffer.append("<td align=\"center\" width=\"79%\">").append(OPEN_B).append(SearchMessages.MissingRefReportConverter_ErrorMessage).append(CLOSE_B).append(CLOSE_TD); //$NON-NLS-1$
+			buffer.append("<td align=\"center\" width=\"7%\">").append(OPEN_B).append(SearchMessages.MissingRefReportConverter_LineNumber).append(CLOSE_B).append(CLOSE_TD); //$NON-NLS-1$
+			buffer.append("<td align=\"left\" width=\"7%\">").append(OPEN_B).append(SearchMessages.MissingRefReportConverter_CharStart).append(CLOSE_B).append(CLOSE_TD); //$NON-NLS-1$
+			buffer.append("<td align=\"center\" width=\"7%\">").append(OPEN_B).append(SearchMessages.MissingRefReportConverter_CharEnd).append(CLOSE_B).append(CLOSE_TD); //$NON-NLS-1$
+			buffer.append(CLOSE_TR);
+
+			buffer.append(OPEN_TR);
+			buffer.append("<td align=\"left\" width=\"79%\">").append(OPEN_B).append(apiProblem.getMessage()).append(CLOSE_B).append(CLOSE_TD); //$NON-NLS-1$ 
+			buffer.append("<td align=\"center\" width=\"7%\">").append(OPEN_B).append(apiProblem.getCharStart()).append(CLOSE_B).append(CLOSE_TD); //$NON-NLS-1$ 
+			buffer.append("<td align=\"center\" width=\"7%\">").append(OPEN_B).append(apiProblem.getCharEnd()).append(CLOSE_B).append(CLOSE_TD); //$NON-NLS-1$
+			buffer.append("<td align=\"center\" width=\"7%\">").append(OPEN_B).append(apiProblem.getCharEnd()).append(CLOSE_B).append(CLOSE_TD); //$NON-NLS-1$
+			buffer.append(CLOSE_TR);
+			buffer.append(CLOSE_TABLE);
+			return buffer;
+		}
+
+		private Object getProblemSummary(Report report) {
+			StringBuffer buffer = new StringBuffer();
+			buffer.append(OPEN_H4).append(SearchMessages.MissingRefReportConverter_Summary).append(CLOSE_H4);
+			buffer.append(OPEN_P).append(NLS.bind(SearchMessages.MissingRefReportConverter_SummaryDesc, new String[] {report.name, Integer.toString(report.apiProblems.size())})).append(CLOSE_P);
+			return buffer.toString();
+		}
+
+		/**
+		 * Returns the HTML markup for the problems table header.
+		 * @param sectionname
+		 * @param type
+		 * @return the default references table header
+		 */
+		String getProblemsTableHeader(String sectionname, String type) {
+			StringBuffer buffer = new StringBuffer();
+			buffer.append(OPEN_H4).append(sectionname).append(CLOSE_H4);
+			buffer.append(OPEN_P).append(SearchMessages.MissingRefReportConverter_ProblemTableHeader).append(CLOSE_P);
+			buffer.append("<div align=\"left\" class=\"main\">"); //$NON-NLS-1$
+			buffer.append("<table border=\"1\" width=\"80%\">\n"); //$NON-NLS-1$
+
+			buffer.append(OPEN_TR);
+			buffer.append("<td bgcolor=\"").append(PROBLEMS_TABLE_HEADER_COLOUR).append("\">").append(OPEN_B).append(type).append("</b></td>\n"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ 
+			buffer.append(CLOSE_TR);
+
+			return buffer.toString();
+		}
+
+		/**
+		 * @param bundle
+		 * @return the page title 
+		 */
+		protected String getProblemTitle(String bundle) {
+			return NLS.bind(SearchMessages.MissingRefReportConverter_ProblemTitle, bundle);
+		}
+
+		public void addToCuurentReport(List apiProblems) {
+			currentreport.add(apiProblems);
+		}
+	}
+
+	/**
+	 * Writes the main index file for the reports
+	 * @param result a list of {@link Report} objects returns from the use scan parser
+	 */
+	void writeIndexPage(List result) throws Exception {
+		Collections.sort(result, new Comparator() {
+			public int compare(Object o1, Object o2) {
+				return ((Report) o1).name.compareTo(((Report) o2).name);
+			}
+		});
+
+		PrintWriter writer = null;
+		try {
+			File reportIndex = new File(getHtmlLocation(), "index.html"); //$NON-NLS-1$
+			if (!reportIndex.exists()) {
+				reportIndex.createNewFile();
+			}
+//			setReportIndex(reportIndex);
+
+			StringBuffer buffer = new StringBuffer();
+			buffer.append(HTML_HEADER);
+			buffer.append(OPEN_HTML).append(OPEN_HEAD).append(CONTENT_TYPE_META);
+			writeMetadataHeaders(buffer);
+			buffer.append(OPEN_TITLE).append(getIndexTitle()).append(CLOSE_TITLE);
+			buffer.append(CLOSE_HEAD);
+			buffer.append(OPEN_BODY);
+			buffer.append(OPEN_H3).append(getIndexTitle()).append(CLOSE_H3);
+
+			writeMetadataSummary(buffer);
+
+			buffer.append(OPEN_H4).append(SearchMessages.MissingRefReportConverter_AddlBundleInfo).append(CLOSE_H4);
+//			if(hasMissing()) {
+//				buffer.append(OPEN_P); 
+//				buffer.append(NLS.bind(SearchMessages.UseReportConverter_missing_bundles_prevented_scan, 
+//						new String[] {" <a href=\"./missing.html\">", "</a>"})); //$NON-NLS-1$ //$NON-NLS-2$
+//				buffer.append(CLOSE_P); 
+//			}
+			buffer.append(OPEN_P);
+			buffer.append(NLS.bind(SearchMessages.MissingRefReportConverter_NotSearched, new String[] {"<a href=\"./not_searched.html\">", "</a></p>\n"}));  //$NON-NLS-1$//$NON-NLS-2$
+//			String additional = getAdditionalIndexInfo(scanResult.size() > 0);
+//			if(additional != null) {
+//				buffer.append(additional);
+//			}
+			if (result.size() > 0) {
+				buffer.append(getProblemSummaryTable());
+				if (result.size() > 0) {
+					Report report = null;
+					for (Iterator iter = result.iterator(); iter.hasNext();) {
+						report = (Report) iter.next();
+						if (report != null) {
+							File refereehtml = new File(getReportsRoot(), report.name + File.separator + "index.html"); //$NON-NLS-1$
+							String link = extractLinkFrom(getReportsRoot(), refereehtml.getAbsolutePath());
+							buffer.append(getReferenceTableEntry(report, link));
+						}
+					}
+					buffer.append(CLOSE_TABLE);
+				}
+			} else {
+//				buffer.append(getNoReportsInformation()); 
+			}
+			buffer.append(W3C_FOOTER);
+			buffer.append(CLOSE_BODY).append(CLOSE_HTML);
+
+			//write the file
+			writer = new PrintWriter(new OutputStreamWriter(new FileOutputStream(reportIndex), IApiCoreConstants.UTF_8));
+			writer.print(buffer.toString());
+			writer.flush();
+		} catch (IOException e) {
+			throw new Exception(NLS.bind(SearchMessages.ioexception_writing_html_file, getReportIndex().getAbsolutePath()));
+		} finally {
+			if (writer != null) {
+				writer.close();
+			}
+		}
+	}
+
+	/**
+	 * Returns the HTML markup for one entry in the problem summary table.
+	 * @param report
+	 * @param link
+	 * @return a single reference table entry
+	 */
+	private Object getReferenceTableEntry(Report report, String link) {
+		StringBuffer buffer = new StringBuffer();
+		buffer.append(OPEN_TR);
+		buffer.append("<td><b><a href=\"").append(link).append("\">").append(getBundleOnlyName(report.name)).append("</a>").append(CLOSE_B).append(CLOSE_TD); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
+		buffer.append("\t<td align=\"left\">").append(getVersion(report.name)).append(CLOSE_TD); //$NON-NLS-1$
+		buffer.append("\t<td align=\"center\">").append(report.typeProblems).append(CLOSE_TD); //$NON-NLS-1$
+		buffer.append("\t<td align=\"center\">").append(report.methodProblems).append(CLOSE_TD); //$NON-NLS-1$ 
+		buffer.append("\t<td align=\"center\">").append(report.fieldProblems).append(CLOSE_TD); //$NON-NLS-1$ 
+		buffer.append("\t<td align=\"center\">").append(report.getTotal()).append(CLOSE_TD); //$NON-NLS-1$ 
+		buffer.append(CLOSE_TR);
+		return buffer.toString();
+	}
+
+	String getBundleOnlyName(String text) {
+		int idx = text.indexOf('(');
+		if (idx > -1) {
+			return text.substring(0, idx - 1);
+		}
+		return text;
+	}
+
+	/**
+	 * Returns the version string from the text (if any)
+	 * @param text
+	 * @return
+	 */
+	String getVersion(String text) {
+		int idx = text.indexOf('(');
+		if (idx > -1) {
+			int idx2 = text.indexOf(')', idx);
+			String version = text.substring(idx + 1, idx2);
+			try {
+				Version ver = new Version(version);
+				return ver.toString();
+			} catch (IllegalArgumentException iae) {
+				//do nothing, not a valid version
+			}
+		}
+		return "-"; //$NON-NLS-1$
+	}
+
+	/**
+	 * Extracts underlying link text from the given absolute filename based off the root file
+	 * @param root
+	 * @param fileName
+	 * @return link text pruned via the given root file
+	 */
+	private String extractLinkFrom(File root, String fileName) {
+		StringBuffer buffer = new StringBuffer();
+		String substring = fileName.substring(root.getAbsolutePath().length()).replace('\\', '/');
+		buffer.append('.');
+		if (substring.charAt(0) != '/') {
+			buffer.append('/');
+		}
+		buffer.append(substring);
+		return buffer.toString();
+	}
+
+	private StringBuffer getProblemSummaryTable() {
+		StringBuffer buffer = new StringBuffer();
+		buffer.append(OPEN_H4).append(SearchMessages.MissingRefReportConverter_ProblemSummaryTitle).append(CLOSE_H4);
+		buffer.append(OPEN_P).append(SearchMessages.MissingRefReportConverter_ProblemSummary).append(CLOSE_P);
+		buffer.append("<table border=\"1\" width=\"80%\">\n"); //$NON-NLS-1$
+		buffer.append(OPEN_TR);
+		buffer.append("\t<td bgcolor=\"").append(PROBLEMS_TABLE_HEADER_COLOUR).append("\" width=\"25%\" title=\""); //$NON-NLS-1$ //$NON-NLS-2$
+		buffer.append(SearchMessages.MissingRefReportConverter_ProblemTable_ColumnBundleTooltip).append("\"\">");  //$NON-NLS-1$
+		buffer.append(OPEN_B).append(SearchMessages.MissingRefReportConverter_ProblemTable_ColumnBundle).append(CLOSE_B).append(CLOSE_TD);
+		//version header
+		buffer.append("\t<td bgcolor=\"").append(PROBLEMS_TABLE_HEADER_COLOUR).append("\" align=\"center\" width=\"15%\" title=\""); //$NON-NLS-1$ //$NON-NLS-2$
+		buffer.append(SearchMessages.MissingRefReportConverter_ProblemTable_ColumnVersionTooltip).append("\"\">");  //$NON-NLS-1$
+		buffer.append(OPEN_B).append(SearchMessages.MissingRefReportConverter_ProblemTable_ColumnVersion).append(CLOSE_B).append(CLOSE_TD);
+		//Missing Types
+		buffer.append("\t<td bgcolor=\"").append(PROBLEMS_TABLE_HEADER_COLOUR).append("\" align=\"center\" width=\"15%\" title=\""); //$NON-NLS-1$ //$NON-NLS-2$
+		buffer.append(SearchMessages.MissingRefReportConverter_ProblemTable_ColumnMissingTypesTooltip).append("\">");  //$NON-NLS-1$
+		buffer.append(OPEN_B).append(SearchMessages.MissingRefReportConverter_ProblemTable_ColumnMissingTypes).append(CLOSE_B).append(CLOSE_TD);
+		//Missing Methods
+		buffer.append("\t<td bgcolor=\"").append(PROBLEMS_TABLE_HEADER_COLOUR).append("\" align=\"center\" width=\"15%\" title=\""); //$NON-NLS-1$ //$NON-NLS-2$
+		buffer.append(SearchMessages.MissingRefReportConverter_ProblemTable_ColumnMissingMethodsTooltip).append("\">");  //$NON-NLS-1$
+		buffer.append(OPEN_B).append(SearchMessages.MissingRefReportConverter_ProblemTable_ColumnMissingMethods).append(CLOSE_B).append(CLOSE_TD);
+		//Missing Fields
+		buffer.append("\t<td bgcolor=\"").append(PROBLEMS_TABLE_HEADER_COLOUR).append("\" align=\"center\" width=\"15%\" title=\""); //$NON-NLS-1$ //$NON-NLS-2$
+		buffer.append(SearchMessages.MissingRefReportConverter_ProblemTable_ColumnMissingFieldsTooltip).append("\">");  //$NON-NLS-1$
+		buffer.append(OPEN_B).append(SearchMessages.MissingRefReportConverter_ProblemTable_ColumnMissingFields).append(CLOSE_B).append(CLOSE_TD);
+		//Total
+		buffer.append("\t<td bgcolor=\"").append(PROBLEMS_TABLE_HEADER_COLOUR).append("\" align=\"center\" width=\"15%\" title=\""); //$NON-NLS-1$ //$NON-NLS-2$
+		buffer.append(SearchMessages.MissingRefReportConverter_ProblemTable_ColumnTotalTooltip).append("\">");  //$NON-NLS-1$
+		buffer.append(OPEN_B).append(SearchMessages.MissingRefReportConverter_ProblemTable_ColumnTotal).append(CLOSE_B).append(CLOSE_TD);
+		return buffer;
+	}
+
+	private void writeMetadataSummary(StringBuffer buffer) throws Exception {
+		MissingRefMetadata metadata = getMetadata();
+		buffer.append(OPEN_H4).append(SearchMessages.MissingRefReportConverter_MetadataTitle).append(CLOSE_H4);
+		buffer.append("<table border=\"0px\" title=\"").append(SearchMessages.MissingRefReportConverter_MetadataTableTitle).append("\"width=\"50%\">"); //$NON-NLS-1$ //$NON-NLS-2$ 
+
+		buffer.append(OPEN_TR);
+		buffer.append(openTD(14)).append(SearchMessages.MissingRefReportConverter_ReportDate).append(CLOSE_TD);
+		buffer.append(openTD(36)).append(metadata.getRunAtDate()).append(CLOSE_TD);
+		buffer.append(CLOSE_TR);
+
+		buffer.append(OPEN_TR);
+		buffer.append(openTD(14)).append(SearchMessages.MissingRefReportConverter_ProfileLocation).append(CLOSE_TD);
+		String value = metadata.getProfile();
+		buffer.append(openTD(36)).append((value != null ? value : SearchMessages.MissingRefReportConverter_NONE)).append(CLOSE_TD);
+		buffer.append(CLOSE_TR);
+
+		buffer.append(OPEN_TR);
+		buffer.append(openTD(14)).append(SearchMessages.MissingRefReportConverter_ReportLocation).append(CLOSE_TD);
+		value = metadata.getReportLocation();
+		buffer.append(openTD(36)).append((value != null ? value : SearchMessages.MissingRefReportConverter_NONE)).append(CLOSE_TD);
+		buffer.append(CLOSE_TR);
+
+		buffer.append(OPEN_TR);
+		buffer.append(openTD(14)).append(SearchMessages.MissingRefReportConverter_ApiUseScanLocations).append(CLOSE_TD);
+		value = metadata.getApiUseScans();
+		buffer.append(openTD(36)).append((value != null ? value : SearchMessages.MissingRefReportConverter_NONE)).append(CLOSE_TD);
+		buffer.append(CLOSE_TR);
+
+		buffer.append(CLOSE_TD);
+		buffer.append(CLOSE_TR);
+		buffer.append(CLOSE_TABLE);
+	}
+
+	private MissingRefMetadata getMetadata() throws Exception {
+		File xmlFile = new File(getReportsRoot(), "meta" + XML_EXTENSION); //$NON-NLS-1$
+		if (!xmlFile.exists()) {
+			//try looking in the default 'xml' directory as a raw report root
+			//might have been specified
+			xmlFile = new File(getReportsRoot() + File.separator + "xml", "meta" + XML_EXTENSION); //$NON-NLS-1$//$NON-NLS-2$
+		}
+		return MissingRefMetadata.getMetadata(xmlFile);
+
+	}
+
+	private String getIndexTitle() {
+		return SearchMessages.MissingRefReportConverter_ReportTitle;
+	}
+
+	private void writeMetadataHeaders(StringBuffer buffer) {
+		buffer.append("<meta name=\"").append("description").append("\" content=\"").append(SearchMessages.MissingRefReportConverter_IndexMetaTag).append("\">"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$ 
+	}
+
+	/**
+	 * Parse the xml directories and report.xml and generate html for them
+	 */
+	protected List parse() throws Exception {
+		MissingRefParser parser = new MissingRefParser();
+		MissingRefVisitor visitor = new MissingRefVisitor();
+		parser.parse(getXmlLocation(), visitor);
+		return visitor.reports;
+	}
+
+	protected String getHtmlLocation() {
+		return this.htmlLocation;
+	}
+
+	protected String getXmlLocation() {
+		return this.xmlLocation;
+	}
+
+	protected File getReportsRoot() {
+		if (this.reportsRoot == null) {
+			this.reportsRoot = new File(getXmlLocation());
+		}
+		return this.reportsRoot;
+	}
+
+	/**
+	 * @return the index.html file created from the report conversion or <code>null</code>
+	 * if the conversion failed
+	 */
+	public File getReportIndex() {
+		//TODO remove if
+		if (htmlIndex == null)
+			return new File(htmlLocation);
+		else
+			return htmlIndex;
+	}
+
+}
Index: src/org/eclipse/pde/api/tools/internal/search/SearchMessages.java
===================================================================
RCS file: /cvsroot/eclipse/pde/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/search/SearchMessages.java,v
retrieving revision 1.27
diff -u -r1.27 SearchMessages.java
--- src/org/eclipse/pde/api/tools/internal/search/SearchMessages.java	2 Dec 2010 17:42:05 -0000	1.27
+++ src/org/eclipse/pde/api/tools/internal/search/SearchMessages.java	4 Mar 2011 15:29:53 -0000
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2009, 2010 IBM Corporation and others.
+ * Copyright (c) 2009, 2011 IBM Corporation and others.
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
@@ -52,6 +52,46 @@
 	public static String MigrationReportConvertor_table_shows_unresolved;
 	public static String MigrationReportConvertor_type_migration_information;
 	public static String MigrationReportConvertor_type_with_unresolved_refs;
+	public static String MissingRefMetadata_CoreExceptionInParsing;
+	public static String MissingRefReportConverter_AddlBundleInfo;
+	public static String MissingRefReportConverter_ApiUseScanLocations;
+	public static String MissingRefReportConverter_BackToIndex;
+	public static String MissingRefReportConverter_CharEnd;
+	public static String MissingRefReportConverter_CharStart;
+	public static String MissingRefReportConverter_ErrorMessage;
+	public static String MissingRefReportConverter_Field;
+	public static String MissingRefReportConverter_IndexMetaTag;
+	public static String MissingRefReportConverter_LineNumber;
+	public static String MissingRefReportConverter_MetadataTableTitle;
+	public static String MissingRefReportConverter_MetadataTitle;
+	public static String MissingRefReportConverter_Method;
+	public static String MissingRefReportConverter_NONE;
+	public static String MissingRefReportConverter_NotSearched;
+	public static String MissingRefReportConverter_ProblemDetails;
+	public static String MissingRefReportConverter_ProblemSummary;
+	public static String MissingRefReportConverter_ProblemSummaryTitle;
+	public static String MissingRefReportConverter_ProblemTable_ColumnMissingFields;
+	public static String MissingRefReportConverter_ProblemTable_ColumnMissingFieldsTooltip;
+	public static String MissingRefReportConverter_ProblemTable_ColumnMissingMethods;
+	public static String MissingRefReportConverter_ProblemTable_ColumnMissingMethodsTooltip;
+	public static String MissingRefReportConverter_ProblemTable_ColumnMissingTypes;
+	public static String MissingRefReportConverter_ProblemTable_ColumnMissingTypesTooltip;
+	public static String MissingRefReportConverter_ProblemTable_ColumnBundle;
+	public static String MissingRefReportConverter_ProblemTable_ColumnBundleTooltip;
+	public static String MissingRefReportConverter_ProblemTable_ColumnTotal;
+	public static String MissingRefReportConverter_ProblemTable_ColumnTotalTooltip;
+	public static String MissingRefReportConverter_ProblemTable_ColumnVersion;
+	public static String MissingRefReportConverter_ProblemTable_ColumnVersionTooltip;
+	public static String MissingRefReportConverter_ProblemTableHeader;
+	public static String MissingRefReportConverter_ProblemTitle;
+	public static String MissingRefReportConverter_ProblemTypes;
+	public static String MissingRefReportConverter_ProfileLocation;
+	public static String MissingRefReportConverter_ReportDate;
+	public static String MissingRefReportConverter_ReportLocation;
+	public static String MissingRefReportConverter_ReportTitle;
+	public static String MissingRefReportConverter_Summary;
+	public static String MissingRefReportConverter_SummaryDesc;
+	public static String MissingRefReportConverter_Type;
 	public static String ReferenceLookupVisitor_0;
 	public static String SkippedComponent_component_was_excluded;
 	public static String UseReportConverter_xslt_file_not_valid;
Index: src/org/eclipse/pde/api/tools/internal/search/searchmessages.properties
===================================================================
RCS file: /cvsroot/eclipse/pde/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/search/searchmessages.properties,v
retrieving revision 1.34
diff -u -r1.34 searchmessages.properties
--- src/org/eclipse/pde/api/tools/internal/search/searchmessages.properties	2 Dec 2010 17:42:05 -0000	1.34
+++ src/org/eclipse/pde/api/tools/internal/search/searchmessages.properties	4 Mar 2011 15:29:53 -0000
@@ -1,5 +1,5 @@
 ###############################################################################
-# Copyright (c) 2008, 2010 IBM Corporation and others.
+# Copyright (c) 2008, 2011 IBM Corporation and others.
 # All rights reserved. This program and the accompanying materials
 # are made available under the terms of the Eclipse Public License v1.0
 # which accompanies this distribution, and is available at
@@ -45,6 +45,46 @@
 MigrationReportConvertor_table_shows_unresolved=The following table shows the complete listing of types that have un-resolvable references to them.
 MigrationReportConvertor_type_migration_information={0} migration information
 MigrationReportConvertor_type_with_unresolved_refs=Types in {0} with un-resolved references
+MissingRefMetadata_CoreExceptionInParsing=CoreException parsing XML file: {0}
+MissingRefReportConverter_AddlBundleInfo=Additional Bundle Information
+MissingRefReportConverter_ApiUseScanLocations=API Use Scan locations
+MissingRefReportConverter_BackToIndex=Back to problem index
+MissingRefReportConverter_CharEnd=Offset End
+MissingRefReportConverter_CharStart=Offset Start
+MissingRefReportConverter_ErrorMessage=Error Message
+MissingRefReportConverter_Field=Field
+MissingRefReportConverter_IndexMetaTag=The root index page for the entire API Use Scan Problem page
+MissingRefReportConverter_LineNumber=Line Number
+MissingRefReportConverter_MetadataTableTitle=Report Parameter Table
+MissingRefReportConverter_MetadataTitle=Report Parameters
+MissingRefReportConverter_Method=Method
+MissingRefReportConverter_NONE=None
+MissingRefReportConverter_NotSearched=Bundles that were {0} not searched {1}
+MissingRefReportConverter_ProblemDetails=Problem Details
+MissingRefReportConverter_ProblemSummary=The table below displays the bundles and the problems reported for them. You can hover over a column header to see its description.
+MissingRefReportConverter_ProblemSummaryTitle=Problem Summary
+MissingRefReportConverter_ProblemTable_ColumnMissingFields=Missing Fields
+MissingRefReportConverter_ProblemTable_ColumnMissingFieldsTooltip=References to fields which are now missing from the profile
+MissingRefReportConverter_ProblemTable_ColumnMissingMethods=Missing Methods
+MissingRefReportConverter_ProblemTable_ColumnMissingMethodsTooltip=References to methods which are now missing from the profile
+MissingRefReportConverter_ProblemTable_ColumnMissingTypes=Missing Types
+MissingRefReportConverter_ProblemTable_ColumnMissingTypesTooltip=References to types which are now missing from the profile
+MissingRefReportConverter_ProblemTable_ColumnBundle=Bundle
+MissingRefReportConverter_ProblemTable_ColumnBundleTooltip=List of Bundles and the problems reported for them
+MissingRefReportConverter_ProblemTable_ColumnTotal=Total
+MissingRefReportConverter_ProblemTable_ColumnTotalTooltip=Total references which are now missing from the profile
+MissingRefReportConverter_ProblemTable_ColumnVersion=Version
+MissingRefReportConverter_ProblemTable_ColumnVersionTooltip=The version or version range of the  bundle
+MissingRefReportConverter_ProblemTableHeader=Click an entry in the table below to reveal the details of the problems related to that element.
+MissingRefReportConverter_ProblemTitle=Problems report for {0}
+MissingRefReportConverter_ProblemTypes=Problem Types
+MissingRefReportConverter_ProfileLocation=Profile location
+MissingRefReportConverter_ReportDate=Report date
+MissingRefReportConverter_ReportLocation=Report Location
+MissingRefReportConverter_ReportTitle=Missing API Use Scan references report
+MissingRefReportConverter_Summary=Summary
+MissingRefReportConverter_SummaryDesc={1} problems were found for the bundle {0}.
+MissingRefReportConverter_Type=Type
 ReferenceLookupVisitor_0=A corresponding bundle does not exist in the migration candidate.
 
 SkippedComponent_component_was_excluded=This component was excluded from the search by the search parameters.
Index: src_ant/org/eclipse/pde/api/tools/internal/tasks/Messages.java
===================================================================
RCS file: /cvsroot/eclipse/pde/apitools/org.eclipse.pde.api.tools/src_ant/org/eclipse/pde/api/tools/internal/tasks/Messages.java,v
retrieving revision 1.28
diff -u -r1.28 Messages.java
--- src_ant/org/eclipse/pde/api/tools/internal/tasks/Messages.java	30 Sep 2010 15:13:26 -0000	1.28
+++ src_ant/org/eclipse/pde/api/tools/internal/tasks/Messages.java	4 Mar 2011 15:29:53 -0000
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2008, 2010 IBM Corporation and others.
+ * Copyright (c) 2008, 2011 IBM Corporation and others.
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
@@ -108,6 +108,10 @@
 	public static String deprecationReportTask_header;
 	public static String deprecationReportTask_missingXmlFileLocation;
 
+	public static String MissingRefProblemsTask_invalidApiUseScanLocation;
+
+	public static String MissingRefProblemsTask_missingArguments;
+
 	static {
 		// initialize resource bundle
 		NLS.initializeMessages(BUNDLE_NAME, Messages.class);
Index: src_ant/org/eclipse/pde/api/tools/internal/tasks/MissingRefProblemsReportConversionTask.java
===================================================================
RCS file: src_ant/org/eclipse/pde/api/tools/internal/tasks/MissingRefProblemsReportConversionTask.java
diff -N src_ant/org/eclipse/pde/api/tools/internal/tasks/MissingRefProblemsReportConversionTask.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src_ant/org/eclipse/pde/api/tools/internal/tasks/MissingRefProblemsReportConversionTask.java	1 Jan 1970 00:00:00 -0000
@@ -0,0 +1,84 @@
+/*******************************************************************************
+ * Copyright (c) 2011 IBM Corporation and others.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *     IBM Corporation - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.pde.api.tools.internal.tasks;
+
+import java.io.File;
+
+import org.apache.tools.ant.BuildException;
+import org.eclipse.osgi.util.NLS;
+import org.eclipse.pde.api.tools.internal.search.MissingRefReportConverter;
+import org.eclipse.pde.api.tools.internal.util.Util;
+
+/**
+ * Default task for converting the XML output from the apitooling.apiuse ants to HTML
+ * 
+ * @noinstantiate This class is not intended to be instantiated by clients.
+ */
+public final class MissingRefProblemsReportConversionTask extends CommonUtilsTask {
+
+	private String xmlReportsLocation = null;
+	private String htmlReportsLocation = null;
+
+	/**
+	 * Set the debug value.
+	 * <p>The possible values are: <code>true</code>, <code>false</code></p>
+	 * <p>Default is <code>false</code>.</p>
+	 *
+	 * @param debugValue the given debug value
+	 */
+	public void setDebug(String debugValue) {
+		this.debug = Boolean.toString(true).equals(debugValue);
+	}
+
+	/**
+	 * Set the location where the html reports are generated.
+	 * 
+	 * <p>This is optional. If not set, the html files are created in the same folder as the
+	 * xml files.</p>
+	 * <p>The location is set using an absolute path.</p>
+	 * 
+	 * @param htmlFilesLocation the given the location where the html reports are generated
+	 */
+	public void setHtmlFiles(String htmlFilesLocation) {
+		this.htmlReportsLocation = htmlFilesLocation;
+	}
+
+	/**
+	 * Set the location where the xml reports are retrieved.
+	 * 
+	 * <p>The location is set using an absolute path.</p>
+	 *
+	 * @param xmlFilesLocation the given location to retrieve the xml reports
+	 */
+	public void setXmlFiles(String xmlFilesLocation) {
+		this.xmlReportsLocation = xmlFilesLocation;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.apache.tools.ant.Task#execute()
+	 */
+	public void execute() throws BuildException {
+		if (this.debug) {
+			System.out.println("XML report location: " + this.xmlReportsLocation); //$NON-NLS-1$
+			System.out.println("HTML report location: " + this.htmlReportsLocation); //$NON-NLS-1$
+		}
+		try {
+			Util.delete(new File(this.htmlReportsLocation));
+			MissingRefReportConverter converter = new MissingRefReportConverter(this.htmlReportsLocation, this.xmlReportsLocation);
+			MissingRefReportConverter.setDebug(this.debug);
+			converter.convert();
+			File index = converter.getReportIndex();
+			System.out.println(NLS.bind(Messages.ApiUseReportConversionTask_conversion_complete, index.getAbsolutePath()));
+		} catch (Exception e) {
+			throw new BuildException(e);
+		}
+	}
+}
Index: src_ant/org/eclipse/pde/api/tools/internal/tasks/MissingRefProblemsTask.java
===================================================================
RCS file: src_ant/org/eclipse/pde/api/tools/internal/tasks/MissingRefProblemsTask.java
diff -N src_ant/org/eclipse/pde/api/tools/internal/tasks/MissingRefProblemsTask.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src_ant/org/eclipse/pde/api/tools/internal/tasks/MissingRefProblemsTask.java	1 Jan 1970 00:00:00 -0000
@@ -0,0 +1,732 @@
+/*******************************************************************************
+ * Copyright (c) 2011 IBM Corporation and others.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *     IBM Corporation - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.pde.api.tools.internal.tasks;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Set;
+
+import org.apache.tools.ant.BuildException;
+import org.eclipse.core.runtime.CoreException;
+import org.eclipse.core.runtime.NullProgressMonitor;
+import org.eclipse.osgi.util.NLS;
+import org.eclipse.pde.api.tools.internal.IApiCoreConstants;
+import org.eclipse.pde.api.tools.internal.IApiXmlConstants;
+import org.eclipse.pde.api.tools.internal.builder.BaseApiAnalyzer;
+import org.eclipse.pde.api.tools.internal.builder.BuildContext;
+import org.eclipse.pde.api.tools.internal.model.StubApiComponent;
+import org.eclipse.pde.api.tools.internal.problems.ApiProblem;
+import org.eclipse.pde.api.tools.internal.problems.ApiProblemFactory;
+import org.eclipse.pde.api.tools.internal.provisional.ApiPlugin;
+import org.eclipse.pde.api.tools.internal.provisional.model.IApiBaseline;
+import org.eclipse.pde.api.tools.internal.provisional.model.IApiComponent;
+import org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblem;
+import org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblemTypes;
+import org.eclipse.pde.api.tools.internal.search.MissingRefMetadata;
+import org.eclipse.pde.api.tools.internal.search.SkippedComponent;
+import org.eclipse.pde.api.tools.internal.search.UseScanManager;
+import org.eclipse.pde.api.tools.internal.util.FilteredElements;
+import org.eclipse.pde.api.tools.internal.util.Util;
+import org.w3c.dom.DOMException;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+
+/**
+ * Ant task to headlessly run the API Analysis builder and generate a report of
+ * missing references in the API Use Scans
+ */
+public class MissingRefProblemsTask extends CommonUtilsTask {
+
+	private FilteredElements excludedElements;
+	private FilteredElements includedElements;
+	private String apiUseScans;
+	private String[] apiUseScanArray;
+	private Properties properties = new Properties();
+
+	public static final String COMPATIBILITY = "compatibility"; //$NON-NLS-1$
+	private static final Summary[] NO_SUMMARIES = new Summary[0];
+
+	private static class Summary {
+		String fComponentID;
+		List fApiProblems;
+
+		public Summary(String componentID, IApiProblem[] apiProblems) {
+			fComponentID = componentID;
+			fApiProblems = Arrays.asList(apiProblems);
+		}
+
+		private void dumpProblems(String title, PrintWriter printWriter) {
+			printWriter.println(title);
+			if (fApiProblems.size() != 0) {
+				for (Iterator iterator = fApiProblems.iterator(); iterator.hasNext();) {
+					IApiProblem problem = (IApiProblem) iterator.next();
+					printWriter.println(problem.getMessage());
+				}
+			} else {
+				printWriter.println("None"); //$NON-NLS-1$
+			}
+		}
+
+		public String getDetails() {
+			StringWriter writer = new StringWriter();
+			PrintWriter printWriter = new PrintWriter(writer);
+
+			printWriter.println("=================================================================================="); //$NON-NLS-1$
+			printWriter.println("Details for " + fComponentID + ":"); //$NON-NLS-1$//$NON-NLS-2$
+			printWriter.println("=================================================================================="); //$NON-NLS-1$
+			dumpProblems("All Problems", printWriter); //$NON-NLS-1$
+			printWriter.println("=================================================================================="); //$NON-NLS-1$
+			printWriter.flush();
+			printWriter.close();
+			return String.valueOf(writer.getBuffer());
+		}
+
+		public String getTitle() {
+			StringWriter writer = new StringWriter();
+			PrintWriter printWriter = new PrintWriter(writer);
+			printTitle(printWriter);
+
+			printWriter.flush();
+			printWriter.close();
+			return String.valueOf(writer.getBuffer());
+		}
+
+		private void printTitle(PrintWriter printWriter) {
+			printWriter.print("Results for " + fComponentID + " : "); //$NON-NLS-1$ //$NON-NLS-2$
+			printWriter.print("(total: " + fApiProblems.size() + ")"); //$NON-NLS-1$//$NON-NLS-2$
+		}
+
+	}
+
+	/**
+	 * Run the api use scan problems task
+	 * 
+	 * @throws BuildException
+	 *             exception is thrown if anything goes wrong during the
+	 *             verification
+	 */
+	public void execute() throws BuildException {
+		if (super.currentBaselineLocation == null || super.reportLocation == null || this.apiUseScans == null) {
+			StringBuffer error = new StringBuffer(NLS.bind(Messages.MissingRefProblemsTask_missingArguments, new String[] {super.currentBaselineLocation, super.reportLocation,}));
+			throw new BuildException(error.toString());
+		}
+		if (apiUseScanArray != null && apiUseScanArray.length > 0) {
+			for (int i = 0; i < apiUseScanArray.length; i++) {
+				File file = new File(apiUseScanArray[i]);
+				if (!file.exists()) {
+					StringBuffer error = new StringBuffer(Messages.MissingRefProblemsTask_invalidApiUseScanLocation);
+					error.append(apiUseScanArray[i]);
+					throw new BuildException(error.toString());
+				}
+			}
+		}
+
+		if (super.debug) {
+			System.out.println("profile to compare : " + super.currentBaselineLocation); //$NON-NLS-1$
+			System.out.println("report location : " + super.reportLocation); //$NON-NLS-1$
+
+			if (super.excludeListLocation != null) {
+				System.out.println("exclude list location : " + super.excludeListLocation); //$NON-NLS-1$
+			} else {
+				System.out.println("No exclude list location"); //$NON-NLS-1$
+			}
+			if (super.includeListLocation != null) {
+				System.out.println("include list location : " + super.includeListLocation); //$NON-NLS-1$
+			} else {
+				System.out.println("No include list location"); //$NON-NLS-1$
+			}
+		}
+		// unzip profile
+		long time = 0;
+		if (super.debug) {
+			time = System.currentTimeMillis();
+		}
+
+		File baselineInstallDir = extractSDK(CURRENT, super.currentBaselineLocation);
+		if (super.debug) {
+			System.out.println("Preparation of profile installation : " + (System.currentTimeMillis() - time) + "ms"); //$NON-NLS-1$ //$NON-NLS-2$
+			time = System.currentTimeMillis();
+		}
+
+		// create baseline = profile
+		IApiBaseline profile = createBaseline(CURRENT_BASELINE_NAME, baselineInstallDir.getAbsolutePath(), null);
+		if (super.debug) {
+			System.out.println("Creation of baseline : " + (System.currentTimeMillis() - time) + "ms"); //$NON-NLS-1$ //$NON-NLS-2$
+			time = System.currentTimeMillis();
+		}
+
+		if (this.excludeListLocation != null) {
+			this.excludedElements = CommonUtilsTask.initializeFilteredElements(this.excludeListLocation, profile, super.debug);
+			if (super.debug) {
+				System.out.println("===================================================================================="); //$NON-NLS-1$
+				System.out.println("Excluded elements list:"); //$NON-NLS-1$
+				System.out.println(this.excludedElements);
+			}
+		}
+		if (this.includeListLocation != null) {
+			this.includedElements = CommonUtilsTask.initializeFilteredElements(this.includeListLocation, profile, super.debug);
+			if (super.debug) {
+				System.out.println("===================================================================================="); //$NON-NLS-1$
+				System.out.println("Included elements list:"); //$NON-NLS-1$
+				System.out.println(this.includedElements);
+			}
+		}
+
+		UseScanManager.getInstance().setReportLocations(apiUseScanArray);
+
+		if (super.debug) {
+			System.out.println("===================================================================================="); //$NON-NLS-1$
+			System.out.println("API Use Scan locations:"); //$NON-NLS-1$
+			for (int i = 0; i < apiUseScanArray.length; i++) {
+				System.out.println("Location " + i + " : " + apiUseScanArray[i]); //$NON-NLS-1$ //$NON-NLS-2$
+			}
+		}
+
+		Map allProblems = new HashMap();
+		List allNonApiBundles = new ArrayList();
+		List notSearchedList = new ArrayList();
+		try {
+			IApiComponent[] apiComponents = profile.getApiComponents();
+			int length = apiComponents.length;
+			Set visitedApiComponentNames = new HashSet();
+			for (int i = 0; i < length; i++) {
+				IApiComponent apiComponent = apiComponents[i];
+				String name = apiComponent.getSymbolicName();
+
+				if (this.excludedElements != null && (this.excludedElements.containsExactMatch(name) || this.excludedElements.containsPartialMatch(name))) {
+					notSearchedList.add(new SkippedComponent(name, apiComponents[i].getVersion(), null));
+					continue;
+				}
+				if (this.includedElements != null && !this.includedElements.isEmpty() && !(this.includedElements.containsExactMatch(name) || this.includedElements.containsPartialMatch(name))) {
+					notSearchedList.add(new SkippedComponent(name, apiComponents[i].getVersion(), null));
+					continue;
+				}
+
+				visitedApiComponentNames.add(name);
+				if (apiComponent.isSystemComponent()) {
+					continue;
+				}
+				if (!Util.isApiToolsComponent(apiComponent)) {
+					allNonApiBundles.add(name);
+					continue;
+				}
+
+				BaseApiAnalyzer analyzer = new BaseApiAnalyzer();
+				try {
+					BaseApiAnalyzer.setDebug(super.debug);
+					if (this.properties.isEmpty()) {
+						addDefaultProperties();
+					}
+					analyzer.checkExternalDependencies(apiComponent, new BuildContext(), this.properties, new NullProgressMonitor());
+					IApiProblem[] problems = analyzer.getProblems();
+					if (problems.length != 0) {
+						allProblems.put(name, problems);
+					}
+				} catch (RuntimeException e) {
+					ApiPlugin.log(e);
+					throw e;
+				} catch (CoreException e) {
+					ApiPlugin.log(e);
+				} finally {
+					analyzer.dispose();
+				}
+			}
+			if (super.debug) {
+				System.out.println("Total number of components in current baseline :" + length); //$NON-NLS-1$
+				System.out.println("=============================================================================="); //$NON-NLS-1$
+				System.out.println("Total number of non-api tools components in current baseline :" + allNonApiBundles.size()); //$NON-NLS-1$
+				System.out.println("Details:"); //$NON-NLS-1$
+				Collections.sort(allNonApiBundles);
+				for (Iterator iterator = allNonApiBundles.iterator(); iterator.hasNext();) {
+					System.out.println(iterator.next());
+				}
+			}
+		} finally {
+			if (super.debug) {
+				System.out.println("API tools verification check : " + (System.currentTimeMillis() - time) + "ms"); //$NON-NLS-1$ //$NON-NLS-2$
+				time = System.currentTimeMillis();
+			}
+			profile.dispose();
+			StubApiComponent.disposeAllCaches();
+			deleteBaseline(super.currentBaselineLocation, baselineInstallDir);
+			if (super.debug) {
+				System.out.println("Cleanup : " + (System.currentTimeMillis() - time) + "ms"); //$NON-NLS-1$ //$NON-NLS-2$
+			}
+			writeMetaData(new File(this.reportLocation, "meta.xml")); //$NON-NLS-1$
+		}
+		Summary[] summaries = createAllSummaries(allProblems);
+
+		try {
+			dumpReport(summaries);
+			reportNonApiBundles(allNonApiBundles);
+			reportNotSearched(notSearchedList);
+		} catch (RuntimeException e) {
+			ApiPlugin.log(e);
+			throw e;
+		}
+	}
+
+	private void addDefaultProperties() {
+		this.properties.put(IApiProblemTypes.API_USE_SCAN_TYPE_SEVERITY, ApiPlugin.VALUE_ERROR);
+		this.properties.put(IApiProblemTypes.API_USE_SCAN_METHOD_SEVERITY, ApiPlugin.VALUE_ERROR);
+		this.properties.put(IApiProblemTypes.API_USE_SCAN_FIELD_SEVERITY, ApiPlugin.VALUE_ERROR);
+	}
+
+	private void writeMetaData(File file) {
+		try {
+			if (!file.exists()) {
+				file.getParentFile().mkdirs();
+				if (!file.createNewFile())
+					return; // could not create meta.xml
+			}
+			if (super.debug) {
+				System.out.println("Writing metadata to " + file.getAbsolutePath()); //$NON-NLS-1$ 
+			}
+
+			MissingRefMetadata metadata = new MissingRefMetadata(super.currentBaselineLocation, super.reportLocation, this.apiUseScans);
+			metadata.serializeToFile(file);
+		} catch (UnsupportedEncodingException e) {
+			ApiPlugin.log(e);
+		} catch (FileNotFoundException e) {
+			ApiPlugin.log(e);
+		} catch (IOException e) {
+			ApiPlugin.log(e);
+		} catch (CoreException e) {
+			ApiPlugin.log(e);
+		}
+	}
+
+	private Summary[] createAllSummaries(Map allProblems) {
+		Set entrySet = allProblems.entrySet();
+		int size = entrySet.size();
+		if (size == 0) {
+			return NO_SUMMARIES;
+		}
+		List allEntries = new ArrayList();
+		allEntries.addAll(entrySet);
+		Collections.sort(allEntries, new Comparator() {
+			public int compare(Object o1, Object o2) {
+				Map.Entry entry1 = (Map.Entry) o1;
+				Map.Entry entry2 = (Map.Entry) o2;
+				return ((String) entry1.getKey()).compareTo((String) entry2.getKey());
+			}
+		});
+		Summary[] summaries = new Summary[size];
+		int i = 0;
+		for (Iterator iterator = allEntries.iterator(); iterator.hasNext();) {
+			Map.Entry entry = (Map.Entry) iterator.next();
+			summaries[i++] = new Summary((String) entry.getKey(), (IApiProblem[]) entry.getValue());
+		}
+		if (super.debug) {
+			dumpSummaries(summaries);
+		}
+		return summaries;
+	}
+
+	private void dumpReport(Summary[] summaries) {
+		for (int i = 0, max = summaries.length; i < max; i++) {
+			Summary summary = summaries[i];
+			String contents = null;
+			String componentID = summary.fComponentID;
+
+			try {
+				Document document = Util.newDocument();
+				Element report = document.createElement(IApiXmlConstants.ELEMENT_API_TOOL_REPORT);
+				report.setAttribute(IApiXmlConstants.ATTR_VERSION, IApiXmlConstants.API_REPORT_CURRENT_VERSION);
+				report.setAttribute(IApiXmlConstants.ATTR_COMPONENT_ID, componentID);
+				document.appendChild(report);
+
+				Element category = document.createElement(IApiXmlConstants.ATTR_CATEGORY);
+				category.setAttribute(IApiXmlConstants.ATTR_KEY, Integer.toString(IApiProblem.CATEGORY_API_USE_SCAN_PROBLEM));
+				category.setAttribute(IApiXmlConstants.ATTR_VALUE, COMPATIBILITY);
+				insertAPIProblems(category, document, summary.fApiProblems);
+				report.appendChild(category);
+
+				contents = Util.serializeDocument(document);
+			} catch (DOMException e) {
+				throw new BuildException(e);
+			} catch (CoreException e) {
+				throw new BuildException(e);
+			}
+			if (contents != null) {
+				saveReport(componentID, contents, "report.xml"); //$NON-NLS-1$
+			}
+		}
+
+	}
+
+	private void reportNonApiBundles(List allNonApiBundles) {
+		if (allNonApiBundles.isEmpty()) {
+			return;
+		}
+		String contents = null;
+		try {
+			Document document = Util.newDocument();
+			Element report = document.createElement(IApiXmlConstants.ELEMENT_API_TOOL_REPORT);
+			report.setAttribute(IApiXmlConstants.ATTR_VERSION, IApiXmlConstants.API_REPORT_CURRENT_VERSION);
+			document.appendChild(report);
+
+			for (Iterator iterator = allNonApiBundles.iterator(); iterator.hasNext();) {
+				String bundleName = (String) iterator.next();
+				Element bundle = document.createElement(IApiXmlConstants.ELEMENT_BUNDLE);
+				bundle.setAttribute(IApiXmlConstants.ATTR_NAME, bundleName);
+				report.appendChild(bundle);
+			}
+
+			contents = Util.serializeDocument(document);
+		} catch (DOMException e) {
+			throw new BuildException(e);
+		} catch (CoreException e) {
+			throw new BuildException(e);
+		}
+		if (contents != null) {
+			saveReport(".", contents, "allNonApiBundles.xml"); //$NON-NLS-1$ //$NON-NLS-2$
+		}
+	}
+
+	public void reportNotSearched(List notSearchedList) {
+		if (notSearchedList.isEmpty()) {
+			return;
+		}
+		BufferedWriter writer = null;
+		try {
+			if (this.debug) {
+				System.out.println("Writing file for projects that were not searched..."); //$NON-NLS-1$
+			}
+			File rootfile = new File(reportLocation);
+			if (!rootfile.exists()) {
+				rootfile.mkdirs();
+			}
+			File file = new File(rootfile, "not_searched.xml"); //$NON-NLS-1$
+			if (!file.exists()) {
+				file.createNewFile();
+			}
+			Document doc = Util.newDocument();
+			Element root = doc.createElement(IApiXmlConstants.ELEMENT_COMPONENTS);
+			root.setAttribute("ShowMissing", "false"); //$NON-NLS-1$ //$NON-NLS-2$
+			doc.appendChild(root);
+			Element comp = null;
+			for (Iterator iterator = notSearchedList.iterator(); iterator.hasNext();) {
+				SkippedComponent component = (SkippedComponent) iterator.next();
+				comp = doc.createElement(IApiXmlConstants.ELEMENT_COMPONENT);
+				comp.setAttribute(IApiXmlConstants.ATTR_ID, component.getComponentId());
+				comp.setAttribute(IApiXmlConstants.ATTR_VERSION, component.getVersion());
+				comp.setAttribute(IApiXmlConstants.SKIPPED_DETAILS, component.getErrorDetails());
+				root.appendChild(comp);
+			}
+			writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(file), IApiCoreConstants.UTF_8));
+			writer.write(Util.serializeDocument(doc));
+			writer.flush();
+		} catch (FileNotFoundException fnfe) {
+		} catch (IOException ioe) {
+		} catch (CoreException ce) {
+		} finally {
+			if (writer != null) {
+				try {
+					writer.close();
+				} catch (IOException e) {
+				}
+			}
+		}
+	}
+
+	private void dumpSummaries(Summary[] summaries) {
+		System.out.println("=================================================================================="); //$NON-NLS-1$);
+		System.out.println("Summaries"); //$NON-NLS-1$
+		for (int i = 0, max = summaries.length; i < max; i++) {
+			System.out.println(summaries[i].getTitle());
+		}
+		for (int i = 0, max = summaries.length; i < max; i++) {
+			System.out.println(summaries[i].getDetails());
+		}
+		System.out.println("=================================================================================="); //$NON-NLS-1$);
+	}
+
+	private void insertAPIProblems(Element root, Document document, List problems) throws CoreException {
+		Element apiProblems = document.createElement(IApiXmlConstants.ELEMENT_API_PROBLEMS);
+		root.appendChild(apiProblems);
+		Element element = null;
+		// sort the problem by type name
+		Collections.sort(problems, new Comparator() {
+			public int compare(Object o1, Object o2) {
+				IApiProblem p1 = (IApiProblem) o1;
+				IApiProblem p2 = (IApiProblem) o2;
+				return p1.getTypeName().compareTo(p2.getTypeName());
+			}
+		});
+		for (Iterator iterator = problems.iterator(); iterator.hasNext();) {
+			IApiProblem problem = (IApiProblem) iterator.next();
+			element = document.createElement(IApiXmlConstants.ELEMENT_API_PROBLEM);
+			element.setAttribute(IApiXmlConstants.ATTR_TYPE_NAME, String.valueOf(problem.getTypeName()));
+			element.setAttribute(IApiXmlConstants.ATTR_ID, Integer.toString(problem.getId()));
+			element.setAttribute(IApiXmlConstants.ATTR_LINE_NUMBER, Integer.toString(problem.getLineNumber()));
+			element.setAttribute(IApiXmlConstants.ATTR_CHAR_START, Integer.toString(problem.getCharStart()));
+			element.setAttribute(IApiXmlConstants.ATTR_CHAR_END, Integer.toString(problem.getCharEnd()));
+			element.setAttribute(IApiXmlConstants.ATTR_ELEMENT_KIND, Integer.toString(problem.getElementKind()));
+			element.setAttribute(IApiXmlConstants.ATTR_NAME_ELEMENT_TYPE, ApiProblem.getProblemElementKind(problem.getCategory(), problem.getElementKind()));
+			element.setAttribute(IApiXmlConstants.ATTR_CATEGORY, ApiProblem.getProblemCategory(problem.getCategory()));
+			element.setAttribute(IApiXmlConstants.ATTR_SEVERITY, this.properties.getProperty(ApiProblemFactory.getProblemSeverityId(problem)));
+			element.setAttribute(IApiXmlConstants.ATTR_KIND, Integer.toString(problem.getKind()));
+			element.setAttribute(IApiXmlConstants.ATTR_FLAGS, Integer.toString(problem.getFlags()));
+			element.setAttribute(IApiXmlConstants.ATTR_MESSAGE, problem.getMessage());
+			String[] extraMarkerAttributeIds = problem.getExtraMarkerAttributeIds();
+			if (extraMarkerAttributeIds != null && extraMarkerAttributeIds.length != 0) {
+				int length = extraMarkerAttributeIds.length;
+				Object[] extraMarkerAttributeValues = problem.getExtraMarkerAttributeValues();
+				Element extraArgumentsElement = document.createElement(IApiXmlConstants.ELEMENT_PROBLEM_EXTRA_ARGUMENTS);
+				for (int j = 0; j < length; j++) {
+					Element extraArgumentElement = document.createElement(IApiXmlConstants.ELEMENT_PROBLEM_EXTRA_ARGUMENT);
+					extraArgumentElement.setAttribute(IApiXmlConstants.ATTR_ID, extraMarkerAttributeIds[j]);
+					extraArgumentElement.setAttribute(IApiXmlConstants.ATTR_VALUE, String.valueOf(extraMarkerAttributeValues[j]));
+					extraArgumentsElement.appendChild(extraArgumentElement);
+				}
+				element.appendChild(extraArgumentsElement);
+			}
+			String[] messageArguments = problem.getMessageArguments();
+			if (messageArguments != null && messageArguments.length != 0) {
+				int length = messageArguments.length;
+				Element messageArgumentsElement = document.createElement(IApiXmlConstants.ELEMENT_PROBLEM_MESSAGE_ARGUMENTS);
+				for (int j = 0; j < length; j++) {
+					Element messageArgumentElement = document.createElement(IApiXmlConstants.ELEMENT_PROBLEM_MESSAGE_ARGUMENT);
+					messageArgumentElement.setAttribute(IApiXmlConstants.ATTR_VALUE, String.valueOf(messageArguments[j]));
+					messageArgumentsElement.appendChild(messageArgumentElement);
+				}
+				element.appendChild(messageArgumentsElement);
+			}
+			apiProblems.appendChild(element);
+		}
+	}
+
+	/**
+	 * Set the debug value.
+	 * <p>
+	 * The possible values are: <code>true</code>, <code>false</code>
+	 * </p>
+	 * <p>
+	 * Default is <code>false</code>.
+	 * </p>
+	 * 
+	 * @param debugValue
+	 *            the given debug value
+	 */
+	public void setDebug(boolean debugValue) {
+		super.debug = debugValue;
+	}
+
+	/**
+	 * Set the exclude list location.
+	 * 
+	 * <p>
+	 * The exclude list is used to know what bundles should excluded from the
+	 * xml report generated by the task execution. Lines starting with '#' are
+	 * ignored from the excluded elements.
+	 * </p>
+	 * <p>
+	 * The format of the exclude list file looks like this:
+	 * </p>
+	 * 
+	 * <pre>
+	 * # DOC BUNDLES
+	 * org.eclipse.jdt.doc.isv
+	 * org.eclipse.jdt.doc.user
+	 * org.eclipse.pde.doc.user
+	 * org.eclipse.platform.doc.isv
+	 * org.eclipse.platform.doc.user
+	 * # NON-ECLIPSE BUNDLES
+	 * com.ibm.icu
+	 * com.jcraft.jsch
+	 * javax.servlet
+	 * javax.servlet.jsp
+	 * ...
+	 * </pre>
+	 * <p>
+	 * The location is set using an absolute path.
+	 * </p>
+	 * 
+	 * @param excludeListLocation
+	 *            the given location for the excluded list file
+	 */
+	public void setExcludeList(String excludeListLocation) {
+		this.excludeListLocation = excludeListLocation;
+	}
+
+	/**
+	 * Set the include list location.
+	 * 
+	 * <p>
+	 * The include list is used to know what bundles should included from the
+	 * xml report generated by the task execution. Lines starting with '#' are
+	 * ignored from the included elements.
+	 * </p>
+	 * <p>
+	 * The format of the include list file looks like this:
+	 * </p>
+	 * 
+	 * <pre>
+	 * # DOC BUNDLES
+	 * org.eclipse.jdt.doc.isv
+	 * org.eclipse.jdt.doc.user
+	 * org.eclipse.pde.doc.user
+	 * org.eclipse.platform.doc.isv
+	 * org.eclipse.platform.doc.user
+	 * # NON-ECLIPSE BUNDLES
+	 * com.ibm.icu
+	 * com.jcraft.jsch
+	 * javax.servlet
+	 * javax.servlet.jsp
+	 * ...
+	 * </pre>
+	 * <p>
+	 * The location is set using an absolute path.
+	 * </p>
+	 * 
+	 * @param includeListLocation
+	 *            the given location for the included list file
+	 */
+	public void setIncludeList(String includeListLocation) {
+		this.includeListLocation = includeListLocation;
+	}
+
+	/**
+	 * Set the preferences for the task.
+	 * 
+	 * <p>
+	 * The preferences are used to configure problem severities. Problem
+	 * severities have three possible values: Ignore, Warning, or Error. The set
+	 * of problems detected is defined by corresponding problem preference keys
+	 * in API tools.
+	 * </p>
+	 * <p>
+	 * If the given location doesn't exist, the preferences won't be set.
+	 * </p>
+	 * <p>
+	 * Lines starting with '#' are ignored. The format of the preferences file
+	 * looks like this:
+	 * </p>
+	 * 
+	 * <pre>
+	 * #Thu Jan 11 17:03:09 IST 2011
+	 * API_USE_SCAN_TYPE_SEVERITY=Error
+	 * API_USE_SCAN_METHOD_SEVERITY=Ignore
+	 * API_USE_SCAN_FIELD_SEVERITY=Ignore
+	 * </pre>
+	 * <p>
+	 * The keys can be found in
+	 * {@link org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblemTypes}
+	 * .
+	 * </p>
+	 * <p>
+	 * The location is set using an absolute path.
+	 * </p>
+	 * 
+	 * @param preferencesLocation
+	 *            the location of the preference file
+	 */
+	public void setPreferences(String preferencesLocation) {
+		File preferencesFile = new File(preferencesLocation);
+		if (!preferencesFile.exists()) {
+			return;
+		}
+		BufferedInputStream inputStream = null;
+		try {
+			inputStream = new BufferedInputStream(new FileInputStream(preferencesFile));
+			Properties temp = new Properties();
+			temp.load(inputStream);
+			this.properties = temp;
+		} catch (IOException e) {
+			// ignore
+		} finally {
+			if (inputStream != null) {
+				try {
+					inputStream.close();
+				} catch (IOException e) {
+					// ignore
+				}
+			}
+		}
+	}
+
+	/**
+	 * Set the location of the current product or baseline that you want to
+	 * compare against the reference baseline.
+	 * 
+	 * <p>
+	 * It can be a .zip, .jar, .tgz, .tar.gz file, or a directory that
+	 * corresponds to the Eclipse installation folder. This is the directory is
+	 * which you can find the Eclipse executable.
+	 * </p>
+	 * 
+	 * @param baselineLocation
+	 *            the given location for the baseline to analyze
+	 */
+	public void setProfile(String baselineLocation) {
+		this.currentBaselineLocation = baselineLocation;
+	}
+
+	/**
+	 * Comma-separated list of the locations of the API Use Scans that you want
+	 * to check against the reference baseline.
+	 * 
+	 * <p>
+	 * It can be a .zip file or a directory that corresponds to the API Use Scan report. 
+	 * This is the directory is which you can find the XML folder.
+	 * </p>
+	 * 
+	 * @param baselineLocation
+	 *            the given location for the baseline to analyze
+	 */
+	public void setAPIUseScans(String apiUseScans) {
+		this.apiUseScans = apiUseScans;
+		this.apiUseScanArray = apiUseScans.split(","); //$NON-NLS-1$		
+	}
+
+	/**
+	 * Set the output location where the reports will be generated.
+	 * 
+	 * <p>
+	 * Once the task is completed, reports are available in this directory using
+	 * a structure similar to the filter root. A sub-folder is created for each
+	 * component that has problems to be reported. Each sub-folder contains a
+	 * file called "report.xml".
+	 * </p>
+	 * 
+	 * <p>
+	 * A special folder called "allNonApiBundles" is also created in this folder
+	 * that contains a xml file called "report.xml". This file lists all the
+	 * bundles that are not using the api tooling nature.
+	 * </p>
+	 * 
+	 * @param baselineLocation
+	 *            the given location for the reference baseline to analyze
+	 */
+	public void setReport(String reportLocation) {
+		this.reportLocation = reportLocation;
+	}
+}
Index: src_ant/org/eclipse/pde/api/tools/internal/tasks/messages.properties
===================================================================
RCS file: /cvsroot/eclipse/pde/apitools/org.eclipse.pde.api.tools/src_ant/org/eclipse/pde/api/tools/internal/tasks/messages.properties,v
retrieving revision 1.47
diff -u -r1.47 messages.properties
--- src_ant/org/eclipse/pde/api/tools/internal/tasks/messages.properties	31 Jan 2011 18:08:32 -0000	1.47
+++ src_ant/org/eclipse/pde/api/tools/internal/tasks/messages.properties	4 Mar 2011 15:29:55 -0000
@@ -212,4 +212,9 @@
 </html>\n
 deprecationReportTask_missingXmlFileLocation=Missing the xml file location argument
 deltaReportTask_xmlFileLocationShouldHaveAnXMLExtension=The report location must be an xml file location
-deltaReportTask_htmlFileLocationShouldHaveAnHtmlExtension=The report location must be an html file location
\ No newline at end of file
+deltaReportTask_htmlFileLocationShouldHaveAnHtmlExtension=The report location must be an html file location
+MissingRefProblemsTask_invalidApiUseScanLocation=Invalid API Use Scan location: 
+MissingRefProblemsTask_missingArguments=Missing arguments:\n\
+profile location : {0}\n\
+api use scan locations : {1}\n\
+report location : {2}
Index: xslt/notsearched.xsl
===================================================================
RCS file: /cvsroot/eclipse/pde/apitools/org.eclipse.pde.api.tools/xslt/notsearched.xsl,v
retrieving revision 1.4
diff -u -r1.4 notsearched.xsl
--- xslt/notsearched.xsl	13 Jan 2010 18:08:34 -0000	1.4
+++ xslt/notsearched.xsl	4 Mar 2011 15:29:55 -0000
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="iso-8859-1"?>
 <!--
-	Copyright (c) IBM Corporation and others 2009. This page is made available under license. For full details see the LEGAL in the documentation book that contains this page.
+	Copyright (c) IBM Corporation and others 2009, 2011. This page is made available under license. For full details see the LEGAL in the documentation book that contains this page.
 	
 	All Platform Debug contexts, those for org.eclipse.debug.ui, are located in this file
 	All contexts are grouped by their relation, with all relations grouped alphabetically.
@@ -56,9 +56,12 @@
 		</h3>
 			<xsl:choose>
 				<xsl:when test="count(components/component) &gt; 0">
+				<xsl:variable name="ShowMissing" select="components/@ShowMissing" />
+				<xsl:if test="$ShowMissing != 'false'">
 				<p>
 					A summary of the missing required bundles is <a href="missing.html">available here</a>.
 				</p>
+				</xsl:if>
 				<p>
 					Click an entry in the table below to reveal the details of why it was not searched.
 				</p>
#P org.eclipse.pde.doc.user
Index: reference/api-tooling/ant-tasks/apiusescan-problems-ant-task.htm
===================================================================
RCS file: reference/api-tooling/ant-tasks/apiusescan-problems-ant-task.htm
diff -N reference/api-tooling/ant-tasks/apiusescan-problems-ant-task.htm
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ reference/api-tooling/ant-tasks/apiusescan-problems-ant-task.htm	1 Jan 1970 00:00:00 -0000
@@ -0,0 +1,186 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta name="copyright" content="Copyright (c) IBM Corporation and others s2011. This page is made available under license. For full details see the LEGAL in the documentation book that contains this page."/>
+<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"/>
+<meta http-equiv="Content-Style-Type" content="text/css"/>
+<link rel="stylesheet" href="../../../apache_style.css" type="text/css"/>
+<title>API Tools Analysis Ant Task</title>
+<script language="JavaScript" src="PLUGINS_ROOT/org.eclipse.help/livehelp.js" type="text/javascript"> </script>
+</head>
+<body>
+<h1>API Use Scan Problems Ant Task</h1>
+<h2>Purpose</h2>
+<p>This task resolves the API Use Scans in a profile relative to a baseline. It reports the references to the types, methods and fields which are now missing from the profile. </p>
+<h2>Usage</h2>
+<h3>Description</h3>
+<p>The name of the Ant task is: <code>apitooling.apiusescanproblems</code>. To be used, the jar file <code>apitooling-ant.jar</code> has to be on the Ant
+classpath.</p>
+<div style="text-align: left;">
+<pre style="margin-left: 40px">
+<b><font color="#0000ff">&lt;apitooling.apiusescanproblems
+	profile=<font color="#008000">"..."</font>
+	report=<font color="#008000">"..."</font>
+	apiusescans=<font color="#008000">"..."</font>
+	excludelist=<font color="#008000">"..."</font>
+	includelist=<font color="#008000">"..."</font>
+	preferences=<font color="#008000">"..."</font>
+	debug=<font color="#008000">"..."</font>
+/&gt;</font></b>
+</pre>
+</div>
+<h3>Parameters</h3>
+<table border="1" cellpadding="2" cellspacing="0">
+  <tr>
+    <td valign="top"><b>Attribute</b></td>
+    <td valign="top"><b>Description</b></td>
+    <td align="center" valign="top"><b>Required</b></td>
+  </tr>
+<tr>
+<td valign="top">profile</td>
+<td valign="top">This attribute specifies the location of the current product or profile that you want to resolved the API Use Scans against.
+<br/><br/>
+It can be a .zip, .jar, .tgz, .tar.gz file, or a directory that corresponds to the Eclipse installation folder. This is the 
+directory is which you can find the Eclipse executable.
+<br/><br/>The location is specified using an absolute path.
+</td>
+<td align="center" valign="top">Yes</td>
+</tr>
+<tr>
+<td valign="top">report</td>
+<td valign="top">Set the output location where the reports will be generated.
+<br/><br/>
+Once the task is completed, reports are available in this directory using a structure similar to the filter root. A sub-folder is created
+for each component that has problems to be reported. Each sub-folder contains a file called "report.xml".
+<br/><br/>The location is specified using an absolute path. 
+</td>
+<td align="center" valign="top">Yes</td>
+</tr>
+<tr>
+<td valign="top">apiusescans</td>
+<td valign="top">This attribute specifies the comma-separated list of the locations of the API Use Scans that you want to check against the profile.
+<br/><br/>
+It can be a .zip file or a directory that corresponds to the API Use Scan report. This is the directory is which you can find the XML folder in the Use Scan.
+</td>
+<td align="center" valign="top">Yes</td>
+</tr>
+<tr>
+<td valign="top">excludelist</td>
+<td valign="top">Set the exclude list location. 
+<br/><br/>The exclude list location specifies a text file listing bundles to be excluded from the analysis.
+By default all bundles in the profile are analyzed. The include and exclude list attributes can be used to 
+selectively include and exclude bundles. The include list seeds the set of bundles to be analyzed (when omitted,
+all bundles are included), and the exclude list is then applied.
+Each line of the file specifies one of:
+<ul>
+<li>a specific bundle name</li>
+<li>a regular expression to match against bundle names (lines being with "R:")</li>
+<li>a comment (lines being with '#')</li>
+</ul>
+<br/>The location is specified using an absolute path.
+<br/>Following is an example exclude list:
+<pre>
+ # DOC BUNDLES
+ org.eclipse.jdt.doc.isv
+ org.eclipse.jdt.doc.user
+ org.eclipse.pde.doc.user
+ org.eclipse.platform.doc.isv
+ org.eclipse.platform.doc.user
+ # NON-ECLIPSE BUNDLES
+ com.ibm.icu
+ com.jcraft.jsch
+ R:javax\..*
+ ...
+</pre>
+</td>
+<td align="center" valign="top">No</td>
+</tr>
+<tr>
+<td valign="top">includelist</td>
+<td valign="top">Set the include list location. 
+<br/><br/>The include list location specifies a text file listing bundles to be included in the analysis.
+By default all bundles in the profile are analyzed. The include and exclude list attributes can be used to 
+selectively include and exclude bundles. The include list seeds the set of bundles to be analyzed (when omitted,
+all bundles are included), and the exclude list is then applied.
+Each line of the file specifies one of:
+<ul>
+<li>a specific bundle name</li>
+<li>a regular expression to match against bundle names (lines being with "R:")</li>
+<li>a comment (lines being with '#')</li>
+</ul>
+<br/>The location is specified using an absolute path.
+<br/>Following is an example include list:
+<pre>
+ # DOC BUNDLES
+ org.eclipse.jdt.doc.isv
+ org.eclipse.jdt.doc.user
+ org.eclipse.pde.doc.user
+ R:org.eclipse.platform.doc.*
+ # NON-ECLIPSE BUNDLES
+ com.ibm.icu
+ com.jcraft.jsch
+ R:javax\..*
+ ...
+</pre>
+</td>
+<td align="center" valign="top">No</td>
+</tr>
+<tr>
+<td valign="top">preferences</td>
+<td valign="top">Set the preferences for the task. 
+<br/><br/>
+The preferences are used to configure problem severities. Problem severities have three possible values: Ignore, Warning, or Error. The set of problems detected is defined by corresponding problem preference keys in API tools.
+<br/>The location is specified using an absolute path. If the given location doesn't exist, the preferences won't be set.
+<br/>
+Lines starting with '#' are ignored. The format of the preferences file looks like this:
+<pre>
+ #Thu Nov 20 17:35:06 EST 2008
+ API_USE_SCAN_TYPE_SEVERITY=Error
+ API_USE_SCAN_METHOD_SEVERITY=Error
+ API_USE_SCAN_FIELD_SEVERITY=Error
+</pre>
+The keys can be found in org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblemTypes.
+</td>
+<td align="center" valign="top">No</td>
+</tr>
+<tr>
+<td valign="top">debug</td>
+<td valign="top">Set the debug value.
+<br/><br/>The possible values are: <code>true</code>, <code>false</code>
+<br/>Default is <code>false</code>.
+</td>
+<td align="center" valign="top">No</td>
+</tr>
+</table>
+
+<h3>Examples</h3>
+
+<pre>
+	<b><font color="#0000ff">&lt;apitooling.apiusescanproblems
+		profile=<font color="#008000">"D:\eclipse\3.7\eclipse"</font>
+		report=<font color="#008000">"D:\reports\xml"</font>
+		apiusescans=<font color="#008000">"D:\APIUseScan\ProductOne,D:\APIUseScan\ProductTwo"</font>
+		excludelist=<font color="#008000">"D:\exclude_list_external.txt"</font>
+		preferences=<font color="#008000">"D:\tests_api\org.eclipse.pde.api.tools.prefs"</font>
+		debug=<font color="#008000">"true"</font>
+	/&gt;</font></b>
+</pre>
+<p>This will run the task creating <code>report.xml</code> files inside the folder <code>D:\reports\xml</code>. The types, methods and fields from the use scans
+will be resolved in the profile at <code>D:\eclipse\3.7\eclipse</code> and the missing ones will be reported.
+It will use the exclude list from the file <code>D:\exclude_list_external.txt</code> to reduce the number of bundles for which problems to report.</p>
+<p>Problem severities will be generated as specified by <code>D:\tests_api\org.eclipse.pde.api.tools.prefs</code>.</p>
+<p>Since debug is enabled, some debug tracing will show up in the Ant console.</p>
+
+<p><img src="../../../images/ngrelr.png" alt="Related reference" border="0"/></p>
+<p><a href="analysis-ant-task.htm">API Analysis Ant Task</a>
+<br/><a href="apifreeze-ant-task.htm">API Freeze Ant Task</a>
+<br/><a href="filegeneration-ant-task.htm">File Generation Ant Task</a>
+<br/><a href="apiuse-ant-task.htm">API Use Ant Task</a>
+<br/><a href="analysis-reportconversion-ant-task.htm">Analysis Report Conversion Ant Task</a>
+<br/><a href="apifreeze-reportconversion-ant-task.htm">API Freeze Report Conversion Ant Task</a>
+<br/><a href="apiuse-reportconversion-ant-task.htm">API Use Report Conversion Ant Task</a>
+<br/><a href="deprecation-ant-task.htm">API Deprecation Ant Task</a>
+<br/><a href="deprecation-reportconversion-ant-task.htm">API Deprecation Report Conversion Ant Task</a>
+</p>
+</body>
+</html>
Index: reference/api-tooling/ant-tasks/apiusescan-problems-reportconversion-ant-task.htm
===================================================================
RCS file: reference/api-tooling/ant-tasks/apiusescan-problems-reportconversion-ant-task.htm
diff -N reference/api-tooling/ant-tasks/apiusescan-problems-reportconversion-ant-task.htm
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ reference/api-tooling/ant-tasks/apiusescan-problems-reportconversion-ant-task.htm	1 Jan 1970 00:00:00 -0000
@@ -0,0 +1,86 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html lang="en">
+<head>
+<meta name="copyright" content="Copyright (c) IBM Corporation and others 2011. This page is made available under license. For full details see the LEGAL in the documentation book that contains this page.">
+<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
+<meta http-equiv="Content-Style-Type" content="text/css">
+<link rel="stylesheet" href="../../../apache_style.css" type="text/css">
+<title>API Tools Analysis Report Conversion Ant Task</title>
+<script language="JavaScript" src="PLUGINS_ROOT/org.eclipse.help/livehelp.js" type="text/javascript"> </script>
+</head>
+<body>
+<h1> API Use Scan Problems Report Conversion Ant Task </h1>
+<h2>Purpose</h2>
+<p>This task converts  XML reports created by the <code>apitooling.apiusescanproblems</code> Ant task into HTML files.
+</p>
+<h2>Usage</h2>
+<h3>Description</h3>
+<p>The name of the Ant task is: <code>apitooling.apiusescanproblem_reportconversion</code>. To be used, the jar file <code>apitooling-ant.jar</code> has to be on the Ant
+classpath.</p>
+<div style="text-align: left;">
+<pre style="margin-left: 40px">
+<b><font color="#0000ff">&lt;apitooling.apiusescanproblem_reportconversion
+	xmlfiles=<font color="#008000">"..."</font>
+	htmlfiles=<font color="#008000">"..."</font>
+	debug=<font color="#008000">"..."</font>
+/&gt;</font></b>
+</pre>
+</div>
+<h3>Parameters</h3>
+<table border="1" cellpadding="2" cellspacing="0">
+  <tr>
+    <td valign="top"><b>Attribute</b></td>
+    <td valign="top"><b>Description</b></td>
+    <td align="center" valign="top"><b>Required</b></td>
+  </tr>
+<tr>
+<td valign="top">xmlfiles</td>
+<td valign="top">Set the location where the xml reports are retrieved.
+<br><br>The location is set using an absolute path.
+</td>
+<td align="center" valign="top">Yes</td>
+</tr>
+<tr>
+<td valign="top">htmlfiles</td>
+<td valign="top">Set the location where the html reports are generated.
+<br><br>If not set, the html files are created in the same folder as the xml files.
+<br><br>The location is set using an absolute path.
+</td>
+<td align="center" valign="top">No</td>
+</tr>
+<tr>
+<td valign="top">debug</td>
+<td valign="top">Set the debug value.
+<br><br>The possible values are: <code>true</code>, <code>false</code>
+<br>Default is <code>false</code>.
+</td>
+<td align="center" valign="top">No</td>
+</tr>
+</table>
+
+<h3>Examples</h3>
+
+<pre>
+	<b><font color="#0000ff">&lt;apitooling.analysis_reportconversion
+		xmlfiles=<font color="#008000">"D:\reports\xml"</font>
+		htmlfiles=<font color="#008000">"D:\reports\html"</font>
+		debug=<font color="#008000">"true"</font>
+	/&gt;</font></b>
+</pre>
+<p>This will create an <code>index.html</code> inside the folder <code>D:\reports\html</code>. A report for each
+bundle will be created inside a sub-folder of <code>D:\reports\html</code>. Each sub-folder will contain a 
+<code>report.html</code>.</p>
+<p>Since debug is enabled, some debug tracing will show up in the Ant console.</p>
+
+<p><img src="../../../images/ngrelr.png" alt="Related reference" border="0"></p>
+<p><a href="apiusescan-problems-ant-task.htm">API Use Scan Problems Ant Task</a>
+<br><a href="analysis-ant-task.htm">Analysis Ant Task</a>
+<br><a href="filegeneration-ant-task.htm">File Generation Ant Task</a>
+<br><a href="apiuse-ant-task.htm">API Use Ant Task</a>
+<br><a href="apifreeze-ant-task.htm">API Freeze Ant Task</a>
+<br><a href="apifreeze-reportconversion-ant-task.htm">API Freeze Report Conversion Ant Task</a>
+<br><a href="deprecation-ant-task.htm">API Deprecation Ant Task</a>
+<br><a href="deprecation-reportconversion-ant-task.htm">API Deprecation Report Conversion Ant Task</a>
+<br><a href="apiuse-reportconversion-ant-task.htm">API Use Report Conversion Ant Task</a></p>
+</body>
+</html>
Index: topics_Reference.xml
===================================================================
RCS file: /cvsroot/eclipse/pde/doc/org.eclipse.pde.doc.user/topics_Reference.xml,v
retrieving revision 1.39
diff -u -r1.39 topics_Reference.xml
--- topics_Reference.xml	23 Feb 2011 21:31:35 -0000	1.39
+++ topics_Reference.xml	4 Mar 2011 15:29:58 -0000
@@ -42,6 +42,10 @@
       </topic>
       <topic href="reference/api-tooling/ant-tasks/compare-ant-task.htm" label="Compare Ant Task">
       </topic>
+      <topic href="reference/api-tooling/ant-tasks/apiusescan-problems-ant-task.htm" label="API Use Scan Problems Ant Task">
+      </topic>
+      <topic href="reference/api-tooling/ant-tasks/apiusescan-problems-reportconversion-ant-task.htm" label="API Use Scan Problems Report Conversion Ant Task">
+      </topic>
    </topic>
    <topic label="Build Configuration">
 		<topic label="Builder Configuration properties" href="reference/pde_builder_config.htm" />