Bug 378317 - Index update mode for resolving unresolved includes and

reindexing files with I/O errors.

17 files changed, 429 insertions, 92 deletions

diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/CIndex.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/CIndex.java
index 1fbc93e4b55..c3dde20b6f0 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/CIndex.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/CIndex.java
@@ -759,6 +759,32 @@ public class CIndex implements IIndex {
 	}
 
 	@Override
+	public IIndexFile[] getDefectiveFiles() throws CoreException {
+		HashMap<IIndexFileLocation, IIndexFile> result= new HashMap<IIndexFileLocation, IIndexFile>();
+		for (IIndexFragment fragment : fFragments) {
+			for (IIndexFragmentFile file : fragment.getDefectiveFiles()) {
+				if (file.hasContent()) { 
+					result.put(file.getLocation(), file);
+				}
+			}
+		}
+		return result.values().toArray(new IIndexFile[result.size()]);
+	}
+
+	@Override
+	public IIndexFile[] getFilesWithUnresolvedIncludes() throws CoreException {
+		HashMap<IIndexFileLocation, IIndexFile> result= new HashMap<IIndexFileLocation, IIndexFile>();
+		for (IIndexFragment fragment : fFragments) {
+			for (IIndexFragmentFile file : fragment.getFilesWithUnresolvedIncludes()) {
+				if (file.hasContent()) { 
+					result.put(file.getLocation(), file);
+				}
+			}
+		}
+		return result.values().toArray(new IIndexFile[result.size()]);
+	}
+
+	@Override
 	public IIndexScope[] getInlineNamespaces() throws CoreException {
 		if (SPECIALCASE_SINGLES && fFragments.length == 1) {
 			return fFragments[0].getInlineNamespaces();
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/EmptyCIndex.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/EmptyCIndex.java
index 503ede13120..9168511d58d 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/EmptyCIndex.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/EmptyCIndex.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2006, 2011 Wind River Systems, Inc. and others.
+ * Copyright (c) 2006, 2012 Wind River Systems, Inc. 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
@@ -190,6 +190,16 @@ final public class EmptyCIndex implements IIndex {
 	}
 
 	@Override
+	public IIndexFile[] getDefectiveFiles() {
+		return IIndexFile.EMPTY_FILE_ARRAY;
+	}
+
+	@Override
+	public IIndexFile[] getFilesWithUnresolvedIncludes() {
+		return IIndexFile.EMPTY_FILE_ARRAY;
+	}
+
+	@Override
 	public IIndexBinding[] findBindings(char[] name, boolean fileScopeOnly,	IndexFilter filter, IProgressMonitor monitor) {
 		return IIndexBinding.EMPTY_INDEX_BINDING_ARRAY;
 	}
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/IIndexFragment.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/IIndexFragment.java
index 2b2ac26362f..7a2bc0ccf72 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/IIndexFragment.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/IIndexFragment.java
@@ -326,6 +326,16 @@ public interface IIndexFragment {
 	IIndexFragmentFile[] getAllFiles() throws CoreException;
 
 	/**
+	 * @return an array of files that were indexed with I/O errors.
+	 */
+	IIndexFragmentFile[] getDefectiveFiles() throws CoreException;
+
+	/**
+	 * @return an array of files containg unresolved includes.
+	 */
+	IIndexFragmentFile[] getFilesWithUnresolvedIncludes() throws CoreException;
+
+	/**
 	 * Caches an object with the key, the cache must be cleared at latest when the fragment no
 	 * longer holds a locks.
 	 * @param replace if <code>false</code> an existing entry will not be replaced.
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/IIndexFragmentFile.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/IIndexFragmentFile.java
index f6ca6b05ca2..0577e408b1b 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/IIndexFragmentFile.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/index/IIndexFragmentFile.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2006, 2011 Wind River Systems, Inc. and others.
+ * Copyright (c) 2006, 2012 Wind River Systems, Inc. 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
@@ -24,11 +24,16 @@ public interface IIndexFragmentFile extends IIndexFile {
 	IIndexFragment getIndexFragment();
 
 	/**
-	 * Sets the timestamp of the file
+	 * Sets the timestamp of the file.
 	 */
 	void setTimestamp(long timestamp) throws CoreException;
 
 	/**
+	 * Sets the file read time.
+	 */
+	void setSourceReadTime(long time) throws CoreException;
+
+	/**
 	 * Sets the hash of the file content. 
 	 */
 	void setContentsHash(long hash) throws CoreException;
@@ -58,6 +63,12 @@ public interface IIndexFragmentFile extends IIndexFile {
 	boolean hasContent() throws CoreException;
 
 	/**
+	 * Checks if the file contains at least one unresolved include.
+	 * @return {@code true} if the file contains an unresolved include
+	 */
+	boolean hasUnresolvedInclude() throws CoreException;
+
+	/**
 	 * Returns the id of the linkage this file belongs to.
 	 */
 	@Override
@@ -74,4 +85,5 @@ public interface IIndexFragmentFile extends IIndexFile {
 	 * The file 'source' must belong to the same fragment as this file.
 	 */
 	void transferContext(IIndexFragmentFile source) throws CoreException;
+
 }
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/InternalParserUtil.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/InternalParserUtil.java
index 37ac0d0b27b..a9de019b08e 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/InternalParserUtil.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/InternalParserUtil.java
@@ -155,6 +155,7 @@ public class InternalParserUtil extends ParserFactory {
 
 		InputStream input;
 		try {
+			long fileReadTime = System.currentTimeMillis();
 			IFileStore store = EFS.getStore(file.getLocationURI());
 			IFileInfo fileInfo = store.fetchInfo();
 			input= file.getContents(true);
@@ -173,7 +174,7 @@ public class InternalParserUtil extends ParserFactory {
 			}
 			try {
 				return createFileContent(path, file.getCharset(), input,
-						fileInfo.getLastModified(), fileInfo.getLength());
+						fileInfo.getLastModified(), fileInfo.getLength(), fileReadTime);
 			} finally {
 				try {
 					input.close();
@@ -201,6 +202,7 @@ public class InternalParserUtil extends ParserFactory {
 	 * canonical path. 
 	 */
 	public static InternalFileContent createExternalFileContent(String externalLocation, String encoding) {
+		long fileReadTime = System.currentTimeMillis();
 		File includeFile = null;
 		String path = null;
 		if (!UNCPathConverter.isUNC(externalLocation)) {
@@ -228,7 +230,7 @@ public class InternalParserUtil extends ParserFactory {
 				return null;
 			}
 			try {
-				return createFileContent(path, encoding, in, timestamp, fileSize);
+				return createFileContent(path, encoding, in, timestamp, fileSize, fileReadTime);
 			} finally {
 				try {
 					in.close();
@@ -240,13 +242,13 @@ public class InternalParserUtil extends ParserFactory {
 	}
 
 	private static InternalFileContent createFileContent(String path, String charset, InputStream in,
-			long fileTimestamp, long fileSize) {
+			long fileTimestamp, long fileSize, long fileReadTime) {
 		try {
 			AbstractCharArray chars= FileCharArray.create(path, charset, in);
 			if (chars == null)
 				return null;
 			
-			return new InternalFileContent(path, chars, fileTimestamp, fileSize);
+			return new InternalFileContent(path, chars, fileTimestamp, fileSize, fileReadTime);
 		} catch (IOException e) {
 			CCorePlugin.log(e);
 		}
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/ASTPreprocessorNode.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/ASTPreprocessorNode.java
index 8cf8471286d..43bc89e7012 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/ASTPreprocessorNode.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/ASTPreprocessorNode.java
@@ -298,6 +298,7 @@ class ASTInclusionStatement extends ASTPreprocessorNode implements IASTPreproces
 	private long fIncludedFileContentsHash;
 	private long fIncludedFileTimestamp = -1;
 	private long fIncludedFileSize;
+	private long fIncludedFileReadTime;
 	private boolean fErrorInIncludedFile;
 
 	public ASTInclusionStatement(IASTTranslationUnit parent, 
@@ -405,6 +406,19 @@ class ASTInclusionStatement extends ASTPreprocessorNode implements IASTPreproces
 	}
 
 	@Override
+	public long getIncludedFileReadTime() {
+		if (fNominationDelegate != null) {
+			return 0;
+		} 	
+		return fIncludedFileReadTime;
+	}
+
+	public void setIncludedFileReadTime(long time) {
+		assert fNominationDelegate == null;
+		fIncludedFileReadTime= time;
+	}
+
+	@Override
 	public long getIncludedFileSize() {
 		if (fNominationDelegate != null) {
 			return 0;
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/CPreprocessor.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/CPreprocessor.java
index 0829535d524..46da6f2a30b 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/CPreprocessor.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/CPreprocessor.java
@@ -302,7 +302,7 @@ public class CPreprocessor implements ILexerLog, IScanner, IAdaptable {
         if (contextPath == null) {
         	contextPath= fRootContent.getFileLocation();
         }
-        configureIncludeSearchPath(new File(contextPath).getParentFile(), info);
+        fIncludeSearchPath = configureIncludeSearchPath(new File(contextPath).getParentFile(), info);
         setupMacroDictionary(configuration, info, language);		
 
         ILocationCtx ctx= fLocationMap.pushTranslationUnit(fRootContent.getFileLocation(), fRootContent.getSource());
@@ -396,37 +396,39 @@ public class CPreprocessor implements ILexerLog, IScanner, IAdaptable {
 		return array == null ? CharArrayUtils.EMPTY_CHAR_ARRAY : array;
 	}
 
-    private void configureIncludeSearchPath(File directory, IScannerInfo info) {
+    public static IncludeSearchPathElement[] configureIncludeSearchPath(File directory, IScannerInfo info) {
+    	IncludeSearchPathElement[] includeSearchPath = null;
     	String[] searchPath= info.getIncludePaths();
     	int idx= 0;
         if (info instanceof IExtendedScannerInfo) {
         	final IExtendedScannerInfo einfo= (IExtendedScannerInfo) info;
             final String[] quoteIncludeSearchPath= einfo.getLocalIncludePath();
             if (quoteIncludeSearchPath != null && quoteIncludeSearchPath.length > 0) {
-            	fIncludeSearchPath= new IncludeSearchPathElement[quoteIncludeSearchPath.length + searchPath.length];
-            	for (String qip : quoteIncludeSearchPath) {
-					fIncludeSearchPath[idx++]= new IncludeSearchPathElement(makeAbsolute(directory, qip), true);
+            	includeSearchPath= new IncludeSearchPathElement[quoteIncludeSearchPath.length + searchPath.length];
+            	for (String path : quoteIncludeSearchPath) {
+            		includeSearchPath[idx++]= new IncludeSearchPathElement(makeAbsolute(directory, path), true);
 				}
             }
         }
-        if (fIncludeSearchPath == null) {
-        	fIncludeSearchPath= new IncludeSearchPathElement[searchPath.length];
+        if (includeSearchPath == null) {
+        	includeSearchPath= new IncludeSearchPathElement[searchPath.length];
         }
         for (String path : searchPath) {
-			fIncludeSearchPath[idx++]= new IncludeSearchPathElement(makeAbsolute(directory, path), false);
+        	includeSearchPath[idx++]= new IncludeSearchPathElement(makeAbsolute(directory, path), false);
 		}
+        return includeSearchPath;
 	}
 
-	private String makeAbsolute(File directory, String inlcudePath) {
-		if (directory == null || new File(inlcudePath).isAbsolute()) {
-			return inlcudePath;
+	private static String makeAbsolute(File directory, String includePath) {
+		if (directory == null || new File(includePath).isAbsolute()) {
+			return includePath;
 		}
-		return ScannerUtility.createReconciledPath(directory.getAbsolutePath(), inlcudePath);
+		return ScannerUtility.createReconciledPath(directory.getAbsolutePath(), includePath);
 	}
 
 	private void setupMacroDictionary(IScannerExtensionConfiguration config, IScannerInfo info,
 			ParserLanguage lang) {
-    	// built in macros
+    	// Built-in macros
     	fMacroDictionary.put(__CDT_PARSER__.getNameCharArray(), __CDT_PARSER__);
         fMacroDictionary.put(__STDC__.getNameCharArray(), __STDC__);
         fMacroDictionary.put(__FILE__.getNameCharArray(), __FILE__);
@@ -1066,20 +1068,10 @@ public class CPreprocessor implements ILexerLog, IScanner, IAdaptable {
     private <T> T findInclusion(final String includeDirective, final boolean quoteInclude,
     		final boolean includeNext, final String currentFile, final IIncludeFileTester<T> tester) {
         T reader = null;
-		// Filename is an absolute path
-		if (new File(includeDirective).isAbsolute()) {
-		    return tester.checkFile(includeDirective, false, null);
-		}
-		// Filename is a Linux absolute path on a windows machine
-		if (File.separatorChar == '\\' && includeDirective.length() > 0) {
-			final char firstChar = includeDirective.charAt(0);
-			if (firstChar == '\\' || firstChar == '/') {
-				if (currentFile != null && currentFile.length() > 1 && currentFile.charAt(1) == ':') {
-					return tester.checkFile(currentFile.substring(0, 2) + includeDirective, false, null);
-				}
-			    return tester.checkFile(includeDirective, false, null);
-			}
-		}
+        String absoluteInclusionPath = getAbsoluteInclusionPath(includeDirective, currentFile);
+        if (absoluteInclusionPath != null) {
+        	return tester.checkFile(absoluteInclusionPath, false, null);
+        }
 
         if (currentFile != null && quoteInclude && !includeNext) {
             // Check to see if we find a match in the current directory
@@ -1134,6 +1126,24 @@ public class CPreprocessor implements ILexerLog, IScanner, IAdaptable {
         return null;
     }
 
+    public static String getAbsoluteInclusionPath(String includeDirective, String currentFile) {
+		// Filename is an absolute path
+		if (new File(includeDirective).isAbsolute()) {
+		    return includeDirective;
+		}
+		// Filename is a Linux absolute path on a Windows machine
+		if (File.separatorChar == '\\' && includeDirective.length() > 0) {
+			final char firstChar = includeDirective.charAt(0);
+			if (firstChar == '\\' || firstChar == '/') {
+				if (currentFile != null && currentFile.length() > 1 && currentFile.charAt(1) == ':') {
+					return currentFile.substring(0, 2) + includeDirective;
+				}
+			    return includeDirective;
+			}
+		}
+		return null;
+    }
+    
     private IncludeSearchPathElement findFileInIncludePath(String file, String includeDirective) {
         for (IncludeSearchPathElement path : fIncludeSearchPath) {
     		String fileLocation = path.getLocation(includeDirective);
@@ -1490,6 +1500,7 @@ public class CPreprocessor implements ILexerLog, IScanner, IAdaptable {
 				stmt.setIncludedFileTimestamp(fi.getTimestamp());
 				stmt.setIncludedFileSize(fi.getFileSize());
 				stmt.setIncludedFileContentsHash(source.getContentsHash());
+				stmt.setIncludedFileReadTime(fi.getReadTime());
 				stmt.setErrorInIncludedFile(source.hasError());
 				if (!fCurrentContext.isPragmaOnce()) {
 					// Track the loaded version count, even in a non-pragma-once context.
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/FileCharArray.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/FileCharArray.java
index 66708a23bb3..94c45ff9255 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/FileCharArray.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/FileCharArray.java
@@ -186,6 +186,7 @@ public class FileCharArray extends LazyCharArray {
 			decode(channel, chunk.fSourceOffset, chunk.fSourceEndOffset, CharBuffer.wrap(dest));
 		} catch (IOException e) {
 			// File cannot be read
+			CCorePlugin.log(e);
 			fHasError = true;
 		} finally {
 			try {
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/IncludeSearchPathElement.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/IncludeSearchPathElement.java
index 7cd2ef5e4da..458dbc3f632 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/IncludeSearchPathElement.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/IncludeSearchPathElement.java
@@ -15,7 +15,7 @@ import java.io.File;
 /** 
  * Represents an entry of the include search path
  */
-final class IncludeSearchPathElement {
+public final class IncludeSearchPathElement {
 	private static final boolean NON_SLASH_SEPARATOR = File.separatorChar != '/';
 	public static final String FRAMEWORK_VAR = "__framework__"; //$NON-NLS-1$
 	public static final String FILE_VAR = "__header__"; //$NON-NLS-1$
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/InternalFileContent.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/InternalFileContent.java
index d8daeb12efb..5ce1b706be9 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/InternalFileContent.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/parser/scanner/InternalFileContent.java
@@ -60,6 +60,7 @@ public class InternalFileContent extends FileContent {
 	private IncludeSearchPathElement fFoundOnPath;
 	private final long fTimestamp;
 	private final long fFileSize;
+	private final long fReadTime;
 	
 	/**
 	 * For skipping include files.
@@ -79,7 +80,8 @@ public class InternalFileContent extends FileContent {
 		fSource= null;
 		fNonPragmaOnceFiles= null;
 		fTimestamp= NULL_TIMESTAMP;
-		fFileSize = NULL_FILE_SIZE;
+		fFileSize= NULL_FILE_SIZE;
+		fReadTime= 0;
 	}
 
 	/**
@@ -87,7 +89,7 @@ public class InternalFileContent extends FileContent {
 	 * @throws IllegalArgumentException in case the codeReader or its location is <code>null</code>.
 	 */
 	public InternalFileContent(String filePath, AbstractCharArray content, long timestamp,
-			long fileSize) throws IllegalArgumentException {
+			long fileSize, long fileReadTime) throws IllegalArgumentException {
 		if (content == null) {
 			throw new IllegalArgumentException();
 		}
@@ -101,7 +103,8 @@ public class InternalFileContent extends FileContent {
 			throw new IllegalArgumentException();
 		}
 		fTimestamp= timestamp;
-		fFileSize = fileSize;
+		fFileSize= fileSize;
+		fReadTime= fileReadTime; 
 	}
 
 	/**
@@ -123,6 +126,7 @@ public class InternalFileContent extends FileContent {
 		}
 		fTimestamp= NULL_TIMESTAMP;
 		fFileSize = NULL_FILE_SIZE;
+		fReadTime= 0;
 	}
 
 	/**
@@ -144,6 +148,7 @@ public class InternalFileContent extends FileContent {
 		fNonPragmaOnceFiles= nonPragmaOnceVersions;
 		fTimestamp= NULL_TIMESTAMP;
 		fFileSize = NULL_FILE_SIZE;
+		fReadTime= 0;
 	}
 
 	/**
@@ -167,6 +172,11 @@ public class InternalFileContent extends FileContent {
 	}
 
 	@Override
+	public long getReadTime() {
+		return fReadTime;
+	}
+
+	@Override
 	public long getFileSize() {
 		return fFileSize;
 	}
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/AbstractIndexerTask.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/AbstractIndexerTask.java
index 8a15c8298a1..b86005f0d7a 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/AbstractIndexerTask.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/AbstractIndexerTask.java
@@ -584,6 +584,7 @@ public abstract class AbstractIndexerTask extends PDOMWriter {
 		final boolean forceAll= (fUpdateFlags & IIndexManager.UPDATE_ALL) != 0;
 		final boolean checkTimestamps= (fUpdateFlags & IIndexManager.UPDATE_CHECK_TIMESTAMPS) != 0;
 		final boolean checkFileContentsHash = (fUpdateFlags & IIndexManager.UPDATE_CHECK_CONTENTS_HASH) != 0;
+		final boolean forceUnresolvedIncludes = (fUpdateFlags & IIndexManager.UPDATE_UNRESOLVED_INCLUDES) != 0;
 		final boolean both = fIndexHeadersWithoutContext == UnusedHeaderStrategy.useBoth;
 		int count= 0;
 		int forceFirst= fForceNumberFiles;
@@ -616,7 +617,9 @@ public abstract class AbstractIndexerTask extends PDOMWriter {
 							if (ifile != null && ifile.getLinkageID() == linkageID && ifile.hasContent()) {
 								foundInLinkage = true;
 								indexFiles[i]= null;  // Take the file.
-								boolean update= force || isModified(checkTimestamps, checkFileContentsHash, ifl, tu, ifile);
+								boolean update= force ||
+										(forceUnresolvedIncludes && ifile.hasUnresolvedInclude()) ||
+										isModified(checkTimestamps, checkFileContentsHash, ifl, tu, ifile);
 								if (update && requestUpdate(linkageID, ifl, ifile, tu, updateKind)) {
 									count++;
 									linkages.set(linkageID);
@@ -639,7 +642,9 @@ public abstract class AbstractIndexerTask extends PDOMWriter {
 						iFilesToRemove.add(ifile);
 						count++;
 					} else {
-						boolean update= force || isModified(checkTimestamps, checkFileContentsHash, ifl, tu, ifile);
+						boolean update= force ||
+								(forceUnresolvedIncludes && ifile.hasUnresolvedInclude()) ||
+								isModified(checkTimestamps, checkFileContentsHash, ifl, tu, ifile);
 						final int linkageID = ifile.getLinkageID();
 						if (update && requestUpdate(linkageID, ifl, ifile, tu, UpdateKind.OTHER_HEADER)) {
 							count++;
@@ -648,7 +653,7 @@ public abstract class AbstractIndexerTask extends PDOMWriter {
 					}
 				}
 			}
-			for (int lid = linkages.nextSetBit(0); lid >= 0; lid= linkages.nextSetBit(lid+1)) {
+			for (int lid = linkages.nextSetBit(0); lid >= 0; lid= linkages.nextSetBit(lid + 1)) {
 				addPerLinkage(lid, ifl, files);
 			}
 		}
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOM.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOM.java
index 3d027cb7c6b..b7f081a4cc9 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOM.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOM.java
@@ -72,6 +72,7 @@ import org.eclipse.cdt.internal.core.pdom.db.BTree;
 import org.eclipse.cdt.internal.core.pdom.db.ChunkCache;
 import org.eclipse.cdt.internal.core.pdom.db.DBProperties;
 import org.eclipse.cdt.internal.core.pdom.db.Database;
+import org.eclipse.cdt.internal.core.pdom.db.IBTreeComparator;
 import org.eclipse.cdt.internal.core.pdom.db.IBTreeVisitor;
 import org.eclipse.cdt.internal.core.pdom.dom.BindingCollector;
 import org.eclipse.cdt.internal.core.pdom.dom.FindBinding;
@@ -215,10 +216,11 @@ public class PDOM extends PlatformObject implements IPDOM {
 	 *  122.0 - Compacting strings
 	 *  123.0 - Combined file size and encoding hash code.
 	 *  124.0 - GCC attributes and NO_RETURN flag for functions.
+	 *  125.0 - Indexes for unresolved includes and files indexed with I/O errors.
 	 */
-	private static final int MIN_SUPPORTED_VERSION= version(124, 0);
-	private static final int MAX_SUPPORTED_VERSION= version(124, Short.MAX_VALUE);
-	private static final int DEFAULT_VERSION = version(124, 0);
+	private static final int MIN_SUPPORTED_VERSION= version(125, 0);
+	private static final int MAX_SUPPORTED_VERSION= version(125, Short.MAX_VALUE);
+	private static final int DEFAULT_VERSION = version(125, 0);
 
 	private static int version(int major, int minor) {
 		return (major << 16) + minor;
@@ -251,8 +253,10 @@ public class PDOM extends PlatformObject implements IPDOM {
 
 	public static final int LINKAGES = Database.DATA_AREA;
 	public static final int FILE_INDEX = Database.DATA_AREA + 4;
-	public static final int PROPERTIES = Database.DATA_AREA + 8;
-	public static final int END= Database.DATA_AREA + 12;
+	public static final int INDEX_OF_DEFECTIVE_FILES = Database.DATA_AREA + 8;
+	public static final int INDEX_OF_FILES_WITH_UNRESOLVED_INCLUDES = Database.DATA_AREA + 12;
+	public static final int PROPERTIES = Database.DATA_AREA + 16;
+	public static final int END= Database.DATA_AREA + 20;
 	static {
 		assert END <= Database.CHUNK_SIZE;
 	}
@@ -303,9 +307,19 @@ public class PDOM extends PlatformObject implements IPDOM {
 		public void handleChange(PDOM pdom, ChangeEvent event);
 	}
 
+	// Primitive comparator that compares database offsets of two records.
+	private static final IBTreeComparator offsetComparator = new IBTreeComparator() {
+		@Override
+		public int compare(long record1, long record2) throws CoreException {
+	        return record1 < record2 ? -1 : record1 == record2 ? 0 : 1;
+		}
+	};
+
 	// Local caches
 	protected Database db;
 	private BTree fileIndex;
+	private BTree indexOfDefectiveFiles;
+	private BTree indexOfFiledWithUnresolvedIncludes;
 	private Map<Integer, PDOMLinkage> fLinkageIDCache = new HashMap<Integer, PDOMLinkage>();
 	private File fPath;
 	private IIndexLocationConverter locationConverter;
@@ -432,6 +446,26 @@ public class PDOM extends PlatformObject implements IPDOM {
 		return fileIndex;
 	}
 
+	/**
+	 * Returns the index of files that were read with I/O errors.
+	 */
+	public BTree getIndexOfDefectiveFiles() throws CoreException {
+		if (indexOfDefectiveFiles == null)
+			indexOfDefectiveFiles = new BTree(getDB(), INDEX_OF_DEFECTIVE_FILES, offsetComparator);
+		return indexOfDefectiveFiles;
+	}
+
+	/**
+	 * Returns the index of files containg unresolved includes.
+	 */
+	public BTree getIndexOfFilesWithUnresolvedIncludes() throws CoreException {
+		if (indexOfFiledWithUnresolvedIncludes == null) {
+			indexOfFiledWithUnresolvedIncludes =
+					new BTree(getDB(), INDEX_OF_FILES_WITH_UNRESOLVED_INCLUDES, offsetComparator);
+		}
+		return indexOfFiledWithUnresolvedIncludes;
+	}
+
 	@Deprecated
 	@Override
 	public PDOMFile getFile(int linkageID, IIndexFileLocation location) throws CoreException {
@@ -471,8 +505,22 @@ public class PDOM extends PlatformObject implements IPDOM {
 
 	@Override
 	public IIndexFragmentFile[] getAllFiles() throws CoreException {
-		final List<PDOMFile> locations = new ArrayList<PDOMFile>();
-		getFileIndex().accept(new IBTreeVisitor() {
+		return getFiles(getFileIndex());
+	}
+
+	@Override
+	public IIndexFragmentFile[] getDefectiveFiles() throws CoreException {
+		return getFiles(getIndexOfDefectiveFiles());
+	}
+
+	@Override
+	public IIndexFragmentFile[] getFilesWithUnresolvedIncludes() throws CoreException {
+		return getFiles(getIndexOfFilesWithUnresolvedIncludes());
+	}
+
+	private IIndexFragmentFile[] getFiles(BTree index) throws CoreException {
+		final List<PDOMFile> files = new ArrayList<PDOMFile>();
+		index.accept(new IBTreeVisitor() {
 			@Override
 			public int compare(long record) throws CoreException {
 				return 0;
@@ -481,13 +529,13 @@ public class PDOM extends PlatformObject implements IPDOM {
 			@Override
 			public boolean visit(long record) throws CoreException {
 				PDOMFile file = PDOMFile.recreateFile(PDOM.this, record);
-				locations.add(file);
+				files.add(file);
 				return true;
 			}
 		});
-		return locations.toArray(new IIndexFragmentFile[locations.size()]);
+		return files.toArray(new IIndexFragmentFile[files.size()]);
 	}
-
+		
 	protected IIndexFragmentFile addFile(int linkageID, IIndexFileLocation location,
 			ISignificantMacros sigMacros) throws CoreException {
 		PDOMLinkage linkage= createLinkage(linkageID);
@@ -1296,6 +1344,8 @@ public class PDOM extends PlatformObject implements IPDOM {
 
 	private void clearCaches() {
 		fileIndex= null;
+		indexOfDefectiveFiles= null;
+		indexOfFiledWithUnresolvedIncludes= null;
 		fLinkageIDCache.clear();
 		clearResultCache();
 	}
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMProxy.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMProxy.java
index 20f4d820d0a..99d43bc24d3 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMProxy.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMProxy.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2007, 2010 Wind River Systems, Inc. and others.
+ * Copyright (c) 2007, 2012 Wind River Systems, Inc. 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
@@ -41,7 +41,7 @@ import org.eclipse.core.runtime.IProgressMonitor;
 /**
  * The PDOMProxy is returned by the PDOMManager before the indexer kicks in. Also and more
  * importantly it is returned when the indexer has been shut down (clients may not be aware
- * of this yet). Doing that prevents the creation of empty pdoms for deleted projects.
+ * of this yet). Doing that prevents the creation of empty PDOMs for deleted projects.
  */
 public class PDOMProxy implements IPDOM {
 	private PDOM fDelegate;
@@ -319,6 +319,20 @@ public class PDOMProxy implements IPDOM {
 	}
 
 	@Override
+	public synchronized IIndexFragmentFile[] getDefectiveFiles() throws CoreException {
+		if (fDelegate != null)
+			return fDelegate.getDefectiveFiles();
+		return IIndexFragmentFile.EMPTY_ARRAY;
+	}
+
+	@Override
+	public synchronized IIndexFragmentFile[] getFilesWithUnresolvedIncludes() throws CoreException {
+		if (fDelegate != null)
+			return fDelegate.getFilesWithUnresolvedIncludes();
+		return IIndexFragmentFile.EMPTY_ARRAY;
+	}
+
+	@Override
 	public synchronized IIndexFragmentBinding[] findMacroContainers(Pattern pattern, IndexFilter filter,
 			IProgressMonitor monitor) throws CoreException {
 		if (fDelegate != null) {
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMWriter.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMWriter.java
index c3b7c051b92..bcdc654fe9f 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMWriter.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMWriter.java
@@ -79,6 +79,7 @@ abstract public class PDOMWriter {
 		final long timestamp;
 		final long fileSize;
 		final long contentsHash;
+		final long sourceReadTime;
 		final boolean hasError;
 
 		public FileInAST(IASTPreprocessorIncludeStatement includeStmt, FileContentKey key) {
@@ -87,6 +88,7 @@ abstract public class PDOMWriter {
 			timestamp= includeStmt.getIncludedFileTimestamp();
 			fileSize = includeStmt.getIncludedFileSize();
 			contentsHash= includeStmt.getIncludedFileContentsHash();
+			sourceReadTime= includeStmt.getIncludedFileReadTime();
 			hasError= includeStmt.isErrorInIncludedFile();
 		}
 
@@ -96,6 +98,7 @@ abstract public class PDOMWriter {
 			timestamp= codeReader.getTimestamp();
 			fileSize= codeReader.getFileSize();
 			contentsHash= codeReader.getContentsHash();
+			sourceReadTime= codeReader.getReadTime();
 			hasError= codeReader.hasError();
 		}
 
@@ -577,6 +580,7 @@ abstract public class PDOMWriter {
 				index.setFileContent(file, linkageID, includeInfoArray, macros, names, fResolver, lock);
 			}
 			file.setTimestamp(astFile.hasError ? 0 : astFile.timestamp);
+			file.setSourceReadTime(astFile.sourceReadTime);
 			file.setSizeAndEncodingHashcode(computeFileSizeAndEncodingHashcode(astFile.fileSize, location));
 			file.setContentsHash(astFile.contentsHash);
 			file = index.commitUncommittedFile();
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/WritablePDOM.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/WritablePDOM.java
index aaeb280dfd8..89b1b26d487 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/WritablePDOM.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/WritablePDOM.java
@@ -87,17 +87,36 @@ public class WritablePDOM extends PDOM implements IWritableIndexFragment {
 	public IIndexFragmentFile commitUncommittedFile() throws CoreException {
 		if (uncommittedFile == null)
 			return null;
+
+		int defectiveStateChange = uncommittedFile.getTimestamp() == 0 ? 1 : 0;
+		int unresolvedIncludeStateChange = uncommittedFile.hasUnresolvedInclude() ? 1 : 0;
+
 		PDOMFile file;
 		if (fileBeingUpdated == null) {
 			// New file, insert it into the index.
 			file = uncommittedFile;
-			getFileIndex().insert(file.getRecord()); 
+			getFileIndex().insert(file.getRecord());
 		} else {
 			// Existing file.
+			if (fileBeingUpdated.getTimestamp() == 0)
+				defectiveStateChange -= 1;
+			if (fileBeingUpdated.hasUnresolvedInclude())
+				unresolvedIncludeStateChange -= 1;
 			fileBeingUpdated.replaceContentsFrom(uncommittedFile);
 			file = fileBeingUpdated;
 			fileBeingUpdated = null;
 		}
+		if (defectiveStateChange > 0) {
+			getIndexOfDefectiveFiles().insert(file.getRecord());
+		} else if (defectiveStateChange < 0) {
+			getIndexOfDefectiveFiles().delete(file.getRecord());
+		}
+		if (unresolvedIncludeStateChange > 0) {
+			getIndexOfFilesWithUnresolvedIncludes().insert(file.getRecord());
+		} else if (unresolvedIncludeStateChange < 0) {
+			getIndexOfFilesWithUnresolvedIncludes().delete(file.getRecord());
+		}
+
 		fEvent.fFilesWritten.add(uncommittedKey.getLocation());
 		uncommittedFile = null;
 		uncommittedKey = null;
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/dom/PDOMFile.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/dom/PDOMFile.java
index 816e1dbcbb1..e44b2170e72 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/dom/PDOMFile.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/dom/PDOMFile.java
@@ -72,13 +72,14 @@ public class PDOMFile implements IIndexFragmentFile {
 	private static final int LOCATION_REPRESENTATION = FIRST_MACRO + Database.PTR_SIZE;
 	private static final int LINKAGE_ID= LOCATION_REPRESENTATION + Database.PTR_SIZE;  // size 3
 	private static final int FLAGS= LINKAGE_ID + 3;  // size 1
-	private static final int TIME_STAMP = FLAGS + 1; // long
-	private static final int CONTENT_HASH= TIME_STAMP + 8;  // long
+	private static final int TIME_STAMP= FLAGS + 1;  // long
+	private static final int SOURCE_READ_TIME= TIME_STAMP + 8;  // long
+	private static final int CONTENT_HASH= SOURCE_READ_TIME + 8;  // long
 	private static final int SIZE_AND_ENCODING_HASH= CONTENT_HASH + 8;
 	private static final int LAST_USING_DIRECTIVE= SIZE_AND_ENCODING_HASH + 4;
 	private static final int FIRST_MACRO_REFERENCE= LAST_USING_DIRECTIVE + Database.PTR_SIZE;
 	private static final int SIGNIFICANT_MACROS= FIRST_MACRO_REFERENCE + Database.PTR_SIZE;
-	private static final int RECORD_SIZE= SIGNIFICANT_MACROS + Database.PTR_SIZE;   // 8*PTR_SIZE + 3+1+8+8+4 = 56
+	private static final int RECORD_SIZE= SIGNIFICANT_MACROS + Database.PTR_SIZE;   // 8*PTR_SIZE + 3+1+8+8+8+4 = 64
 
 	private static final int FLAG_PRAGMA_ONCE_SEMANTICS	= 0x01;
 
@@ -205,6 +206,7 @@ public class PDOMFile implements IIndexFragmentFile {
 		}
 
 		setTimestamp(sourceFile.getTimestamp());
+		setSourceReadTime(sourceFile.getSourceReadTime());
 		setSizeAndEncodingHashcode(sourceFile.getSizeAndEncodingHashcode());
 		setContentsHash(sourceFile.getContentsHash());
 
@@ -310,6 +312,18 @@ public class PDOMFile implements IIndexFragmentFile {
 	}
 
 	@Override
+	public long getSourceReadTime() throws CoreException {
+		Database db = fLinkage.getDB();
+		return db.getLong(record + SOURCE_READ_TIME);
+	}
+
+	@Override
+	public void setSourceReadTime(long time) throws CoreException {
+		Database db= fLinkage.getDB();
+		db.putLong(record + SOURCE_READ_TIME, time);
+	}
+
+	@Override
 	public long getContentsHash() throws CoreException {
 		Database db = fLinkage.getDB();
 		return db.getLong(record + CONTENT_HASH);
@@ -571,6 +585,7 @@ public class PDOMFile implements IIndexFragmentFile {
 			m.delete();
 		}
 		setFirstMacroReference(null);
+		setSourceReadTime(0);
 		setTimestamp(-1);
 	}
 
@@ -645,6 +660,17 @@ public class PDOMFile implements IIndexFragmentFile {
 	}
 
 	@Override
+	public boolean hasUnresolvedInclude() throws CoreException {
+		PDOMInclude include = getFirstInclude();
+		while (include != null) {
+			if (!include.isResolved() && include.isActive())
+				return true;
+			include = include.getNextInIncludes();
+		}
+		return false;
+	}
+
+	@Override
 	public IIndexMacro[] getMacros() throws CoreException {
 		List<PDOMMacro> result= new ArrayList<PDOMMacro>();
 		PDOMMacro macro = getFirstMacro();
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/indexer/PDOMUpdateTask.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/indexer/PDOMUpdateTask.java
index 349ea0fde3f..df8621199c4 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/indexer/PDOMUpdateTask.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/indexer/PDOMUpdateTask.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2007, 2010 Wind River Systems, Inc. and others.
+ * Copyright (c) 2007, 2012 Wind River Systems, Inc. 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
@@ -11,6 +11,7 @@
 ******************************************************************************/ 
 package org.eclipse.cdt.internal.core.pdom.indexer;
 
+import java.io.File;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -22,13 +23,18 @@ import org.eclipse.cdt.core.dom.IPDOMManager;
 import org.eclipse.cdt.core.index.IIndex;
 import org.eclipse.cdt.core.index.IIndexFile;
 import org.eclipse.cdt.core.index.IIndexFileLocation;
+import org.eclipse.cdt.core.index.IIndexInclude;
 import org.eclipse.cdt.core.index.IIndexManager;
 import org.eclipse.cdt.core.index.IndexLocationFactory;
 import org.eclipse.cdt.core.model.CoreModel;
 import org.eclipse.cdt.core.model.ICElement;
 import org.eclipse.cdt.core.model.ICProject;
 import org.eclipse.cdt.core.model.ITranslationUnit;
+import org.eclipse.cdt.core.parser.IScannerInfo;
 import org.eclipse.cdt.internal.core.model.ExternalTranslationUnit;
+import org.eclipse.cdt.internal.core.parser.scanner.CPreprocessor;
+import org.eclipse.cdt.internal.core.parser.scanner.IncludeSearchPathElement;
+import org.eclipse.cdt.internal.core.parser.scanner.ScannerUtility;
 import org.eclipse.cdt.internal.core.pdom.IndexerProgress;
 import org.eclipse.core.resources.IFile;
 import org.eclipse.core.resources.IResource;
@@ -42,19 +48,18 @@ import org.eclipse.osgi.util.NLS;
  * A task for updating an index, suitable for all indexers.
  */
 public class PDOMUpdateTask implements IPDOMIndexerTask {
-	protected static final String TRUE= String.valueOf(true);
-	protected static final ITranslationUnit[] NO_TUS = {};
+	private static final ITranslationUnit[] NO_TUS = {};
 	
 	private final IPDOMIndexer fIndexer;
-	private final IndexerProgress fProgress;
 	private final int fUpdateOptions;
+	private final IndexerProgress fProgress;
 	private volatile IPDOMIndexerTask fDelegate;
 	private ArrayList<ICElement> fFilesAndFolders;
 
 	public PDOMUpdateTask(IPDOMIndexer indexer, int updateOptions) {
 		fIndexer= indexer;
-		fProgress= createProgress();
 		fUpdateOptions= updateOptions;
+		fProgress= createProgress();
 	}
 
 	private IndexerProgress createProgress() {
@@ -92,40 +97,65 @@ public class PDOMUpdateTask implements IPDOMIndexerTask {
 	private void createDelegate(ICProject project, IProgressMonitor monitor)
 			throws CoreException, InterruptedException {
 		HashSet<ITranslationUnit> set= new HashSet<ITranslationUnit>();
-		TranslationUnitCollector collector= new TranslationUnitCollector(set, set, monitor);
-		boolean haveProject= false;
-		if (fFilesAndFolders == null) {
-			project.accept(collector);
-		} else {
-			for (ICElement elem : fFilesAndFolders) {
-				if (elem.getElementType() == ICElement.C_PROJECT) {
-					haveProject= true;
+		if ((fUpdateOptions & (IIndexManager.UPDATE_ALL | IIndexManager.UPDATE_CHECK_TIMESTAMPS)) != 0) {
+			TranslationUnitCollector collector= new TranslationUnitCollector(set, set, monitor);
+			boolean haveProject= false;
+			if (fFilesAndFolders == null) {
+				project.accept(collector);
+			} else {
+				for (ICElement elem : fFilesAndFolders) {
+					if (elem.getElementType() == ICElement.C_PROJECT) {
+						haveProject= true;
+					}
+					elem.accept(collector);
+				}
+			}
+			if (haveProject && (fUpdateOptions & IIndexManager.UPDATE_EXTERNAL_FILES_FOR_PROJECT) != 0) {
+				final String projectPrefix= project.getProject().getFullPath().toString() + IPath.SEPARATOR;
+				IIndex index= CCorePlugin.getIndexManager().getIndex(project);
+				index.acquireReadLock();
+				try {
+					IIndexFile[] files= index.getAllFiles();
+					for (IIndexFile indexFile : files) {
+						IIndexFileLocation floc= indexFile.getLocation();
+						final String fullPath = floc.getFullPath();
+						if (fullPath == null || !fullPath.startsWith(projectPrefix)) {
+							ITranslationUnit tu = getTranslationUnit(floc, project);
+							if (tu != null) {
+								set.add(tu);
+							}
+						}
+					}
+				} finally {
+					index.releaseReadLock();
 				}
-				elem.accept(collector);
 			}
 		}
-		if (haveProject && (fUpdateOptions & IIndexManager.UPDATE_EXTERNAL_FILES_FOR_PROJECT) != 0) {
-			final String projectPrefix= project.getProject().getFullPath().toString() + IPath.SEPARATOR;
+
+		if ((fUpdateOptions & IIndexManager.UPDATE_UNRESOLVED_INCLUDES) != 0) {
 			IIndex index= CCorePlugin.getIndexManager().getIndex(project);
 			index.acquireReadLock();
 			try {
-				IIndexFile[] files= index.getAllFiles();
-				for (IIndexFile indexFile : files) {
-					IIndexFileLocation floc= indexFile.getLocation();
-					final String fullPath = floc.getFullPath();
-					if (fullPath == null || !fullPath.startsWith(projectPrefix)) {
-						IPath path= IndexLocationFactory.getAbsolutePath(floc);
-						if (path != null) {
-							ITranslationUnit tu= CoreModel.getDefault().createTranslationUnitFrom(project, path);
-							if (tu != null) {
-								if (fullPath != null) {
-									if (tu instanceof ExternalTranslationUnit) {
-										IResource file= ResourcesPlugin.getWorkspace().getRoot().findMember(fullPath);
-										if (file instanceof IFile) {
-											((ExternalTranslationUnit) tu).setResource((IFile) file);
-										}
-									}
-								}
+				// Files that were indexed with I/O errors.
+				IIndexFile[] files= index.getDefectiveFiles();
+				for (IIndexFile file : files) {
+					ITranslationUnit tu = getTranslationUnit(file.getLocation(), project);
+					if (tu != null) {
+						set.add(tu);
+					}
+				}
+
+				// Files with unresolved includes.
+				files= index.getFilesWithUnresolvedIncludes();
+				if (files.length > 0) {
+					ProjectIndexerInputAdapter inputAdapter = new ProjectIndexerInputAdapter(project, true);
+			        ProjectIndexerIncludeResolutionHeuristics includeResolutionHeuristics =
+			        		new ProjectIndexerIncludeResolutionHeuristics(project.getProject(), inputAdapter);
+			        for (IIndexFile file : files) {
+						ITranslationUnit tu = getTranslationUnit(file.getLocation(), project);
+						if (tu != null) {
+							IScannerInfo scannerInfo = tu.getScannerInfo(true);
+							if (canResolveUnresolvedInclude(file, scannerInfo, includeResolutionHeuristics)) {
 								set.add(tu);
 							}
 						}
@@ -135,15 +165,108 @@ public class PDOMUpdateTask implements IPDOMIndexerTask {
 				index.releaseReadLock();
 			}
 		}
+
 		ITranslationUnit[] tus= set.toArray(new ITranslationUnit[set.size()]);
 		IPDOMIndexerTask delegate= fIndexer.createTask(NO_TUS, tus, NO_TUS);
 		if (delegate instanceof PDOMIndexerTask) {
 			final PDOMIndexerTask task = (PDOMIndexerTask) delegate;
 			task.setUpdateFlags(fUpdateOptions);
 		}
-		synchronized (this) {
-			fDelegate= delegate;
+		setDelegate(delegate);
+	}
+
+	private ITranslationUnit getTranslationUnit(IIndexFileLocation location, ICProject project) {
+		IPath path= IndexLocationFactory.getAbsolutePath(location);
+		if (path == null)
+			return null;
+		ITranslationUnit tu= CoreModel.getDefault().createTranslationUnitFrom(project, path);
+		if (tu != null) {
+			final String fullPath = location.getFullPath();
+			if (fullPath != null) {
+				if (tu instanceof ExternalTranslationUnit) {
+					IResource file= ResourcesPlugin.getWorkspace().getRoot().findMember(fullPath);
+					if (file instanceof IFile) {
+						((ExternalTranslationUnit) tu).setResource((IFile) file);
+					}
+				}
+			}
+		}
+		return tu;
+	}
+
+	private boolean canResolveUnresolvedInclude(IIndexFile file, IScannerInfo scannerInfo,
+			ProjectIndexerIncludeResolutionHeuristics includeResolutionHeuristics) {
+		try {
+			String filePath = IndexLocationFactory.getAbsolutePath(file.getLocation()).toOSString();
+			long fileReadTime = file.getSourceReadTime();
+			IncludeSearchPathElement[] includeSearchPath =
+					CPreprocessor.configureIncludeSearchPath(new File(filePath).getParentFile(), scannerInfo);
+			for (IIndexInclude include : file.getIncludes()) {
+				if (!include.isResolved() && include.isActive() &&
+						canResolveInclude(include, filePath, fileReadTime, includeSearchPath, includeResolutionHeuristics)) {
+					return true;
+				}
+			}
+		} catch (CoreException e) {
+			CCorePlugin.log(e);
 		}
+		return false;
+	}
+
+	private boolean canResolveInclude(IIndexInclude include, String currentFile, long timestamp,
+			IncludeSearchPathElement[] includeSearchPath,
+			ProjectIndexerIncludeResolutionHeuristics includeResolutionHeuristics) throws CoreException {
+		String includeName = include.getFullName();
+        String filePath = CPreprocessor.getAbsoluteInclusionPath(includeName, currentFile);
+        if (filePath != null && fileIsNotOlderThanTimestamp(filePath, timestamp)) {
+        	return true;
+        }
+
+        if (currentFile != null && !include.isSystemInclude()) {
+            // Check to see if we find a match in the current directory
+    		final File currentDir= new File(currentFile).getParentFile();
+    		if (currentDir != null) {
+        		filePath = ScannerUtility.createReconciledPath(currentDir.getAbsolutePath(), includeName);
+        		if (!filePath.equals(currentFile) && fileIsNotOlderThanTimestamp(filePath, timestamp)) {
+        			return true;
+        		}
+    		}
+        }
+
+        // Unlike CPreprocessor.findInclusion we are searching include path from the beginning.
+        // This simplification may produce false positives, but by checking file modification time
+        // we guarantee that any false positive won't be produced again when this task runs
+        // next time.
+        for (IncludeSearchPathElement path : includeSearchPath) {
+        	if (!include.isSystemInclude() || !path.isForQuoteIncludesOnly()) {
+        		filePath = path.getLocation(includeName);
+        		if (filePath != null && fileIsNotOlderThanTimestamp(filePath, timestamp)) {
+        			return true;
+        		}
+        	}
+        }
+        if (includeResolutionHeuristics != null) {
+        	filePath= includeResolutionHeuristics.findInclusion(includeName, currentFile);
+    		if (filePath != null && fileIsNotOlderThanTimestamp(filePath, timestamp)) {
+    			return true;
+    		}
+        }
+
+        return false;
+	}
+
+	/**
+	 * Returns true if the file exists and is not older than the given timestamp.
+	 */
+	private boolean fileIsNotOlderThanTimestamp(String filename, long timestamp) {
+		// We are subtracting 1 second from the timestamp to account for limited precision
+		// of File.lastModified() method and possible asynchrony between clocks on multi-CPU
+		// systems. This may produce false positives, but they are pretty harmless.
+		return new File(filename).lastModified() >= timestamp - 1000;
+	}
+
+	private synchronized void setDelegate(IPDOMIndexerTask delegate) {
+		fDelegate= delegate;
 	}
 
 	@Override