### Eclipse Workspace Patch 1.0
#P org.eclipse.jdt.core
Index: antadapter/org/eclipse/jdt/core/JDTCompilerAdapter.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/antadapter/org/eclipse/jdt/core/JDTCompilerAdapter.java,v
retrieving revision 1.69
diff -u -r1.69 JDTCompilerAdapter.java
--- antadapter/org/eclipse/jdt/core/JDTCompilerAdapter.java	25 Apr 2010 20:10:09 -0000	1.69
+++ antadapter/org/eclipse/jdt/core/JDTCompilerAdapter.java	28 Sep 2010 17:56:46 -0000
@@ -119,8 +119,6 @@
 			}
 		}
 
-		Path classpath = new Path(this.project);
-
 		/*
 		 * Eclipse compiler doesn't support -extdirs.
 		 * It is emulated using the classpath. We add extdirs entries after the
@@ -131,11 +129,17 @@
 			cmd.createArgument().setPath(this.extdirs);
 		}
 
+		Path classpath = new Path(this.project);
 		/*
 		 * The java runtime is already handled, so we simply want to retrieve the
 		 * ant runtime and the compile classpath.
 		 */
 		classpath.append(getCompileClasspath());
+		/*
+		 * Set the classpath for the Eclipse compiler.
+		 */
+		cmd.createArgument().setValue("-classpath"); //$NON-NLS-1$
+		createClasspathArgument(cmd, classpath);
 
 		// For -sourcepath, use the "sourcepath" value if present.
 		// Otherwise default to the "srcdir" value.
@@ -164,12 +168,8 @@
 		} else {
 			sourcepath = this.src;
 		}
-		classpath.append(sourcepath);
-		/*
-		 * Set the classpath for the Eclipse compiler.
-		 */
-		cmd.createArgument().setValue("-classpath"); //$NON-NLS-1$
-		createClasspathArgument(cmd, classpath);
+		cmd.createArgument().setValue("-sourcepath"); //$NON-NLS-1$
+		createClasspathArgument(cmd, sourcepath);
 
 		final String javaVersion = JavaEnvUtils.getJavaVersion();
 		String memoryParameterPrefix = javaVersion.equals(JavaEnvUtils.JAVA_1_1) ? "-J-" : "-J-X";//$NON-NLS-1$//$NON-NLS-2$
Index: batch/org/eclipse/jdt/internal/compiler/batch/ClasspathDirectory.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/batch/org/eclipse/jdt/internal/compiler/batch/ClasspathDirectory.java,v
retrieving revision 1.57
diff -u -r1.57 ClasspathDirectory.java
--- batch/org/eclipse/jdt/internal/compiler/batch/ClasspathDirectory.java	19 Aug 2010 06:26:31 -0000	1.57
+++ batch/org/eclipse/jdt/internal/compiler/batch/ClasspathDirectory.java	28 Sep 2010 17:56:46 -0000
@@ -28,7 +28,7 @@
 
 private Hashtable directoryCache;
 private String[] missingPackageHolder = new String[1];
-private int mode; // ability to only consider one kind of files (source vs. binaries), by default use both
+int mode; // ability to only consider one kind of files (source vs. binaries), by default use both
 private String encoding; // only useful if referenced in the source path
 
 ClasspathDirectory(File directory, String encoding, int mode,
Index: batch/org/eclipse/jdt/internal/compiler/batch/FileSystem.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/batch/org/eclipse/jdt/internal/compiler/batch/FileSystem.java,v
retrieving revision 1.55
diff -u -r1.55 FileSystem.java
--- batch/org/eclipse/jdt/internal/compiler/batch/FileSystem.java	21 Feb 2010 03:35:52 -0000	1.55
+++ batch/org/eclipse/jdt/internal/compiler/batch/FileSystem.java	28 Sep 2010 17:56:46 -0000
@@ -201,13 +201,37 @@
 			fileName = CharOperation.subarray(fileName, 0, lastIndexOf);
 		}
 		CharOperation.replace(fileName, '\\', '/');
+		boolean sourcePathMatches = false;
+		// a source path folder should match over a classpath entry set up for both source and binary
 		for (int j = 0, max = this.classpaths.length; j < max; j++) {
 			char[] matchCandidate = this.classpaths[j].normalizedPath();
-			if (this.classpaths[j] instanceof  ClasspathDirectory &&
-					CharOperation.prefixEquals(matchCandidate, fileName) &&
-					(matchingPathName == null ||
-							matchCandidate.length < matchingPathName.length)) {
-				matchingPathName = matchCandidate;
+			boolean currentSourcePathMatch = false;
+			if (this.classpaths[j] instanceof ClasspathDirectory
+					&& CharOperation.prefixEquals(matchCandidate, fileName)) {
+				ClasspathDirectory classpathDirectory = (ClasspathDirectory) this.classpaths[j];
+				if ((classpathDirectory.mode & (ClasspathLocation.SOURCE | ClasspathLocation.BINARY)) == ClasspathLocation.SOURCE) {
+					currentSourcePathMatch = true;
+				}
+				if (matchingPathName == null) {
+					matchingPathName = matchCandidate;
+				} else {
+					// if not null, we must keep the current classpath directory if this is a source path folder
+					if (currentSourcePathMatch) {
+						// we have a second source folder that matches the path of the source file
+						if (matchCandidate.length > matchingPathName.length) {
+							// we want to preserve the shortest possible path
+							matchingPathName = matchCandidate;
+						}
+					} else {
+						// if (sourcePathMatches) one former source paths matched - ignore the current match
+						if (!sourcePathMatches && matchCandidate.length < matchingPathName.length) {
+							matchingPathName = matchCandidate;
+						}
+					}
+				}
+				if (currentSourcePathMatch) {
+					sourcePathMatches = true;
+				}
 			}
 		}
 		if (matchingPathName == null) {