### Eclipse Workspace Patch 1.0
#P org.eclipse.jdt.core
Index: model/org/eclipse/jdt/core/IJavaProject.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/core/IJavaProject.java,v
retrieving revision 1.106
diff -u -r1.106 IJavaProject.java
--- model/org/eclipse/jdt/core/IJavaProject.java	24 Feb 2011 16:51:58 -0000	1.106
+++ model/org/eclipse/jdt/core/IJavaProject.java	3 Mar 2011 07:51:21 -0000
@@ -520,7 +520,9 @@
 	 * does not include package fragment roots in other projects referenced
 	 * on this project's classpath.
 	 *
-	 * <p>NOTE: This is equivalent to <code>getChildren()</code>.
+	 * <p>The package fragment roots appear in the order they are defined 
+	 * by the classpath.
+	 * </p>
 	 *
 	 * @return all of the  package fragment roots contained in this
 	 * project, identified on this project's resolved classpath
Index: model/org/eclipse/jdt/internal/core/DeltaProcessor.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/internal/core/DeltaProcessor.java,v
retrieving revision 1.341
diff -u -r1.341 DeltaProcessor.java
--- model/org/eclipse/jdt/internal/core/DeltaProcessor.java	2 Dec 2010 07:51:52 -0000	1.341
+++ model/org/eclipse/jdt/internal/core/DeltaProcessor.java	3 Mar 2011 07:51:21 -0000
@@ -282,8 +282,56 @@
 		if (parent != null && parent.isOpen()) {
 			try {
 				OpenableElementInfo info = (OpenableElementInfo) parent.getElementInfo();
-				info.addChild(child);
-			} catch (JavaModelException e) {
+				// https://bugs.eclipse.org/bugs/show_bug.cgi?id=338006
+				// Insert the package fragment roots in the same order as the classpath order.
+				iterate: if (child instanceof IPackageFragmentRoot) {
+					IJavaElement[] roots = info.getChildren();
+					if (roots.length == 0)
+						break iterate;
+					
+					IPackageFragmentRoot root = (IPackageFragmentRoot) child;
+					IClasspathEntry[] resolvedClasspath = ((JavaProject)root.getJavaProject()).getResolvedClasspath();
+					IClasspathEntry currentEntry = root.getResolvedClasspathEntry();
+					
+					int indexToInsert = -1;
+					int lastComparedIndex = -1;
+					for (int i =0, j=0; i < roots.length && j < resolvedClasspath.length; ) {
+						
+						// If the new root is already among the children, no need to proceed further. Just return.
+						// This condition will be checked even if indexToInsert has already been found 
+						if(roots[i].getPath().equals(child.getPath())) {
+							return;
+						}
+						
+						if (indexToInsert == -1) {
+							if ( lastComparedIndex != j && currentEntry.getPath().equals(resolvedClasspath[j].getPath())) {
+								indexToInsert = i;
+								break;
+							}
+							lastComparedIndex = j;
+
+							IClasspathEntry rootEntry = ((IPackageFragmentRoot)roots[i]).getResolvedClasspathEntry();
+							if (rootEntry.getPath().equals(resolvedClasspath[j].getPath()))
+								i++;
+							else
+								j++;
+						}
+					}
+					if (indexToInsert >= 0) {
+						int newSize = roots.length + 1;
+						IPackageFragmentRoot[] newChildren = new IPackageFragmentRoot[newSize];
+						
+						if(indexToInsert > 0) 
+							System.arraycopy(roots, 0, newChildren, 0, indexToInsert);
+						
+						newChildren[indexToInsert] = (IPackageFragmentRoot)child;
+						System.arraycopy(roots, indexToInsert, newChildren, indexToInsert+1, (newSize - indexToInsert -1));
+						info.setChildren(newChildren);
+						return;
+					}
+				}
+ 				info.addChild(child);
+ 			} catch (JavaModelException e) {
 				// do nothing - we already checked if open
 			}
 		}
#P org.eclipse.jdt.core.tests.model
Index: src/org/eclipse/jdt/core/tests/model/AbstractJavaModelTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.model/src/org/eclipse/jdt/core/tests/model/AbstractJavaModelTests.java,v
retrieving revision 1.243
diff -u -r1.243 AbstractJavaModelTests.java
--- src/org/eclipse/jdt/core/tests/model/AbstractJavaModelTests.java	21 Feb 2011 00:53:28 -0000	1.243
+++ src/org/eclipse/jdt/core/tests/model/AbstractJavaModelTests.java	3 Mar 2011 07:51:25 -0000
@@ -955,6 +955,25 @@
 		}
 		assertEquals(expected, actual);
 	}
+	protected void assertPackageFragmentRootsEqual(IPackageFragmentRoot[] roots, String expected) {
+		String actual;
+		if (roots == null) {
+			actual = "<null>";
+		} else {
+			StringBuffer buffer = new StringBuffer();
+			int length = roots.length;
+			for (int i=0; i<length; i++) {
+				buffer.append(roots[i]);
+				if (i < length-1)
+					buffer.append('\n');
+			}
+			actual = buffer.toString();
+		}
+		if (!actual.equals(expected)) {
+		 	System.out.print(displayString(actual, 2));
+		}
+		assertEquals(expected, actual);		
+	}
 	/**
 	 * Ensures the element is present after creation.
 	 */
Index: src/org/eclipse/jdt/core/tests/model/ClasspathTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.model/src/org/eclipse/jdt/core/tests/model/ClasspathTests.java,v
retrieving revision 1.223
diff -u -r1.223 ClasspathTests.java
--- src/org/eclipse/jdt/core/tests/model/ClasspathTests.java	14 Feb 2011 04:50:05 -0000	1.223
+++ src/org/eclipse/jdt/core/tests/model/ClasspathTests.java	3 Mar 2011 07:51:26 -0000
@@ -6912,4 +6912,45 @@
 	}	
 }
 
+	/**
+	 * @bug 338006: IJavaProject#getPackageFragmentRoots() should return roots in order
+	 * 
+	 * Test whether the {@link IJavaProject#getPackageFragmentRoots()} returns the package fragment
+	 * roots in the same order as defined by the .classpath even when the elements are added in a 
+	 * different order.
+	 * 
+	 * @see "https://bugs.eclipse.org/bugs/show_bug.cgi?id=338006"
+	 */
+	public void testBug338006() throws Exception {
+		try {
+			IJavaProject p = this
+					.createJavaProject("P", new String[] {}, "bin");
+
+			String content = new String(
+					"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
+							+ "<classpath>\n"
+							+ "<classpathentry kind=\"src\" path=\"src a\"/>\n"
+							+ "<classpathentry kind=\"src\" path=\"src x\"/>\n"
+							+ "<classpathentry kind=\"lib\" path=\""
+							+ getExternalJCLPath()
+							+ "\"/>\n"
+							+ "<classpathentry kind=\"output\" path=\"bin\"/>\n"
+							+ "</classpath>\n");
+
+			editFile("/P/.classpath", content);
+			p.open(null);
+			createFolder("/P/src x");
+			createFolder("/P/src a");
+
+			IPackageFragmentRoot[] roots = p.getPackageFragmentRoots();
+			assertPackageFragmentRootsEqual(roots, 
+					"src a (not open) [in P]\n" + 
+					"src x (not open) [in P]\n" + 
+					""+ getExternalJCLPathString() + " (not open)");
+
+		} finally {
+			deleteProject("P");
+		}
+	}
+
 }