Index: src/main/java/org/apache/maven/plugin/eclipse/EclipsePlugin.java
===================================================================
--- src/main/java/org/apache/maven/plugin/eclipse/EclipsePlugin.java	(revision 688519)
+++ src/main/java/org/apache/maven/plugin/eclipse/EclipsePlugin.java	(working copy)
@@ -32,7 +32,6 @@
 import java.util.ListIterator;
 import java.util.Map;
 import java.util.Set;
-import java.util.TreeSet;
 
 import org.apache.maven.artifact.Artifact;
 import org.apache.maven.artifact.handler.ArtifactHandler;
@@ -1275,15 +1274,10 @@
         File projectBaseDir = project.getFile().getParentFile();
 
         // avoid duplicated entries
-        Set directories = new TreeSet();
+        Set directories = new LinkedHashSet();
 
-        extractSourceDirs( directories, project.getCompileSourceRoots(), basedir, projectBaseDir, false, null );
-
         String relativeOutput = IdeUtils.toRelativeAndFixSeparator( projectBaseDir, buildOutputDirectory, false );
 
-        extractResourceDirs( directories, project.getBuild().getResources(), project, basedir, projectBaseDir, false,
-                             relativeOutput );
-
         // If using the standard output location, don't mix the test output into it.
         String testOutput = null;
         boolean useStandardOutputDir =
@@ -1300,9 +1294,14 @@
         }
 
         extractSourceDirs( directories, project.getTestCompileSourceRoots(), basedir, projectBaseDir, true, testOutput );
+        
+        extractSourceDirs( directories, project.getCompileSourceRoots(), basedir, projectBaseDir, false, null );
 
         extractResourceDirs( directories, project.getBuild().getTestResources(), project, basedir, projectBaseDir,
                              true, testOutput );
+        
+        extractResourceDirs( directories, project.getBuild().getResources(), project, basedir, projectBaseDir, false,
+                             relativeOutput );
 
         return (EclipseSourceDir[]) directories.toArray( new EclipseSourceDir[directories.size()] );
     }