diff --git a/com.ibm.wala.j2ee/src/com/ibm/wala/j2ee/client/AnalysisEngine.java b/com.ibm.wala.j2ee/src/com/ibm/wala/j2ee/client/AnalysisEngine.java
deleted file mode 100644
index 3cfbb214b..000000000
--- a/com.ibm.wala.j2ee/src/com/ibm/wala/j2ee/client/AnalysisEngine.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2002 - 2006 IBM Corporation.
- * 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 com.ibm.wala.j2ee.client;
-
-import java.util.jar.JarFile;
-
-import com.ibm.wala.classLoader.Module;
-
-/**
- * 
- * An AnalysisEngine analyzes one or more J2EE modules, including
- * ear files, J2EE clients, web modules, and ejb modules.
- * 
- * @author Logan Colby
- * @author Stephen Fink
- */
-
-public interface AnalysisEngine extends com.ibm.wala.client.AnalysisEngine {
-
-  /**
-   * Specify the jar file that represent the contents of the j2ee.jar 
-   * that the application relies on
-   * 
-   * @param libs an array of jar files; for WAS, j2ee.jar and webcontainer.jar
-   */
-  void setJ2EELibraries(JarFile[] libs);
-  
-  /**
-   * Specify the mdoules that represent the contents of the j2ee.jar 
-   * that the application relies on
-   * 
-   * @param libs an array of Modules; for WAS, j2ee.jar and webcontainer.jar
-   */
-  void setJ2EELibraries(Module[] libs);
-
-}
diff --git a/com.ibm.wala.j2ee/src/com/ibm/wala/j2ee/client/impl/AbstractAnalysisEngine.java b/com.ibm.wala.j2ee/src/com/ibm/wala/j2ee/client/impl/AbstractAnalysisEngine.java
deleted file mode 100644
index 22fb2f5d2..000000000
--- a/com.ibm.wala.j2ee/src/com/ibm/wala/j2ee/client/impl/AbstractAnalysisEngine.java
+++ /dev/null
@@ -1,157 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2002 - 2006 IBM Corporation.
- * 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 com.ibm.wala.j2ee.client.impl;
-
-import java.util.Iterator;
-import java.util.jar.JarFile;
-
-import org.eclipse.jst.j2ee.commonarchivecore.internal.Archive;
-
-import com.ibm.wala.classLoader.JarFileModule;
-import com.ibm.wala.classLoader.Module;
-import com.ibm.wala.ipa.callgraph.AnalysisOptions;
-import com.ibm.wala.ipa.callgraph.CallGraphBuilder;
-import com.ibm.wala.ipa.cha.ClassHierarchy;
-import com.ibm.wala.j2ee.DeploymentMetaData;
-import com.ibm.wala.j2ee.J2EEAnalysisScope;
-import com.ibm.wala.j2ee.client.AnalysisEngine;
-import com.ibm.wala.j2ee.client.CallGraphBuilderFactory;
-import com.ibm.wala.j2ee.util.TopLevelArchiveModule;
-import com.ibm.wala.j2ee.util.TopLevelArchiveModule.BloatedArchiveModule;
-import com.ibm.wala.types.ClassLoaderReference;
-import com.ibm.wala.util.debug.Assertions;
-
-/**
- * 
- * abstract base class for analysis engine implementations
- * 
- * @author sfink
- */
-public abstract class AbstractAnalysisEngine extends com.ibm.wala.client.impl.AbstractAnalysisEngine implements AnalysisEngine {
-
-  /**
-   * A representation of the deployment descriptor
-   */
-  private DeploymentMetaData dmd;
-
-  /**
-   * The J2EE libraries to analysze
-   */
-  private Module[] j2eeLibs;
-
-  /**
-   * Should we analyze dependent jar files?
-   */
-  private boolean dependentJars = true;
-
-  protected AbstractAnalysisEngine() {}
-
-  protected CallGraphBuilder getCallGraphBuilder(ClassHierarchy cha, AnalysisOptions options) {
-    return ((CallGraphBuilderFactory) getCallGraphBuilderFactory()).make(options, cha, (J2EEAnalysisScope) getScope(), getDmd(),
-        getWarnings(), false);
-  }
-
-  /**
-   * Set up the AnalysisScope object
-   */
-  protected void buildAnalysisScope() {
-    buildAnalysisScope(null);
-  }
-  /**
-   * Set up the AnalysisScope object
-   */
-  protected void buildAnalysisScope(String exclusionsFile) {
-    // set up the scope of the analysis
-    ClassLoader cl = AbstractAnalysisEngine.class.getClassLoader();
-    if (j2seLibs == null) {
-      Assertions.UNREACHABLE("no j2selibs specificed. You probably did not call AppAnalysisEngine.setJ2SELibrary.");
-    } else if (j2eeLibs == null) {
-      Assertions.UNREACHABLE("j2ee.jar is null. You probably did not call AnalysisEngine.setJ2EELibrary.");
-    } else {
-      scope = J2EEAnalysisScope.make(j2seLibs, j2eeLibs, exclusionsFile, cl, true);
-    }
-
-    addApplicationModulesToScope();
-  }
-
-  /**
-   * Add the application modules to the analyis scope.
-   */
-  @SuppressWarnings({ "restriction", "unchecked" })
-  protected void addApplicationModulesToScope() {
-    ClassLoaderReference app = scope.getApplicationLoader();
-    for (Iterator<Archive> it = moduleFiles.iterator(); it.hasNext();) {
-      Archive A = (Archive) it.next();
-      // TODO: redesign to avoid holding onto BloatedArchives?
-      TopLevelArchiveModule M = new BloatedArchiveModule(A);
-      if (!dependentJars) {
-        M.setIgnoreDependentJars(true);
-      }
-      scope.addToScope(app, M);
-    }
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see com.ibm.wala.atk.AppAnalysisEngine#setJ2EELibrary(java.util.jar.JarFile)
-   */
-  public void setJ2EELibraries(JarFile[] libs) {
-    if (libs == null) {
-      Assertions.UNREACHABLE("Illegal to setJ2EELibrary(null)");
-    }
-    this.j2eeLibs = new Module[libs.length];
-    for (int i = 0; i < libs.length; i++) {
-      j2eeLibs[i] = new JarFileModule(libs[i]);
-    }
-  }
-
-  public void setJ2EELibraries(Module[] libs) {
-    if (libs == null) {
-      Assertions.UNREACHABLE("Illegal to setJ2EELibrary(null)");
-    }
-    this.j2eeLibs = new Module[libs.length];
-    for (int i = 0; i < libs.length; i++) {
-      j2eeLibs[i] = libs[i];
-    }
-  }
-
-  /**
-   * @return Returns the dmd.
-   */
-  protected DeploymentMetaData getDmd() {
-    return dmd;
-  }
-
-  /**
-   * @param dmd
-   *          The dmd to set.
-   */
-  protected void setDmd(DeploymentMetaData dmd) {
-    this.dmd = dmd;
-  }
-
-  /**
-   * @return Returns the dependentJars.
-   */
-  public boolean isDependentJars() {
-    return dependentJars;
-  }
-
-  /**
-   * @param dependentJars
-   *          The dependentJars to set.
-   */
-  public void setDependentJars(boolean dependentJars) {
-    this.dependentJars = dependentJars;
-  }
-
-}