diff --git a/main/pom.xml b/main/pom.xml
index 4e88805..dc11fa9 100644
--- a/main/pom.xml
+++ b/main/pom.xml
@@ -9,10 +9,8 @@
     <artifactId>butterfly-container</artifactId>
     <version>1.2.7-SNAPSHOT</version>
   </parent>
-  
-  <groupId>org.openrefine.dependencies</groupId>
+
   <artifactId>butterfly</artifactId>
-  <version>1.2.7-SNAPSHOT</version>
 
   <name>SIMILE Butterfly Engine</name>
   <url>https://github.com/OpenRefine/simile-butterfly/</url>
@@ -81,9 +79,14 @@
 
   <dependencies>
     <dependency>
-      <groupId>commons-collections</groupId>
-      <artifactId>commons-collections</artifactId>
-      <version>3.2.2</version>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-collections4</artifactId>
+      <version>4.4</version>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-configuration2</artifactId>
+      <version>2.10.1</version>
     </dependency>
     <dependency>
       <groupId>commons-io</groupId>
diff --git a/main/src/edu/mit/simile/butterfly/Butterfly.java b/main/src/edu/mit/simile/butterfly/Butterfly.java
index e6ff843..390b1c2 100644
--- a/main/src/edu/mit/simile/butterfly/Butterfly.java
+++ b/main/src/edu/mit/simile/butterfly/Butterfly.java
@@ -36,7 +36,11 @@
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.collections.ExtendedProperties;
+import org.apache.commons.configuration2.AbstractConfiguration;
+import org.apache.commons.configuration2.CombinedConfiguration;
+import org.apache.commons.configuration2.PropertiesConfiguration;
+import org.apache.commons.configuration2.ex.ConfigurationException;
+import org.apache.commons.configuration2.tree.OverrideCombiner;
 import org.apache.velocity.app.VelocityEngine;
 import org.apache.velocity.runtime.RuntimeConstants;
 import org.mozilla.javascript.Context;
@@ -156,7 +160,7 @@ public static boolean isGAE(ServletConfig config) {
     transient protected ServletContext _context;
     transient protected ButterflyMounter _mounter;
 
-    protected ExtendedProperties _properties;
+    protected PropertiesConfiguration _properties;
     protected File _contextDir;
     protected File _homeDir;
     protected File _webInfDir;
@@ -188,27 +192,17 @@ public void init(ServletConfig config) throws ServletException {
                 
         _contextDir = new File(_context.getRealPath("/"));
         _webInfDir = new File(_contextDir, "WEB-INF");
-        _properties = new ExtendedProperties();
+        _properties = new PropertiesConfiguration();
         _mounter = new ButterflyMounter();
 
         // Load the butterfly properties
         String props = System.getProperty("butterfly.properties");
         File butterflyProperties = (props == null) ? new File(_webInfDir, "butterfly.properties") : new File(props);
 
-        BufferedInputStream is = null;
-        try {
-            is = new BufferedInputStream(new FileInputStream(butterflyProperties));
-            _properties.load(is);
-        } catch (FileNotFoundException e) {
+        try (BufferedInputStream is = new BufferedInputStream(Files.newInputStream(butterflyProperties.toPath()))){
+            _properties.read(new InputStreamReader(is, StandardCharsets.UTF_8));
+        } catch (IOException|ConfigurationException e) {
             throw new ServletException("Could not find butterfly properties file",e);
-        } catch (IOException e) {
-            throw new ServletException("Could not read butterfly properties file",e);
-        } finally {
-            try {
-                is.close();
-            } catch (Exception e) {
-                // ignore
-            }
         }
 
         // Process eventual properties includes
@@ -216,27 +210,20 @@ public void init(ServletConfig config) throws ServletException {
         if (includes != null) {
             for (String prop : includes.split(",")) {
                 File prop_file = (prop.startsWith("/")) ? new File(prop) : new File(_webInfDir, prop);
-                try {
-                    is = new BufferedInputStream(new FileInputStream(prop_file));
-                    ExtendedProperties p = new ExtendedProperties();
-                    p.load(is);
-                    _properties.combine(p);
-                } catch (Exception e) {
-                    // ignore
-                } finally {
-                    try {
-                        is.close();
-                    } catch (Exception e) {
-                        // ignore
-                    }
+                try (BufferedInputStream is = new BufferedInputStream(Files.newInputStream(prop_file.toPath()))){
+                    PropertiesConfiguration p = new PropertiesConfiguration();
+                    p.read(new InputStreamReader(is, StandardCharsets.UTF_8));
+                    _properties.append(p);
+                } catch (ConfigurationException | IOException e) {
+                    _logger.warn("Error loading included properties file: " + prop_file, e);
                 }
             }
         }
         // Overload with properties set from the command line 
         // using the -Dkey=value parameters to the JVM
         Properties systemProperties = System.getProperties();
-        for (Iterator<Object> i = systemProperties.keySet().iterator(); i.hasNext(); ) {
-            String key = (String) i.next();
+        for (Object o : systemProperties.keySet()) {
+            String key = (String) o;
             String value = systemProperties.getProperty(key);
             _properties.setProperty(key, value);
         }
@@ -326,8 +313,7 @@ public void configure() {
             }
             _logger.info("Butterfly home: {}", _homeDir);
             
-            Iterator<String> i = _properties.getKeys(ZONE);
-            while (i.hasNext()) {
+            for(Iterator<String> i = _properties.getKeys(ZONE); i.hasNext(); ) {
                 String zone = i.next();
                 String path = _properties.getString(zone);
                 zone = zone.substring(ZONE.length() + 1);
@@ -373,7 +359,7 @@ public void configure() {
 
         _logger.info("> load modules");
         // load modules from the properties found in the butterfly.properties
-        List<String> paths = _properties.getList(MODULES_PATH);
+        List<String> paths = _properties.getList(String.class, MODULES_PATH);
         for (String path : paths) {
             findModulesIn(absolutize(_homeDir, path.trim()));
         }
@@ -394,16 +380,15 @@ public void configure() {
         _logger.info("< create modules");
         
         _logger.info("> load module wirings");
-        ExtendedProperties wirings = new ExtendedProperties();
-        try {
-            // Load the wiring properties
-            File moduleWirings = absolutize(_homeDir, _properties.getString("butterfly.modules.wirings","WEB-INF/modules.properties"));
-            _logger.info("Loaded module wirings from: {}", moduleWirings);
-            _classLoader.watch(moduleWirings); // reload if the module wirings change
-            FileInputStream fis = new FileInputStream(moduleWirings);
-            wirings.load(fis);
-            fis.close();
-        } catch (Exception e) {
+        PropertiesConfiguration wirings = new PropertiesConfiguration();
+
+        // Load the wiring properties
+        File moduleWirings = absolutize(_homeDir, _properties.getString("butterfly.modules.wirings","WEB-INF/modules.properties"));
+        _logger.info("Loaded module wirings from: {}", moduleWirings);
+        _classLoader.watch(moduleWirings); // reload if the module wirings change
+        try (FileInputStream fis = new FileInputStream(moduleWirings)) {
+            wirings.read(new InputStreamReader(fis, StandardCharsets.UTF_8));
+        } catch (IOException | ConfigurationException e) {
             _configurationException = new Exception("Failed to load module wirings", e);
         }
         _logger.info("< load module wirings");
@@ -526,7 +511,7 @@ public void service(HttpServletRequest request, HttpServletResponse response) th
     
     protected Map<String,ButterflyModule> _modulesByName = new HashMap<String,ButterflyModule>();
     protected Map<String,Map<String,ButterflyModule>> _modulesByInterface = new HashMap<String,Map<String,ButterflyModule>>();
-    protected Map<String,ExtendedProperties> _moduleProperties = new HashMap<String,ExtendedProperties>();
+    protected Map<String,AbstractConfiguration> _moduleProperties = new HashMap<String,AbstractConfiguration>();
     protected Map<String,Boolean> _created = new HashMap<String,Boolean>();
 
     final static private String routingCookie = "host";
@@ -573,13 +558,13 @@ protected void findModulesIn(File f) {
             try {
                 String name = f.getName();
 
-                ExtendedProperties p  = new ExtendedProperties();
+                PropertiesConfiguration p  = new PropertiesConfiguration();
                 File propFile = new File(modFile,"module.properties");
                 if (propFile.exists()) {
-                    _classLoader.watch(propFile); // reload if the the module properties change
-                    BufferedInputStream stream = new BufferedInputStream(new FileInputStream(propFile));
-                    p.load(stream);
-                    stream.close();
+                    _classLoader.watch(propFile); // reload if the module properties change
+                    try (BufferedInputStream stream = new BufferedInputStream(Files.newInputStream(propFile.toPath()))) {
+                        p.read(new InputStreamReader(stream, StandardCharsets.UTF_8));
+                    }
                 }
 
                 p.addProperty(PATH_PROP, f.getAbsolutePath());
@@ -624,7 +609,7 @@ protected ButterflyModule createModule(String name) {
             return _modulesByName.get(name);
         }
 
-        ExtendedProperties p = _moduleProperties.get(name);
+        AbstractConfiguration p = _moduleProperties.get(name);
         File path = new File(p.getString(PATH_PROP));
         _logger.debug("Module path: {}", path);
             
@@ -685,8 +670,7 @@ protected ButterflyModule createModule(String name) {
         return m; 
     }
 
-    @SuppressWarnings("unchecked")
-	protected void wireModules(ExtendedProperties wirings) {
+    protected void wireModules(PropertiesConfiguration wirings) {
         _logger.trace("> wireModules()");
 
         _logger.info("mounting modules");
@@ -714,21 +698,32 @@ protected void wireModules(ExtendedProperties wirings) {
         for (String name : _moduleProperties.keySet()) {
             _logger.trace("> Expanding properties for module: {}", name);
             ButterflyModule m = _modulesByName.get(name);
-            ExtendedProperties p = _moduleProperties.get(name);
             ButterflyModule extended = m.getExtendedModule();
 
+            // Highest priority properties need to be added first, so we need to collect them all first
+            List<AbstractConfiguration> propertiesList = new ArrayList<>();
+            propertiesList.add(_moduleProperties.get(name));
             while (extended != null) {
                 _logger.trace("> Merging properties from extended module: {}", name);
-                ExtendedProperties temp = p;
-                p = _moduleProperties.get(extended.getName());
-                p.combine(temp);
+                AbstractConfiguration p = _moduleProperties.get(extended.getName());
+                propertiesList.add(p);
                 _logger.trace("< Merging properties from extended module: {} -> {}", name, p);
                 extended = extended.getExtendedModule();
             }
+            AbstractConfiguration p;
+            if (propertiesList.size() == 1) {
+                p = propertiesList.get(0);
+            } else {
+                p = new CombinedConfiguration(new OverrideCombiner());
+                // Add files in reverse order to maintain priority
+                for (int i = propertiesList.size() - 1; i >= 0; i--) {
+                    ((CombinedConfiguration) p).addConfiguration(propertiesList.get(i));
+                }
+            }
 
-            _moduleProperties.put(name,p);
+            _moduleProperties.put(name, p);
 
-            List<String> implementations = p.getList(implementsProperty);
+            List<String> implementations = p.getList(String.class, implementsProperty);
             if (implementations != null) {
                 for (String i : implementations) {
                     Map<String, ButterflyModule> map = _modulesByInterface.get(i);
@@ -745,11 +740,11 @@ protected void wireModules(ExtendedProperties wirings) {
         
         for (String name : _moduleProperties.keySet()) {
             _logger.trace("> Inject dependencies in module: {}", name);
-            ExtendedProperties p = _moduleProperties.get(name);
+            AbstractConfiguration p = _moduleProperties.get(name);
             ButterflyModule m = _modulesByName.get(name);
 
-            for (Object o : p.keySet()) {
-                String s = (String) o;
+            for (Iterator<String> keys = p.getKeys(); keys.hasNext(); ) {
+                String s = keys.next();
                 if (s.equals(dependencyPrefix)) {
                     for (Object oo : p.getList(s)) {
                         String dep = (String) oo;
@@ -800,12 +795,12 @@ protected void wireModules(ExtendedProperties wirings) {
         _logger.trace("< wireModules()");
     }    
 
-    @SuppressWarnings("unchecked")
+
     protected void configureModules() {
         _logger.trace("> configureModules()");
         for (String name : _moduleProperties.keySet()) {
             _logger.trace("> Configuring module: {}", name);
-            ExtendedProperties p = _moduleProperties.get(name);
+            AbstractConfiguration p = _moduleProperties.get(name);
             ButterflyModule m = _modulesByName.get(name);
             
             // make the system properties accessible to the modules
@@ -818,16 +813,16 @@ protected void configureModules() {
                     Properties properties = new Properties();
                     File velocityProperties = new File(_webInfDir, "velocity.properties");
                     _classLoader.watch(velocityProperties); // reload if the velocity properties change
-                    FileInputStream fis = new FileInputStream(velocityProperties);
-                    properties.load(fis);
-                    fis.close();
+                    try (FileInputStream fis = new FileInputStream(velocityProperties)) {
+                        properties.load(fis);
+                    }
         
                     // set properties for resource loading
-                    properties.setProperty("resource.loader", "butterfly");
-                    properties.setProperty("butterfly.resource.loader.class", ButterflyResourceLoader.class.getName());
-                    properties.setProperty("butterfly.resource.loader.cache", "true");
-                    properties.setProperty("butterfly.resource.loader.modificationCheckInterval", "1");
-                    properties.setProperty("butterfly.resource.loader.description", "Butterfly Resource Loader");
+                    properties.setProperty("resource.loaders", "butterfly");
+                    properties.setProperty("resource.loader.butterfly.class", ButterflyResourceLoader.class.getName());
+                    properties.setProperty("resource.loader.butterfly.cache", "true");
+                    properties.setProperty("resource.loader.butterfly.modification_check_interval", "1");
+                    properties.setProperty("resource.loader.butterfly.description", "Butterfly Resource Loader");
                         
                     // set properties for macros
                     properties.setProperty("velocimacro.library.path", p.getString("templating.macros", ""));
@@ -854,8 +849,8 @@ protected void configureModules() {
                     _logger.trace("< enabling templating");
                 }
 
-                List<String> scriptables = p.getList("scriptables");
-                if (scriptables.size() > 0) {
+                List<String> scriptables = p.getList(String.class, "scriptables");
+                if (scriptables != null && !scriptables.isEmpty()) {
                     Context context = Context.enter();
 
                     BufferedReader initializerReader = null; 
@@ -887,7 +882,7 @@ protected void configureModules() {
                     Context.exit();
                 }
                 
-                List<String> controllers = p.getList("controller", CONTROLLER);
+                List<String> controllers = p.getList(String.class, "controller", CONTROLLER);
                 Set<URL> controllerURLs = new HashSet<URL>(controllers.size());
                 for (String controller : controllers) {
                     URL controllerURL = m.getResource("MOD-INF/" + controller);
diff --git a/main/src/edu/mit/simile/butterfly/ButterflyModule.java b/main/src/edu/mit/simile/butterfly/ButterflyModule.java
index 68b8869..fc8a64b 100644
--- a/main/src/edu/mit/simile/butterfly/ButterflyModule.java
+++ b/main/src/edu/mit/simile/butterfly/ButterflyModule.java
@@ -14,7 +14,7 @@
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.collections.ExtendedProperties;
+import org.apache.commons.configuration2.FileBasedConfiguration;
 import org.apache.velocity.VelocityContext;
 import org.apache.velocity.app.VelocityEngine;
 import org.mozilla.javascript.Context;
@@ -65,7 +65,7 @@ public interface ButterflyModule {
 
     public void setTemplateEngine(VelocityEngine velocity);
         
-    public void setProperties(ExtendedProperties properties);
+    public void setProperties(FileBasedConfiguration properties);
     
     public void setTimer(Timer timer);
     
@@ -77,7 +77,7 @@ public interface ButterflyModule {
     
     public String getName();
     
-    public ExtendedProperties getProperties();
+    public FileBasedConfiguration getProperties();
 
     public File getPath();
     
diff --git a/main/src/edu/mit/simile/butterfly/ButterflyModuleImpl.java b/main/src/edu/mit/simile/butterfly/ButterflyModuleImpl.java
index b6cc49a..7645c7a 100644
--- a/main/src/edu/mit/simile/butterfly/ButterflyModuleImpl.java
+++ b/main/src/edu/mit/simile/butterfly/ButterflyModuleImpl.java
@@ -32,10 +32,10 @@
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.collections.ExtendedProperties;
-import org.apache.commons.collections.OrderedMap;
-import org.apache.commons.collections.OrderedMapIterator;
-import org.apache.commons.collections.map.ListOrderedMap;
+import org.apache.commons.collections4.OrderedMap;
+import org.apache.commons.collections4.OrderedMapIterator;
+import org.apache.commons.collections4.map.ListOrderedMap;
+import org.apache.commons.configuration2.FileBasedConfiguration;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.velocity.VelocityContext;
@@ -76,7 +76,7 @@ public class ButterflyModuleImpl implements ButterflyModule {
     protected Set<ButterflyModule> _extendedBy = new LinkedHashSet<ButterflyModule>();
     protected Set<String> _implementations = new LinkedHashSet<String>();
     protected Map<String,ButterflyModule> _dependencies = new HashMap<String,ButterflyModule>();
-    protected ExtendedProperties _properties;
+    protected FileBasedConfiguration _properties;
     protected Map<String,ButterflyModule> _modules;
     protected VelocityEngine _templateEngine;
     protected OrderedMap _scripts = new ListOrderedMap();
@@ -170,7 +170,7 @@ public void setTemplateEngine(VelocityEngine templateEngine) {
         this._templateEngine = templateEngine;
     }
         
-    public void setProperties(ExtendedProperties properties) {
+    public void setProperties(FileBasedConfiguration properties) {
         _logger.trace("{} gets loaded with properties", this);
         this._properties = properties;
     }
@@ -206,7 +206,7 @@ public File getPath() {
         return this._path;
     }
 
-    public ExtendedProperties getProperties() {
+    public FileBasedConfiguration getProperties() {
         return this._properties;
     }
     
@@ -585,7 +585,7 @@ public void initScope(Context context, Scriptable scope) {
             m.initScope(context, scope);
         }
         
-        OrderedMapIterator i = _scripts.orderedMapIterator();
+        OrderedMapIterator i = _scripts.mapIterator();
         while (i.hasNext()) {
             URL url = (URL) i.next();
             _logger.debug("Executing script: {}", url);
diff --git a/main/src/edu/mit/simile/butterfly/ButterflyScriptableObject.java b/main/src/edu/mit/simile/butterfly/ButterflyScriptableObject.java
index 9249e4c..72c3103 100644
--- a/main/src/edu/mit/simile/butterfly/ButterflyScriptableObject.java
+++ b/main/src/edu/mit/simile/butterfly/ButterflyScriptableObject.java
@@ -1,6 +1,6 @@
 package edu.mit.simile.butterfly;
 
-import org.apache.commons.collections.ExtendedProperties;
+import org.apache.commons.configuration2.FileBasedConfiguration;
 import org.mozilla.javascript.Context;
 import org.mozilla.javascript.Scriptable;
 import org.mozilla.javascript.ScriptableObject;
@@ -16,7 +16,7 @@ public abstract class ButterflyScriptableObject extends ScriptableObject {
     private static final long serialVersionUID = 6392807122149170350L;
 
     protected ButterflyModule _module;
-    protected ExtendedProperties _properties;
+    protected FileBasedConfiguration _properties;
 
     public void init(ButterflyModule module) {
         _module = module;