diff --git a/modules/swagger-codegen-cli/src/main/java/com/wordnik/swagger/codegen/cmd/Generate.java b/modules/swagger-codegen-cli/src/main/java/com/wordnik/swagger/codegen/cmd/Generate.java
index 0e88a947b476..47449d842865 100644
--- a/modules/swagger-codegen-cli/src/main/java/com/wordnik/swagger/codegen/cmd/Generate.java
+++ b/modules/swagger-codegen-cli/src/main/java/com/wordnik/swagger/codegen/cmd/Generate.java
@@ -54,10 +54,16 @@ public class Generate implements Runnable {
                     "Pass in a URL-encoded string of name:header with a comma separating multiple values")
     private String auth;
 
+    @Option( name= {"-D"}, title = "system properties", description = "sets specified system properties in " +
+            "the format of name=value,name=value")
+    private String systemProperties;
+
     @Override
     public void run() {
         verbosed(verbose);
 
+        setSystemProperties();
+
         ClientOptInput input = new ClientOptInput();
 
         if (isNotEmpty(auth)) {
@@ -77,6 +83,17 @@ public class Generate implements Runnable {
         new DefaultGenerator().opts(input.opts(new ClientOpts()).swagger(swagger)).generate();
     }
 
+    private void setSystemProperties() {
+        if( systemProperties != null && systemProperties.length() > 0 ){
+            for( String property : systemProperties.split(",")) {
+                int ix = property.indexOf('=');
+                if( ix > 0 && ix < property.length()-1 ){
+                    System.setProperty( property.substring(0, ix), property.substring(ix+1) );
+                }
+            }
+        }
+    }
+
     /**
      * If true parameter, adds system properties which enables debug mode in generator
      * @param verbose - if true, enables debug mode
diff --git a/modules/swagger-codegen/src/main/java/com/wordnik/swagger/codegen/languages/JaxRSServerCodegen.java b/modules/swagger-codegen/src/main/java/com/wordnik/swagger/codegen/languages/JaxRSServerCodegen.java
index f4f16ca63f90..0bc8097d671e 100644
--- a/modules/swagger-codegen/src/main/java/com/wordnik/swagger/codegen/languages/JaxRSServerCodegen.java
+++ b/modules/swagger-codegen/src/main/java/com/wordnik/swagger/codegen/languages/JaxRSServerCodegen.java
@@ -1,8 +1,6 @@
 package com.wordnik.swagger.codegen.languages;
 
 import com.wordnik.swagger.models.Operation;
-import com.wordnik.swagger.models.Path;
-import com.wordnik.swagger.util.Json;
 import com.wordnik.swagger.codegen.*;
 import com.wordnik.swagger.models.properties.*;
 
@@ -14,7 +12,6 @@ public class JaxRSServerCodegen extends JavaClientCodegen implements CodegenConf
   protected String groupId = "io.swagger";
   protected String artifactId = "swagger-jaxrs-server";
   protected String artifactVersion = "1.0.0";
-  protected String sourceFolder = "src/main/java";
   protected String title = "Swagger Server";
 
   public CodegenType getTag() {
@@ -32,7 +29,9 @@ public class JaxRSServerCodegen extends JavaClientCodegen implements CodegenConf
   public JaxRSServerCodegen() {
     super();
 
-    outputFolder = "generated-code/javaJaxRS";
+    sourceFolder = "src/gen/java";
+
+    outputFolder = System.getProperty( "swagger.codegen.jaxrs.genfolder", "generated-code/javaJaxRS" );
     modelTemplateFiles.put("model.mustache", ".java");
     apiTemplateFiles.put("api.mustache", ".java");
     apiTemplateFiles.put("apiService.mustache", ".java");
@@ -40,8 +39,8 @@ public class JaxRSServerCodegen extends JavaClientCodegen implements CodegenConf
     apiTemplateFiles.put("apiServiceFactory.mustache", ".java");
 
     templateDir = "JavaJaxRS";
-    apiPackage = "io.swagger.api";
-    modelPackage = "io.swagger.model";
+    apiPackage = System.getProperty( "swagger.codegen.jaxrs.apipackage", "io.swagger.api") ;
+    modelPackage = System.getProperty( "swagger.codegen.jaxrs.modelpackage", "io.swagger.model" );
 
     additionalProperties.put("invokerPackage", invokerPackage);
     additionalProperties.put("groupId", groupId);
@@ -158,20 +157,35 @@ public class JaxRSServerCodegen extends JavaClientCodegen implements CodegenConf
     String result = super.apiFilename(templateName, tag);
 
     if( templateName.endsWith( "Impl.mustache")){
-       int ix = result.lastIndexOf( '/' );
-       result = result.substring( 0, ix ) + "/impl" + result.substring( ix, result.length()-5 ) + "ServiceImpl.java";
-    } else if( templateName.endsWith( "Service.mustache")){
-      int ix = result.lastIndexOf( '.' );
-      result = result.substring( 0, ix ) + "Service.java";
+      int ix = result.lastIndexOf( '/' );
+      result = result.substring( 0, ix ) + "/impl" + result.substring( ix, result.length()-5 ) + "ServiceImpl.java";
+
+      String output = System.getProperty( "swagger.codegen.jaxrs.impl.source" );
+      if( output != null ){
+        result = result.replace( apiFileFolder(), implFileFolder(output));
+      }
     }
     else if( templateName.endsWith( "Factory.mustache")){
       int ix = result.lastIndexOf( '/' );
       result = result.substring( 0, ix ) + "/factories" + result.substring( ix, result.length()-5 ) + "ServiceFactory.java";
+
+      String output = System.getProperty( "swagger.codegen.jaxrs.impl.source" );
+      if( output != null ){
+        result = result.replace( apiFileFolder(), implFileFolder(output));
+      }
+    }
+    else if( templateName.endsWith( "Service.mustache")) {
+        int ix = result.lastIndexOf('.');
+        result = result.substring(0, ix) + "Service.java";
     }
 
     return result;
   }
 
+  private String implFileFolder(String output) {
+    return outputFolder + "/" + output + "/" + apiPackage().replace('.', File.separatorChar);
+  }
+
   public boolean shouldOverwrite( String filename ){
 
     return !filename.endsWith( "ServiceImpl.java") && !filename.endsWith( "ServiceFactory.java");
diff --git a/modules/swagger-codegen/src/main/resources/JavaJaxRS/pom.mustache b/modules/swagger-codegen/src/main/resources/JavaJaxRS/pom.mustache
index 1bd168af7476..bf2055bb133d 100644
--- a/modules/swagger-codegen/src/main/resources/JavaJaxRS/pom.mustache
+++ b/modules/swagger-codegen/src/main/resources/JavaJaxRS/pom.mustache
@@ -62,6 +62,25 @@
           </execution>
         </executions>
       </plugin>
+      <plugin>
+        <groupId>org.codehaus.mojo</groupId>
+        <artifactId>build-helper-maven-plugin</artifactId>
+        <version>1.9.1</version>
+        <executions>
+          <execution>
+            <id>add-source</id>
+            <phase>generate-sources</phase>
+            <goals>
+              <goal>add-source</goal>
+            </goals>
+            <configuration>
+              <sources>
+                <source>src/gen/java</source>
+              </sources>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
     </plugins>
   </build>
   <dependencies>