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Difference between maven clean and eclipse clean

I have a cucumber project which runs fine when u run cucumberrunner file alone [Run as -->Junit test].
When i try to run same file using maven command it failed : mvn clean test
T E S T S
Running com.myapp.test.CucumberRunnerTest
None of the features at [classpath:com//myapp/datafiles] matched the filters: [#test1]
Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.853 sec - in com.myapp.test.CucumberRunnerTest
Results :
Tests run: 0, Failures: 0, Errors: 0, Skipped: 0
But it works when i do following steps
Select project -->Project -->Clean and then run mvn test
I am confused what i am missing and what is the difference.
below is the maven file
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.mobile.app</groupId>
<artifactId>MobileAutomation</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>jar</packaging>
<name>MobileAutomation</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.target>1.8</maven.compiler.target>
<maven.compiler.source>1.8</maven.compiler.source>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.10</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.seleniumhq.selenium/selenium-java -->
<dependency>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-java</artifactId>
<version>3.4.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.seleniumhq.selenium/selenium-api -->
<dependency>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-api</artifactId>
<version>3.4.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.seleniumhq.selenium/selenium-server -->
<dependency>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-server</artifactId>
<version>3.4.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.seleniumhq.selenium/selenium-remote-driver -->
<dependency>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-remote-driver</artifactId>
<version>3.4.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.seleniumhq.selenium/selenium-firefox-driver -->
<dependency>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-firefox-driver</artifactId>
<version>3.4.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/io.appium/java-client -->
<dependency>
<groupId>io.appium</groupId>
<artifactId>java-client</artifactId>
<version>4.1.2</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.taobao.gecko/gecko -->
<dependency>
<groupId>com.taobao.gecko</groupId>
<artifactId>gecko</artifactId>
<version>1.1.4</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.poi/poi -->
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>3.16</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.poi/poi-ooxml -->
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>3.16</version>
</dependency>
<dependency>
<groupId>com.aventstack</groupId>
<artifactId>extentreports</artifactId>
<version>3.0.6</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.relevantcodes/extentreports -->
<dependency>
<groupId>com.relevantcodes</groupId>
<artifactId>extentreports</artifactId>
<version>2.40.2</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
<version>4.3.10.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>4.3.10.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
<version>4.3.10.RELEASE</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.springframework/spring-context -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>4.3.9.RELEASE</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.springframework/spring-tx -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-tx</artifactId>
<version>4.3.9.RELEASE</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.springframework/spring-test -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-test</artifactId>
<version>4.3.9.RELEASE</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>info.cukes</groupId>
<artifactId>cucumber-spring</artifactId>
<version>1.2.4</version>
<scope>test</scope>
</dependency>
<!-- https://mvnrepository.com/artifact/info.cukes/cucumber-java -->
<dependency>
<groupId>info.cukes</groupId>
<artifactId>cucumber-java</artifactId>
<version>1.2.4</version>
</dependency>
<!-- https://mvnrepository.com/artifact/info.cukes/cucumber-junit -->
<dependency>
<groupId>info.cukes</groupId>
<artifactId>cucumber-junit</artifactId>
<version>1.2.4</version>
<scope>test</scope>
</dependency>
<!-- https://mvnrepository.com/artifact/net.masterthought/cucumber-reporting -->
<dependency>
<groupId>net.masterthought</groupId>
<artifactId>cucumber-reporting</artifactId>
<version>3.0.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.vimalselvam/cucumber-extentsreport -->
<dependency>
<groupId>com.vimalselvam</groupId>
<artifactId>cucumber-extentsreport</artifactId>
<version>3.0.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache/apache-jar-resource-bundle -->
<dependency>
<groupId>org.apache</groupId>
<artifactId>apache-jar-resource-bundle</artifactId>
<version>1.4</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.oracle/ojdbc7 -->
<dependency>
<groupId>com.oracle</groupId>
<artifactId>ojdbc7</artifactId>
<version>12.1.0.2</version>
<scope>system</scope>
<systemPath>${basedir}/src/main/resources/lib/ojdbc7-12.1.0.2.jar</systemPath>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.19.1</version>
<configuration>
<includes>
<exclude>**/*RunnerTest.java</exclude>
</includes>
</configuration>
</plugin>
</plugins>
</build>
</project>

I am still analyzing diff but below pom version works finally
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.test.mobile.app</groupId>
<artifactId>testAutomation</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>jar</packaging>
<name>TestAutomation</name>
<url>http://maven.apache.org</url>
<dependencies>
<dependency>
<groupId>info.cukes</groupId>
<artifactId>cucumber-java</artifactId>
<version>1.2.5</version>
</dependency>
<dependency>
<groupId>info.cukes</groupId>
<artifactId>cucumber-junit</artifactId>
<version>1.2.5</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>io.appium</groupId>
<artifactId>java-client</artifactId>
<version>4.1.2</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
<version>4.3.10.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>4.3.10.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
<version>4.3.10.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>4.3.9.RELEASE</version>
</dependency>
<!-- https://mvnrepository.com/artifact/commons-io/commons-io -->
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.6</version>
</dependency>
<dependency>
<groupId>com.oracle</groupId>
<artifactId>ojdbc7</artifactId>
<version>12.1.0.2</version>
<scope>system</scope>
<systemPath>${basedir}/src/main/resources/lib/ojdbc7-12.1.0.2.jar</systemPath>
</dependency>
<dependency>
<groupId>com.vimalselvam</groupId>
<artifactId>cucumber-extentsreport</artifactId>
<version>3.0.2</version>
</dependency>
<dependency>
<groupId>com.aventstack</groupId>
<artifactId>extentreports</artifactId>
<version>3.1.2</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.0.0-M3</version>
<configuration>
<encoding>UTF-8</encoding>
<source>1.8</source>
<target>1.8</target>
<compilerArgument>-Werror</compilerArgument>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
</plugin>
</plugins>
</build>
</project>

Problems with deploying war on openshift

I'm trying to deploy my war file of my Java Spring Application to openshift.
I'm trying to do this with git.
My pom file is build succesfully but my ROOT.war is not deployed...
In Filezilla I can see that my war is in the webapps folder but when I'm trying to reach my website I got a 404 error.
UPDATE:
I've added my project structure to my question. In filezilla I saw that there is a ROOT.war file deployed but this is empty....
Click here to see project structure
Attached you can find my pom:
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>SussolWebservice</groupId>
<artifactId>SussolWebservice</artifactId>
<version>ROOT</version>
<packaging>war</packaging>
<properties>
<spring.version>4.0.1.RELEASE</spring.version>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
<!-- Spring dependencies -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
<version>1.9.13</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.5.3</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.2.3</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>1.4</version>
</dependency>
<dependency>
<groupId>commons-fileupload</groupId>
<artifactId>commons-fileupload</artifactId>
<version>1.2.2</version> <!-- makesure correct version here -->
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>2.2.3</version>
</dependency>
<dependency>
<groupId>org.eclipse.jdt.core.compiler</groupId>
<artifactId>ecj</artifactId>
<version>4.4.2</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>3.0.1</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>weka</groupId>
<artifactId>weka</artifactId>
<scope>system</scope>
<version>1.0</version>
<systemPath>${basedir}\WebContent\WEB-INF\lib\weka.jar</systemPath>
</dependency>
<dependency>
<groupId>opencsv</groupId>
<artifactId>opencsv</artifactId>
<scope>system</scope>
<version>1.0</version>
<systemPath>${basedir}\WebContent\WEB-INF\lib\opencsv-3.7.jar</systemPath>
</dependency>
<dependency>
<groupId>logging</groupId>
<artifactId>logging</artifactId>
<scope>system</scope>
<version>1.0</version>
<systemPath>${basedir}\WebContent\WEB-INF\lib\slf4j-log4j12-1.7.1.jar</systemPath>
</dependency>
<dependency>
<groupId>log</groupId>
<artifactId>log</artifactId>
<scope>system</scope>
<version>1.0</version>
<systemPath>${basedir}\WebContent\WEB-INF\lib\slf4j-api-1.7.1.jar</systemPath>
</dependency>
<dependency>
<groupId>loggger</groupId>
<artifactId>logger</artifactId>
<scope>system</scope>
<version>1.0</version>
<systemPath>${basedir}\WebContent\WEB-INF\lib\log4j-1.2.17.jar</systemPath>
</dependency>
<dependency>
<groupId>packagemgr</groupId>
<artifactId>packagemgr</artifactId>
<scope>system</scope>
<version>1.0</version>
<systemPath>${basedir}\WebContent\WEB-INF\lib\packageManager.jar</systemPath>
</dependency>
<dependency>
<groupId>SOM</groupId>
<artifactId>SOM</artifactId>
<scope>system</scope>
<version>1.0</version>
<systemPath>${basedir}\WebContent\WEB-INF\lib\SelfOrganizingMap.jar</systemPath>
</dependency>
</dependencies>
<build>
<finalName>ROOT</finalName>
<sourceDirectory>src</sourceDirectory>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-war-plugin</artifactId>
<version>2.6</version>
<configuration>
<warSourceDirectory>WebContent</warSourceDirectory>
<failOnMissingWebXml>false</failOnMissingWebXml>
</configuration>
</plugin>
</plugins>
</build>
</project>

How to change the location of compiled code to WAR file in maven

I have a project where I need to put the complied source code into WAR file instead of default location target/classses folder in maven.
I tried a lot of things but it in not working does anyone has any idea what can be done here.
http://fusesource.com/docs/esbent/7.0/esb_deploy_osgi/BuildWar-Modify.html#BuildWar-Modify-WebInf
I tried the above link and its help but it is not working.
Pom.xml:
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.Avizva.FBVision</groupId>
<artifactId>Enrollment_GUID</artifactId>
<packaging>war</packaging>
<name>Enrollment_GUID</name>
<build>
<sourceDirectory>${basedir}/src</sourceDirectory>
<resources>
<resource>
<directory>${basedir}/src</directory>
<includes>
<include>**/*.properties</include>
<include>**/*.java</include>
</includes>
</resource>
</resources>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-war-plugin</artifactId>
<version>2.3</version>
<configuration>
<warSourceDirectory>${basedir}/WebContent</warSourceDirectory>
<warName>Enrollment_GUID</warName>
<packagingIncludes>WEB-INF/lib/*.jar,WEB-INF/wsdl/*.xsd,WEB-INF/wsdl/*.wsdl,WEB-INF/properties/*.properties,**/*.xml</packagingIncludes>
<webResources>
<resource>
<directory>${basedir}/src</directory>
<targetPath>WEB-INF</targetPath>
</resource>
</webResources>
<failOnMissingWebXml>false</failOnMissingWebXml>
</configuration>
</plugin>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>2.4</version>
<configuration>
<encoding>UTF-8</encoding>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-1.2-api</artifactId>
<version>2.0-rc1</version>
</dependency>
<dependency>
<groupId>org.kie.modules</groupId>
<artifactId>org-apache-commons-lang3</artifactId>
<version>6.1.0.CR1</version>
<type>pom</type>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-jdk14</artifactId>
<version>1.7.7</version>
</dependency>
<dependency>
<groupId>joda-time</groupId>
<artifactId>joda-time</artifactId>
<version>2.3</version>
</dependency>
<dependency>
<groupId>org.apache.directory.studio</groupId>
<artifactId>org.apache.commons.lang</artifactId>
<version>2.6</version>
</dependency>
<dependency>
<groupId>aspectj</groupId>
<artifactId>aspectjweaver</artifactId>
<version>1.5.4</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-aop</artifactId>
<version>3.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-asm</artifactId>
<version>3.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
<version>3.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>3.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>3.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-expression</artifactId>
<version>3.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
<version>3.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<version>3.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>3.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>net.sf.dozer</groupId>
<artifactId>dozer</artifactId>
<version>5.3.2</version>
</dependency>
<dependency>
<groupId>org.apache.axis2</groupId>
<artifactId>axis2-adb</artifactId>
<version>1.6.2</version>
</dependency>
<dependency>
<groupId>org.apache.axis2</groupId>
<artifactId>axis2-kernel</artifactId>
<version>1.6.2</version>
</dependency>
<dependency>
<groupId>org.apache.axis2</groupId>
<artifactId>axis2-transport-local</artifactId>
<version>1.6.2</version>
</dependency>
<dependency>
<groupId>org.apache.axis2</groupId>
<artifactId>axis2-transport-http</artifactId>
<version>1.6.2</version>
</dependency>
<dependency>
<groupId>org.apache.ws.commons.axiom</groupId>
<artifactId>axiom-api</artifactId>
<version>1.2.13</version>
</dependency>
<dependency>
<groupId>org.apache.ws.commons.axiom</groupId>
<artifactId>axiom-impl</artifactId>
<version>1.2.13</version>
</dependency>
<dependency>
<groupId>antlr</groupId>
<artifactId>antlr</artifactId>
<version>2.7.5</version>
</dependency>
<dependency>
<groupId>aspectj</groupId>
<artifactId>aspectjrt</artifactId>
<version>1.5.4</version>
</dependency>
<dependency>
<groupId>org.apache.ws.schema</groupId>
<artifactId>XmlSchema</artifactId>
<version>1.4.5</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient-cache</artifactId>
<version>4.2.3</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
<version>4.2.2</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpmime</artifactId>
<version>4.2.3</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.2.3</version>
</dependency>
</dependencies>
<version>1</version>
</project>

google app engine with struts2, spring and JPA using maven

I am trying to create an application on google app engine using Struts2, Spring and JPA to connect to appengine datastore.
I have created a maven project and I am able to configure struts2 and spring properly but whenever i try to connect to appengine non-relation database I get the below mentioned error
could not resolve type: javax.persistence.Persistence
My pom file is as below
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<packaging>war</packaging>
<version>1.0-SNAPSHOT</version>
<groupId>com.sis.rho</groupId>
<artifactId>rho_v1.0</artifactId>
<properties>
<appengine.app.version>1</appengine.app.version>
<appengine.target.version>1.8.3</appengine.target.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<!-- Compile/runtime dependencies -->
<dependency>
<groupId>com.google.appengine</groupId>
<artifactId>appengine-api-1.0-sdk</artifactId>
<version>${appengine.target.version}</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<version>2.5</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>jstl</groupId>
<artifactId>jstl</artifactId>
<version>1.2</version>
</dependency>
<!-- Test Dependencies -->
<dependency>
<groupId>com.google.appengine</groupId>
<artifactId>appengine-testing</artifactId>
<version>${appengine.target.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.google.appengine</groupId>
<artifactId>appengine-api-stubs</artifactId>
<version>${appengine.target.version}</version>
<scope>test</scope>
</dependency>
<!-- Struts 2 -->
<dependency>
<groupId>org.apache.struts</groupId>
<artifactId>struts2-core</artifactId>
<version>2.1.8</version>
</dependency>
<!-- Spring framework -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring</artifactId>
<version>2.5.6</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>2.5.6</version>
</dependency>
<!-- Struts 2 + Spring plugins -->
<dependency>
<groupId>org.apache.struts</groupId>
<artifactId>struts2-spring-plugin</artifactId>
<version>2.1.8</version>
</dependency>
<!-- Javax persistence -->
<dependency>
<groupId>org.datanucleus</groupId>
<artifactId>datanucleus-core</artifactId>
<!-- version>3.1.0-m3</version -->
<version>[3.1.1, 3.2)</version>
</dependency>
<dependency>
<groupId>org.datanucleus</groupId>
<artifactId>datanucleus-enhancer</artifactId>
<version>[3.1.0-release, )</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-jpa_2.0_spec</artifactId>
<version>1.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.datanucleus</groupId>
<artifactId>datanucleus-api-jpa</artifactId>
<version>[3.1.1, 3.2)</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>com.google.appengine.orm</groupId>
<artifactId>datanucleus-appengine</artifactId>
<version>2.1.1</version>
</dependency>
<!-- for log4J -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.6.1</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>1.6.1</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.6.1</version>
</dependency>
<!-- struts 2 velocity dependency -->
<dependency>
<groupId>org.apache.velocity</groupId>
<artifactId>velocity</artifactId>
<version>1.6.2</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<version>2.5.1</version>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.6</source>
<target>1.6</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.3</version>
<configuration>
<archiveClasses>true</archiveClasses>
<webResources>
<!-- in order to interpolate version from pom into appengine-web.xml -->
<resource>
<directory>${basedir}/src/main/webapp/WEB-INF</directory>
<filtering>true</filtering>
<targetPath>WEB-INF</targetPath>
</resource>
</webResources>
</configuration>
</plugin>
<plugin>
<groupId>com.google.appengine</groupId>
<artifactId>appengine-maven-plugin</artifactId>
<version>${appengine.target.version}</version>
<configuration>
<enableJarClasses>false</enableJarClasses>
<jvmFlags>
<jvmFlag>-Xdebug</jvmFlag>
<jvmFlag>-Xrunjdwp:transport=dt_socket,address=8080,server=y,suspend=y</jvmFlag>
</jvmFlags>
<disableUpdateCheck>true</disableUpdateCheck>
</configuration>
</plugin>
</plugins>
</build>
I have checked a lot of threads discussing similar issues (sample) but none of the fixes provided are able to solve my issue. I included nearly all the dependencies but none worked.
Please help

issue was fixed once i removed optional from geronimo
i am able to run a GAE application with JPA :)
My latest POM where its working is below
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<packaging>war</packaging>
<version>1.0-SNAPSHOT</version>
<groupId>com.sis.rho</groupId>
<artifactId>rho_v1.0</artifactId>
<properties>
<appengine.app.version>1</appengine.app.version>
<appengine.target.version>1.8.3</appengine.target.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<!-- Compile/runtime dependencies -->
<dependency>
<groupId>com.google.appengine</groupId>
<artifactId>appengine-api-1.0-sdk</artifactId>
<version>${appengine.target.version}</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<version>2.5</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>jstl</groupId>
<artifactId>jstl</artifactId>
<version>1.2</version>
</dependency>
<!-- Test Dependencies -->
<dependency>
<groupId>com.google.appengine</groupId>
<artifactId>appengine-testing</artifactId>
<version>${appengine.target.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.google.appengine</groupId>
<artifactId>appengine-api-stubs</artifactId>
<version>${appengine.target.version}</version>
<scope>test</scope>
</dependency>
<!-- Struts 2 -->
<dependency>
<groupId>org.apache.struts</groupId>
<artifactId>struts2-core</artifactId>
<version>2.1.8</version>
</dependency>
<!-- Spring framework -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring</artifactId>
<version>2.5.6</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>2.5.6</version>
</dependency>
<!-- Struts 2 + Spring plugins -->
<dependency>
<groupId>org.apache.struts</groupId>
<artifactId>struts2-spring-plugin</artifactId>
<version>2.1.8</version>
</dependency>
<!-- Javax persistence -->
<dependency>
<groupId>org.datanucleus</groupId>
<artifactId>datanucleus-core</artifactId>
<!-- version>3.1.0-m3</version -->
<version>3.1.1</version>
</dependency>
<dependency>
<groupId>org.datanucleus</groupId>
<artifactId>datanucleus-enhancer</artifactId>
<version>3.1.0-release</version>
</dependency>
<dependency>
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-jpa_2.0_spec</artifactId>
<version>1.1</version>
</dependency>
<dependency>
<groupId>org.datanucleus</groupId>
<artifactId>datanucleus-api-jpa</artifactId>
<version>3.1.1</version>
</dependency>
<dependency>
<groupId>com.google.appengine.orm</groupId>
<artifactId>datanucleus-appengine</artifactId>
<version>2.1.1</version>
</dependency>
<!-- for log4J -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.6.1</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>1.6.1</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.6.1</version>
</dependency>
<!-- struts 2 velocity dependency -->
<dependency>
<groupId>org.apache.velocity</groupId>
<artifactId>velocity</artifactId>
<version>1.6.2</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<version>2.5.1</version>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.6</source>
<target>1.6</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.3</version>
<configuration>
<archiveClasses>true</archiveClasses>
<webResources>
<!-- in order to interpolate version from pom into appengine-web.xml -->
<resource>
<directory>${basedir}/src/main/webapp/WEB-INF</directory>
<filtering>true</filtering>
<targetPath>WEB-INF</targetPath>
</resource>
</webResources>
</configuration>
</plugin>
<plugin>
<groupId>com.google.appengine</groupId>
<artifactId>appengine-maven-plugin</artifactId>
<version>${appengine.target.version}</version>
<configuration>
<enableJarClasses>false</enableJarClasses>
<jvmFlags>
<jvmFlag>-Xdebug</jvmFlag>
<jvmFlag>-Xrunjdwp:transport=dt_socket,address=8080,server=y,suspend=y</jvmFlag>
</jvmFlags>
<disableUpdateCheck>true</disableUpdateCheck>
</configuration>
</plugin>
</plugins>
</build>
</project>

Unexpected exception parsing XML document from ServletContext resource [/WEB-INF/applicationContext.xml];

In my pom.xml I am getting the following error. The reason why I have <version>2.0.3</version> is to use Spring 2 NTLM authentication.
org.springframework.beans.factory.BeanDefinitionStoreException:
Unexpected exception parsing XML document from
ServletContext resource [/WEB-INF/applicationContext.xml]; nested exception
is java.lang.NoSuchMethodError:org.springframework.aop.config.AopNamespaceUtils.
registerAutoProxyCreatorIfNecessary(Lorg/springframework/beans
/factory/xml/ParserContext;Lorg/w3c/dom/Element;)V
If I add the below.
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-core</artifactId>
<version>2.0.3</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-core-tiger</artifactId>
<version>2.0.3</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-ntlm</artifactId>
<version>2.0.3</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-taglibs</artifactId>
<version>2.0.3</version>
</dependency>
My pom.xml without the above with no errors
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>test</groupId>
<artifactId>app</artifactId>
<packaging>war</packaging>
<version>1.0-SNAPSHOT</version>
<name>app</name>
<url>http://maven.apache.org</url>
<repositories>
<repository>
<id>prime-repo</id>
<name>PrimeFaces Maven Repository</name>
<url>http://repository.primefaces.org</url>
<layout>default</layout>
</repository>
</repositories>
<properties>
<spring.version>3.1.1.RELEASE</spring.version>
<spring.security.version>2.0.2. RELEASE</spring.security.version>
</properties>
<dependencies>
<!-- Spring 3 dependencies -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-tx</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-test</artifactId>
<version>${spring.version}</version>
</dependency>
<!-- JSF library -->
<dependency>
<groupId>com.sun.faces</groupId>
<artifactId>jsf-api</artifactId>
<version>2.1.6</version>
</dependency>
<dependency>
<groupId>com.sun.faces</groupId>
<artifactId>jsf-impl</artifactId>
<version>2.1.6</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>jstl</artifactId>
<version>1.2</version>
</dependency>
<!-- Primefaces library -->
<dependency>
<groupId>org.primefaces</groupId>
<artifactId>primefaces</artifactId>
<version>3.4.2</version>
</dependency>
<dependency>
<groupId>org.primefaces.themes</groupId>
<artifactId>afterwork</artifactId>
<version>1.0.8</version>
</dependency>
<!-- Hibernate library -->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>4.1.0.Final</version>
</dependency>
<dependency>
<groupId>javassist</groupId>
<artifactId>javassist</artifactId>
<version>3.12.1.GA</version>
</dependency>
<dependency>
<groupId>javax.inject</groupId>
<artifactId>javax.inject</artifactId>
<version>1</version>
</dependency>
<!-- Oracle Java Connector library -->
<dependency>
<groupId>com.oracle</groupId>
<artifactId>ojdbc6</artifactId>
<version>11.2.0.3</version>
</dependency>
<dependency>
<groupId>c3p0</groupId>
<artifactId>c3p0</artifactId>
<version>0.9.1.2</version>
</dependency>
<!-- Log4j library -->
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.16</version>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.4</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-jpamodelgen</artifactId>
<version>1.2.0.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>4.1.0.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate.javax.persistence</groupId>
<artifactId>hibernate-jpa-2.0-api</artifactId>
<version>1.0.1.Final</version>
</dependency>
<dependency>
<groupId>org.apache.myfaces.extensions.cdi.core</groupId>
<artifactId>myfaces-extcdi-core-api</artifactId>
<version>1.0.5</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-ehcache</artifactId>
<version>4.0.1.Final</version>
</dependency>
<dependency>
<groupId>p6spy</groupId>
<artifactId>p6spy</artifactId>
<version>1.3</version>
</dependency>
</dependencies>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.6</source>
<target>1.6</target>
<compilerArgument>-proc:none</compilerArgument>
</configuration>
</plugin>
<plugin>
<groupId>org.bsc.maven</groupId>
<artifactId>maven-processor-plugin</artifactId>
<version>2.0.6</version>
<executions>
<execution>
<id>process</id>
<goals>
<goal>process</goal>
</goals>
<phase>generate-sources</phase>
<configuration>
<!-- source output directory -->
<outputDirectory>target/metamodel</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
Edit 1
As per PSR's suggestion, the error occurs when the following dependency is added
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-core</artifactId>
<version>2.0.3</version>
</dependency>

The problem will come because of one of the dependency.Try to remove all dependencies first what you shown.Then try to add one by one then we can find out the problem where it is

Check for multiple version for spring jars in your class path. we have spring-dao and spring-tx in class path. removing spring-dao fixed issue.