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Why Eclipse displayed the error " <failOnMissingWebXml> is set to true" whereas I set it to false?

I just created a simple Maven project, i want it without web.xml.
Eclipse display this error while I set it to true (see pom.xml) :
<build>
<finalName>ROOT</finalName>
<!-- <sourceDirectory>src</sourceDirectory> -->
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-war-plugin</artifactId>
<version>3.2.1</version>
<configuration>
<failOnMissingWebXml>false</failOnMissingWebXml>
</configuration>
</plugin>
</plugins>
</build>
Does anybody has an idea of what is involved here ?

maven-jar-plugin not finding my main class

I've got a Java/Selenium/TestNG/Maven project. I can successfully create the myproj-0.0.1-SNAPSHOT.jar file. When I try to run it I'm getting an error:
$ java -jar myproj-0.0.1-SNAPSHOT.jar
Error: Could not find or load main class utilities.MavenTestInvoker
My main goal is to be able to run this SNAPSHOT.jar file to run my test cases on a remote machine.
I'm using a build plugin in my pom.xml:
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.6.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.19.1</version>
<configuration>
<suiteXmlFiles>
<suiteXmlFile>testng.xml</suiteXmlFile>
</suiteXmlFiles>
<skipTests>true</skipTests>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>utilities.MavenTestInvoker</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
When I build the project I'm using the maven command: "mvn clean package shade:shade"
That creates my uber jar.
Here are the dependencies:
<dependencies>
<dependency>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.1</version>
</dependency>
<dependency>
<groupId>org.apache.maven.shared</groupId>
<artifactId>maven-invoker</artifactId>
<version>2.2</version>
</dependency>
<dependency>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.3</version>
</dependency>
plus some others
</dependencies>
What am I doing incorrectly?

The correct usage of including plugin dependencies is as follows, you can merge the plugin dependencies at a single place -
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.6.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.19.1</version>
<configuration>
<suiteXmlFiles>
<suiteXmlFile>testng.xml</suiteXmlFile>
</suiteXmlFiles>
<skipTests>true</skipTests>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.3.2</version>
<!--Notice I have removed the configs here. Not required to generate the jar-->
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.shared</groupId>
<artifactId>maven-invoker</artifactId>
<version>2.2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.3</version>
</plugin>
</plugins>
</pluginManagement>
</build>
Further you can edit the respective plugin configs within the same declaration.
Also for using maven-shade-plugin and maven-jar-plugin, you might want to look into the samples here and here respectively.

Remember that your project must have the right folder structure, for example your code must be in src/main/java

Maven putting META-INF and WEB-INF contents into classes

my pom.xml contents for build -
<build>
<sourceDirectory>src/main/java</sourceDirectory>
<plugins>
<plugin>
<artifactId>maven-war-plugin</artifactId>
<version>2.1.1</version>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
</plugins>
</build>
my directory structure is standard -
But this is what happening in target folder , META and WEB INF are again copied to classes -

No classes in war maven

I'm pretty new in using og maven, an I got stuck. mvn clean install does not generate classes :(
I'm using the following code in my pom :
<plugin>
<artifactId>maven-war-plugin</artifactId>
<version>2.4</version>
<configuration>
<webXml>WebContent\WEB-INF\web.xml</webXml>
<archiveClasses>true</archiveClasses>
</configuration>
</plugin>

Please read the usage page first, it will show the expected folder structure.
So java sources are expected in src/main/java.
BTW: If you still want to use WebContent, set the warSourceDirectory to WebContent, remove all other configuration.

<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.6</source>
<target>1.6</target>
<optimize>true</optimize>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<webResources>
<resource>
<directory>src/main/webapp</directory>
<filtering>true</filtering>
</resource>
</webResources>
</configuration>
</plugin>
</plugins>

maven 3 + pmd fails when code has annotations and generics

When I run mvn pmd:pmd I get an warning / error from PMD saying that the code cannot use generics, annotations or Enums with java 1.4 or 1.5. This is supposed to be a error when the targetJdk property is not set (which I did set).
Here is an example of the error I get
[WARNING] Error while parsing /Users/augusto/Downloads/PMD-Clover2-Cobertura-Maven2-Test/PMDTest/src/main/java/org/xh/studies/quality/App.java: Can't use generics unless running in JDK 1.5 mode!
and here's a snippet of the pom I'm using (there's a link to the whole app below)
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
</configuration>
</plugin>
</plugins>
</build>
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-pmd-plugin</artifactId>
<version>2.5</version>
<configuration>
<targetJdk>1.6</targetJdk>
</configuration>
</plugin>
</plugins>
</reporting>
I'm using Maven 3.0.2 on mac, with the latest java patch 1.6.0_24.
Click here to download the full project (8kb)

EDIT (26/03/2014)
Since version 3.3 of the maven site plugin, maven can also use the old style configuration (and in fact the maven 2 style is now recommended). Links: docs, jira.
Original answer
Pain, the answer is that the site generation changed completely from maven 2 to maven 3. There is an explanation on this blog. Note that mvn pmd:pmd doesn't work anyway with the new reporting configuration, but it works as part of the site generation.
And here's an example of a pom that works.
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>${java-version}</source>
<target>${java-version}</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>3.0-beta-2</version>
<configuration>
<reportPlugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>2.3.1</version>
<configuration>
<dependencyDetailsEnabled>false</dependencyDetailsEnabled>
<dependencyLocationsEnabled>false</dependencyLocationsEnabled>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>javancss-maven-plugin</artifactId>
<version>2.0</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>jdepend-maven-plugin</artifactId>
<version>2.0-beta-2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-pmd-plugin</artifactId>
<version>2.5</version>
<configuration>
<linkXRef>false</linkXRef>
<sourceEncoding>utf-8</sourceEncoding>
<minimumTokens>100</minimumTokens>
<targetJdk>${java-version}</targetJdk>
<verbose>true</verbose>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>findbugs-maven-plugin</artifactId>
<version>2.3.2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>2.6</version>
</plugin>
</reportPlugins>
</configuration>
</plugin>
</plugins>
</build>