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Deploy JAR and WAR to Nexus

I'm working on a JAVA based application. The POM has been so configured that the packaging phase generates an executable JAR (with the maven-shade-plugin) and a WAR (with the war-plugin). The main packaging in the POM is set to jar.
When i execute locally a
mvn clean package
I obtain in my target folder the expected result (WAR + shaded JAR). But for some reason, in the Jenkins CI, in the deploy phase, only the JAR is being send to Nexus, the WAR is ignored.
Is there anything specific I should do to have the WAR sent to NEXUS ?
Here below the plugin-configs:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>3.2.3</version>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
</manifest>
<manifestEntries>
<Build-Time>${maven.build.timestamp}</Build-Time>
</manifestEntries>
-->
</archive>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>war</goal>
</goals>
</execution>
</executions>
</plugin>
and
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.2.4</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<finalName>${project.build.finalName}-jar-with-dependencies</finalName>
</configuration>
</execution>
</executions>
<configuration>
<createDependencyReducedPom>false</createDependencyReducedPom>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>**/Log4j2Plugins.dat</exclude>
<exclude>module-info.class</exclude>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
<shadedArtifactAttached>false</shadedArtifactAttached>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>my.main.class</mainClass>
</transformer>
</transformers>
</configuration>
</plugin>

Maven Shade overlapping classes warning

I am using commons-io in my project and want to shade it. I am running into a warning that I can't seem to figure out:
[WARNING] commons-io-2.7.jar, murder-1.0-SNAPSHOT.jar define 180 overlapping classes and resources:
...
I find this strange, as murder-1.0-SNAPSHOT.jar is the jar I am trying to build and which should include the commons-io jar.
I define my commons-io dependency as such:
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.7</version>
<scope>compile</scope>
</dependency>
(I thought I was supposed to use the runtime scope, but then I can't run package because it complains that FileUtils cannot be found)
Here's my config for the shade plugin:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.2.4</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<artifactSet>
<includes>
<include>commons-io:commons-io</include>
</includes>
</artifactSet>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/MANIFEST.MF</exclude>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
</plugin>
If I remove the <filters> entirely, I only get this warning:
commons-io-2.7.jar, murder-1.0-SNAPSHOT.jar define 1 overlapping resource
[WARNING] - META-INF/MANIFEST.MF
Everything still seems to work fine, but I want to get rid of this warning when I package.
EDIT:
If I run mvn clean first, the next mvn package produces no such warning. Subsequent runs however introduces the warning again.

In this end, this is what I ended up with that seems to work and produces no warnings:
<properties>
<!-- replace this with wherever you want your shaded dependencies to end up -->
<shaded-dependencies>io.vapidlinus.shade</shaded-dependencies>
</properties>
....
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<artifactSet>
<includes>
<include>commons-io:commons-io</include>
</includes>
</artifactSet>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>module-info.class</exclude>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.MF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
<exclude>META-INF/**</exclude>
</excludes>
</filter>
</filters>
<relocations>
<relocation>
<pattern>org.apache.commons.io</pattern>
<shadedPattern>${shaded-dependencies}.org.apache.commons.io</shadedPattern>
</relocation>
</relocations>
</configuration>
</execution>
</executions>

maven-shade-plugin doesn't replace the original jar

It is weird that my maven-shade-plugin doesn't replace the original jar with the shaded jar. Does anyone know what could be the reason?
Here's my plugin in pom.xml
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>${plugin.shade.version}</version>
<configuration>
<artifactSet>
<excludes>
<!-- Leave slf4j unshaded so downstream users can configure logging. -->
<exclude>org.slf4j:slf4j-api</exclude>
<exclude>org.slf4j:slf4j-log4j12</exclude>
<!-- Leave commons-logging unshaded so downstream users can configure logging. -->
<exclude>commons-logging:commons-logging</exclude>
<!-- Leave commons-exec unshaded so downstream users can use ProcessLauncher. -->
<exclude>org.apache.commons:commons-exec</exclude>
<!-- Leave log4j unshaded so downstream users can configure logging. -->
<exclude>log4j:log4j</exclude>
</excludes>
</artifactSet>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
<transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>reference.conf</resource>
</transformer>
<transformer implementation="org.apache.maven.plugins.shade.resource.ApacheLicenseResourceTransformer"/>
<transformer implementation="org.apache.maven.plugins.shade.resource.DontIncludeResourceTransformer">
<resource>NOTICE.txt</resource>
</transformer>
<transformer implementation="org.apache.maven.plugins.shade.resource.IncludeResourceTransformer">
<resource>META-INF/LICENSE.txt</resource>
<file>${basedir}/../../LICENSE.txt</file>
</transformer>
<transformer implementation="org.apache.maven.plugins.shade.resource.IncludeResourceTransformer">
<resource>META-INF/NOTICE.txt</resource>
<file>${basedir}/../../NOTICE.txt</file>
</transformer>
</transformers>
<relocations>
<relocation>
<pattern>org</pattern>
<shadedPattern>${shaded.dependency.prefix}.org</shadedPattern>
<excludes>
<exclude>org/apache/zeppelin/*</exclude>
<exclude>org/apache/zeppelin/**/*</exclude>
<exclude>org/apache/thrift/*</exclude>
<exclude>org/apache/thrift/**/*</exclude>
<exclude>org/slf4j/*</exclude>
<exclude>org/slf4j/**/*</exclude>
<exclude>org/apache/commons/logging/*</exclude>
<exclude>org/apache/commons/logging/**/*</exclude>
<exclude>org/apache/commons/exec/*</exclude>
<exclude>org/apache/commons/exec/**/*</exclude>
<exclude>org/apache/log4j/*</exclude>
<exclude>org/apache/log4j/**/*</exclude>
<exclude>org/sonatype/*</exclude>
<exclude>org/sonatype/**/*</exclude>
<exclude>**/pom.xml</exclude>
<!-- Not the org/ packages that are a part of the jdk -->
<exclude>org/ietf/jgss/*</exclude>
<exclude>org/omg/**/*</exclude>
<exclude>org/w3c/dom/*</exclude>
<exclude>org/w3c/dom/**/*</exclude>
<exclude>org/xml/sax/*</exclude>
<exclude>org/xml/sax/**/*</exclude>
</excludes>
</relocation>
<relocation>
<pattern>com.google</pattern>
<shadedPattern>${shaded.dependency.prefix}.com.google</shadedPattern>
</relocation>
<relocation>
<pattern>io</pattern>
<shadedPattern>${shaded.dependency.prefix}.io</shadedPattern>
</relocation>
<relocation>
<pattern>com.esotericsoftware</pattern>
<shadedPattern>${shaded.dependency.prefix}.com.esotericsoftware</shadedPattern>
</relocation>
</relocations>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>

Shaded plugin by default save original file as -original.jar, if you want to replace original file with the new generated (shaded), put this line in your configuration plugin section:
<configuration>
...
<outputFile>${output.directory}\${project.artifactId}-${project.version}.jar</outputFile>
...
</configuration>
Replace output.directory with your shade plugin outputDirectory.
Check this post with more details: post

Looks like Configuration tag should come inside execution tag in the hierarchy, as shown below. Please re-organize executions and execution tag and include your configuration under it as shown below.
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>${maven.shade.plugin}</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<relocations>
<relocation>
<pattern>org.apache*</pattern>
<shadedPattern>shaded.org.apache*</shadedPattern>
</relocation>
<relocation>
<pattern>com.cookie*</pattern>
<shadedPattern>shaded.com.cookie*</shadedPattern>
</relocation>
</relocations>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
For more information, please refer the maven documentation http://maven.apache.org/plugins/maven-shade-plugin/examples/class-relocation.html

Create jar with dependencies and excluding specific source files

I would like to use Maven to create a jar that includes a specific dependent artifact and excludes some of the source java files.
Currently I use this snippet:
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<id>shadedJar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<shadedClassifierName>classifier</shadedClassifierName>
<shadedArtifactAttached>true</shadedArtifactAttached>
<createDependencyReducedPom>false</createDependencyReducedPom>
<artifactSet>
<includes>
<include>com.google.guava:guava</include>
</includes>
</artifactSet>
</configuration>
</execution>
</executions>
Thus, the jar does contain the 'guava' artifact files, however I would also like to exclude some source files (for example a specific file under src/main/java/my.package/), How can I do that?

I use shade to create a jar, but I do not need some files of eclipse, txt and other things that they are relevant only to development.
This is the code I have, maybe you can addapt it and use it.
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.2</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<createDependencyReducedPom>false</createDependencyReducedPom>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
<exclude>.settings/**</exclude>
<exclude>*.classpath</exclude>
<exclude>*.project</exclude>
<exclude>*.txt</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
</plugin>

Maven shade copy WEB-INF

Using maven-shade-plugin I am trying to create a project file structure as follows:
The problem is that the following pom configuration is not creating the WEB-INF directory.
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
<createDependencyReducedPom>true</createDependencyReducedPom>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>com.my.package.Main</mainClass>
</transformer>
</transformers>
</configuration>
</execution>
</executions>
</plugin>
Basically I need to copy my web.xml file, classes and lib files into a directory called WEB-INF in the root of the project.
Update: SORRY, I copied the wrong plugin from my pom into the original question!
Update: If I add the packaging from the pom declaration: <packaging>war</packaging> The WEB-INF file structure is completed as per the OQ. However, with this declaration the com directory now does not contain my packages so the main class cannot be found.
How it looks with the <packaging>war</packaging>:
How it should look:

maven-assembly plugin allows much more flexibility, it would be easily accomplished by using assembly plugin
See
assembly descriptor examples

There are lots of possible answer to achieve the desired effect with maven. However, based on the update I gave I found that adding the maven-antrun-plugin with the following solved my issue:
<plugin>
<artifactId>maven-antrun-plugin</artifactId>
<executions>
<execution>
<id>move-main-class</id>
<phase>compile</phase>
<configuration>
<tasks>
<copy todir="${project.build.directory}/${project.artifactId}">
<fileset dir="${project.build.directory}/classes/">
</fileset>
</copy>
</tasks>
</configuration>
<goals>
<goal>run</goal>
</goals>
</execution>
</executions>
</plugin>