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Invalid signature file digest for Manifest main attributes while running jar

I am trying to run the jar file of my project. I am working on STS. a But every time i am trying to run my jar file its giving me exception like Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.SecurityException: Invalid signature file digest for Manifest main attributes
my pom.xml is
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.3</version>
<executions>
<!-- <execution> <id>copy-dependencies</id> <phase>prepare-package</phase>
<goals> <goal>copy-dependencies</goal> </goals> <configuration> <outputDirectory>
${project.build.directory}/${environment}/dependencies ${project.build.directory}/dependency-jars/
</outputDirectory> <overWriteReleases>false</overWriteReleases> <overWriteSnapshots>false</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer> <includeScope>runtime</includeScope>
</configuration> </execution> -->
<execution>
<id>unpack-dependencies</id>
<phase>package</phase>
<goals>
<goal>unpack-dependencies</goal>
</goals>
<!-- <configuration> <excludeScope>system</excludeScope> <excludes>META-INF/*.SF</excludes>
<excludes>META-INF/*.DSA</excludes> <excludes>META-INF/*.RSA</excludes> <excludeGroupIds>junit,org.mockito,org.hamcrest</excludeGroupIds>
<outputDirectory>${project.build.directory}/dependency-jars/</outputDirectory>
</configuration> -->
<configuration>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
<!-- Additional configuration. -->
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>2.5</version>
<executions>
<execution>
<id>copy-resources</id>
<!-- here the phase you need -->
<phase>validate</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${basedir}/target/resources
</outputDirectory>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<mainClass>com.emo.process.EmoBatchProcess</mainClass>
<classpathPrefix>dependency-jars/</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>1.4</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<finalName>EMOBatchProcess</finalName>
<outputDirectory>${basedir}/target/LOCAL</outputDirectory>
<shadedArtifactAttached>true</shadedArtifactAttached>
<shadedClassifierName>all</shadedClassifierName>
</configuration>
</execution>
</executions>
</plugin>
</plugins>

How to use JPA-Entities as a dependency with maven

I got in a multimodule-maven-project an entities project in which there are some Entity and DAO classes. Also there are some integration-tests which I'd like to seperate in an own project called entities-IT.
Now I've put the entities-project as an dependency to the entites-IT-project but if I run the build there occurs an error message like this:
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:testCompile (default-testCompile) on project entities-IT: Compilation failure
[ERROR] /some/path/to/project/entities-IT/src/it/java/com/example/persistence/dao/ExampleDaoIT.java:[25,38] cannot access com.example.persistence.ExampleEntity
[ERROR] bad class file: /some/path/to/project/persistence/ExampleEntity.class
[ERROR] illegal start of class file
[ERROR] Please remove or make sure it appears in the correct subdirectory of the classpath.
This is strange because in the target folder there are all of mentioned .class files and the folderstructure is also correct.
Is there anything to take notice if using Entities as a dependency in another project?
In the pom.xml of the entities-project there is some code-generation going on:
<build>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.7.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<compilerArguments>
<processor>org.hibernate.jpamodelgen.JPAMetaModelEntityProcessor</processor>
</compilerArguments>
</configuration>
</plugin>
<plugin>
<groupId>org.bsc.maven</groupId>
<artifactId>maven-processor-plugin</artifactId>
<version>2.2.4</version>
<executions>
<execution>
<id>process</id>
<configuration>
<outputDirectory>${project.build.directory}/generated-sources/metamodel</outputDirectory>
<compilerArguments>
-Aeclipselink.persistencexml=${project.basedir}/src/main/java/META-INF/persistence.xml
</compilerArguments>
<processors>
<processor>org.eclipse.persistence.internal.jpa.modelgen.CanonicalModelProcessor
</processor>
</processors>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
...
</build>
and then I have the dependency set in the entities-IT-project:
<dependency>
<groupId>example</groupId>
<artifactId>entities</artifactId>
<version>${parent.version}</version>
</dependency>
and run the tests with the failsafe-plugin:
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.0.0</version>
<executions>
<execution>
<id>add-integration-test-sources</id>
<phase>generate-test-sources</phase>
<goals>
<goal>add-test-source</goal>
</goals>
<configuration>
<sources>
<source>src/it/java</source>
</sources>
</configuration>
</execution>
<execution>
<id>add-integration-test-resources</id>
<phase>generate-test-resources</phase>
<goals>
<goal>add-test-resource</goal>
</goals>
<configuration>
<resources>
<resource>
<filtering>true</filtering>
<directory>src/it/resources</directory>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>3.0.0-M3</version>
<executions>
<execution>
<id>integration-test</id>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>

Running test categories separately

I need to run groups of my tests in separate stages (first run group A, then run group B as if you had just started running tests)
So i decided to use a combination of maven-failsafe-plugin and junit test categories
I have the following configuration:
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<includes>
<include>**/*Test.java</include>
</includes>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<configuration>
<skip>${skipTests}</skip>
<includes>
<include>**/*IT.java</include>
</includes>
<groups>my.categories.IntegrationTest</groups>
<excludedGroups>my.categories.ProfiledIntegrationTest, my.categories.MvcTest, my.categories.ExchangeRateTest</excludedGroups>
</configuration>
<executions>
<execution>
<id>integration-test</id>
<phase>integration-test</phase>
<goals>
<goal>integration-test</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<configuration>
<skip>${skipTests}</skip>
<includes>
<include>**/*IT.java</include>
</includes>
<groups>my.categories.ProfiledIntegrationTest</groups>
<excludedGroups>my.categories.IntegrationTest, my.categories.MvcTest, my.categories.ExchangeRateTest</excludedGroups>
</configuration>
<executions>
<execution>
<id>profiled-integration-test</id>
<phase>integration-test</phase>
<goals>
<goal>integration-test</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<configuration>
<skip>${skipTests}</skip>
<includes>
<include>**/*IT.java</include>
</includes>
<groups>my.categories.MvcTest</groups>
<excludedGroups>my.categories.ProfiledIntegrationTest, my.categories.IntegrationTest, my.categories.ExchangeRateTest</excludedGroups>
</configuration>
<executions>
<execution>
<id>mvc-integration-tests</id>
<phase>integration-test</phase>
<goals>
<goal>integration-test</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<configuration>
<skip>${skipTests}</skip>
<includes>
<include>**/*IT.java</include>
</includes>
<groups>my.categories.ExchangeRateTest</groups>
<excludedGroups>my.categories.MvcTest, my.categories.ProfiledIntegrationTest, my.categories.IntegrationTest</excludedGroups>
</configuration>
<executions>
<execution>
<id>exchange-rate-integration-tests</id>
<phase>integration-test</phase>
<goals>
<goal>integration-test</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>2.7</version>
</plugin>
</plugins>
However maven runs my unit tests (surefire) and then the last instance of the maven failsafe plugin only (it ignores the previous 3)
How can i make it run them as well please?

The solution was as mentioned by JF Meier
you need to only have one instance of the plugin, and run them as seperate executions
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<includes>
<include>**/*Test.java</include>
</includes>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<configuration>
<skip>${skipTests}</skip>
<includes>
<include>**/*IT.java</include>
</includes>
</configuration>
<executions>
<execution>
<id>integration-test</id>
<phase>integration-test</phase>
<goals>
<goal>integration-test</goal>
</goals>
<configuration>
<groups>my.categories.IntegrationTest</groups>
<excludedGroups>my.categories.ProfiledIntegrationTest, my.categories.MvcTest, my.categories.ExchangeRateTest</excludedGroups>
</configuration>
</execution>
<execution>
<id>profiled-integration-test</id>
<phase>integration-test</phase>
<goals>
<goal>integration-test</goal>
</goals>
<configuration>
<groups>my.categories.ProfiledIntegrationTest</groups>
<excludedGroups>my.categories.IntegrationTest, my.categories.MvcTest, my.categories.ExchangeRateTest</excludedGroups>
</configuration>
</execution>
<execution>
<id>mvc-integration-tests</id>
<phase>integration-test</phase>
<goals>
<goal>integration-test</goal>
</goals>
<configuration>
<groups>my.categories.MvcTest</groups>
<excludedGroups>my.categories.ProfiledIntegrationTest, my.categories.IntegrationTest, my.categories.ExchangeRateTest</excludedGroups>
</configuration>
</execution>
<execution>
<id>exchange-rate-integration-tests</id>
<phase>integration-test</phase>
<goals>
<goal>integration-test</goal>
</goals>
<configuration>
<groups>my.categories.ExchangeRateTest</groups>
<excludedGroups>my.categories.MvcTest, my.categories.ProfiledIntegrationTest, my.categories.IntegrationTest</excludedGroups>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>2.7</version>
</plugin>
</plugins>

maven - why is my pom.xml NOT removing META-INF/*.SF, META-INF/*.DSA and META-INF/*.RSA?

On my pom.xml I have the following <plugin> section:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.8</version>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>prepare-package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<excludeScope>system</excludeScope>
<excludes>META-INF/*.SF</excludes>
<excludes>META-INF/*.DSA</excludes>
<excludes>META-INF/*.RSA</excludes>
<excludeGroupIds>junit,org.mockito,org.hamcrest</excludeGroupIds>
<outputDirectory>${project.build.directory}/classes/lib/</outputDirectory>
<includeScope>runtime</includeScope>
</configuration>
</execution>
</executions>
</plugin>
But, whenever I build the project with a mvn clean install -U, some .SF, .DSA and .RSA are copied to the built jar file and I need to remove them manually.
How to correct this?

The correct usage of tag <excludes> is following:
<excludes>META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA</excludes>

My mixed Scala/Java Maven project doesn't compile

I have a mixed Scala/Java project that doesn't compile well.
The problem arises when Java code is trying to call Scala code in the same package.
Of course, I have the standard layout:
src/main/java
src/main/scala
src/test/java
src/test/scala
I've looked at other similar Stackoverflow questions but this question is a little outdated. This other question doesn't help either.
I have also followed the scala-maven-plugin documentation page.
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>3.1.6</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.0.2</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>process-resources</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<executions>
<execution>
<phase>compile</phase>
<goals>
<goal>compile</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
I have tried unsuccessfully to follow this blog post.
IDEA project with Scala plugin imported from the pom.xml can compile and run my project successfully.
What is the right way of doing it?
Does the Java code gets compiled twice? First by the Scala plugin and the by the Java plugin?.

Here is a working example of pom.xml :
<?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>
<groupId>stackoverflow</groupId>
<artifactId>q24448582</artifactId>
<version>1.0-SNAPSHOT</version>
<properties>
<scala.version>2.10.3</scala.version>
</properties>
<dependencies>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>${scala.version}</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.scala-tools</groupId>
<artifactId>maven-scala-plugin</artifactId>
<version>2.15.2</version>
<executions>
<execution>
<id>compile</id>
<goals>
<goal>compile</goal>
</goals>
<phase>compile</phase>
</execution>
<execution>
<id>test-compile</id>
<goals>
<goal>testCompile</goal>
</goals>
<phase>test-compile</phase>
</execution>
<execution>
<phase>process-resources</phase>
<goals>
<goal>compile</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>

Problem 1
At first I thought the problem was due to using a modern version of the maven-compiler-plugin. I was using version 3.0 instead of 2.0.2.
The solution has been:
- Remove the maven-compiler-plugin
- Add this setting: incremental
Finally my pom.xml is this:
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>3.1.6</version>
<configuration>
<recompileMode>incremental</recompileMode>
<args>
<arg>-deprecation</arg>
<arg>-explaintypes</arg>
<arg>-target:jvm-1.7</arg>
</args>
</configuration>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>process-resources</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile</id>
<phase>process-test-resources</phase>
<goals>
<goal>add-source</goal>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
</plugin>
Problem 2
Another problem I was experiencing is this:
<dependencies>
<dependency>
<groupId>org.json4s</groupId>
<artifactId>json4s-native_${scala.version}</artifactId>
<version>3.2.9</version>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>${scala.version}.4</version>
</dependency>
</dependencies>
<properties>
<scala.version>2.10</scala.version>
</properties>
This make this solved problem arise:
https://issues.scala-lang.org/browse/SI-5733
Probably it was using an old version of the Scala compiler.
The solution has been to rename scala.version to scala.major, as this property has a special meaning.

In order to get the scala-maven-plugin to respect Java 1.8, but still allow mixed compilation of java and scala, we use this:
...
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.5</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
<executions>
<execution>
<id>default-compile</id>
<phase>none</phase>
</execution>
</executions>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>3.2.2</version>
<configuration>
<recompileMode>incremental</recompileMode>
</configuration>
<executions>
<execution>
<goals>
<goal>compile</goal>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
</plugin>
...

I add blow code at pom.xml file <build> block and working good!
<build>
<finalName>${project.artifactId}</finalName>
<plugins>
<!-- SCALA AND JAVA MIX COMPILATION -->
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<executions>
<execution>
<id>scala-compile</id>
<goals>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile</id>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.2</version>
<configuration>
<artifactSet>
<includes>
<include>*:*</include>
</includes>
</artifactSet>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<finalName>${project.artifactId}-shaded-${project.version}</finalName>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
<pluginManagement>
...
</pluginManagement>
<resources>
...
</resources>
</build>