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Problem with building jar file with dependencies

I need to export a jar file which could be execute in server. I try many of answers in this site and other site, but I guess my main problem is :
[ERROR] Failed to parse plugin descriptor for mybot:energyBot:0.0.1-SNAPSHOT (/Users/narges/.m2/repository/bot/mBot/0.0.1-SNAPSHOT/energyBot-0.0.1-SNAPSHOT.jar): No plugin descriptor found at META-INF/maven/plugin.xml -> [Help 1]
Here is part of my pom.xml:
<plugins>
<plugin>
<groupId>mybot</groupId>
<artifactId>myBot</artifactId>
<executions>
<execution>
<phase>install</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>$/Users/narges/eclipse-workspace/Bot/lib</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
</plugins>

Use this in your pom.xml, plugin works fine with boot applications as well.
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.3.1</version>
<configuration>
<outputDirectory>/your/path</outputDirectory>
</configuration>
</plugin>
</plugins>
</build>

You probably wrote myBot/energyBot yourself? You added it as a Maven plugin, but it seems like it is not a Maven plugin, but maybe just a plain jar.
If you want to put all dependencies into your jar, you need the assembly plugin or the shade plugin.

How do I make IntelliJ IDEA automatically extract a dependency to the artifact jar?

Let's say I'm adding the following dependency to my pom.xml:
<dependency>
<groupId>org.ini4j</groupId>
<artifactId>ini4j</artifactId>
<version>0.5.4</version>
</dependency>
I can now use the Ini class as expected, but if I try to build the jar and run it, it will give me a "noclassdeffounderror" error. When I check the content of the jar, it does not contain org/ini4j.
I was able to fix this by going into File -> Project Structure -> Artifacts
If I want to add another dependency, I'll have to do this every time, which is quite tedious (I didn't need to do this on NetBeans). I then tried to use the following plugins (which I used on NetBeans) to have Maven create a jar with dependencies automatically.
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
<configuration>
<archive>
<manifest>
<mainClass>main.Main</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>1.7.1</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
On NetBeans, this automatically adds all dependencies to the jar file, but it doesn't do anything on IntelliJ IDEA. I have no idea what I'm doing anymore; nothing works. How can I make IntelliJ IDEA automatically extract a dependency into the output root?

Dose your intellij use the same version on maven that your Netbeans uses? if it checks fine, try another plugin for making a fat jar such as the folowing:
<build>
<plugins>
<!-- any other plugins -->
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>

scala maven plugin not packaging scala files into jar

I'm new to maven and currently try to assemble a scala project with it. Project structure:
dir
|
|--src/main/java
|
|--src/main/scala
|
|--pom.xml
I was kind of surprised that classes compiled from *.java end up in jar, but one compiled from *.scala do not. I added these plugins to pom.xml
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>3.1.3</version>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>HelloWorld</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
I though maven-jar-plugin is responsible for assembling jar files. But for some reason, it does not add scala-compiled classes.
QUESTION: Who adds .class file into a final jar after executing mvn install? How to add .class-files compiled with scala compiler?

mvn package will build your jar, however maven-compiler-plugin will only compile your java source files not your scala source files. Scala-maven-plugin can be used to compile both java and scala sources.
I wrote a blog post on this a while ago, that may help http://blog.rizvn.com/2016/04/scala-and-maven.html
You will need to tell maven about src/main/scala, since you are putting your scala code under src/main/java. This is done through the build section like so:
<build>
<sourceDirectory>src/main/scala</sourceDirectory>
<testSourceDirectory>src/test/scala</testSourceDirectory>
...
</build>

Can you try something like this, using "scala-maven-plugin" instead. Then execute maven goal : mvn clean package
<build>
<sourceDirectory>${basedir}/src</sourceDirectory>
<resources>
<resource>
<directory>${basedir}/src/test/resources</directory>
</resource>
</resources>
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>${scala-maven-plugin.version}</version>
<configuration>
<sourceDir>${basedir}/src</sourceDir>
<outputDir>${basedir}/target/classes</outputDir>
</configuration>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>process-resources</phase>
<goals>
<goal>compile</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>

Maven: Where to put generated resources for tomcat-maven-plugin?

I have CSS and JavaScript files in src/main/webapp directory of my project.
I want to join add joined and minified version of these resources to my WAR file and to the place where tomcat-maven-plugin picks it up.
I used yuicompressor-maven-plugin to create the files and put it to ${project.build.directory}/${project.build.finalName}. It works great for maven package and those resources make their way to WAR file, but somehow tomcat-maven-plugin does not see those at all. Should I use a different directory for it?
My pom:
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>tomcat-maven-plugin</artifactId>
<version>1.1</version>
<configuration>
<path>/MyApp</path>
<warDirectory>${project.build.directory}/${project.build.finalName}</warDirectory>
</configuration>
</plugin>
<plugin>
<version>2.5.1</version>
<inherited>true</inherited>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.6</source>
<target>1.6</target>
<optimize>true</optimize>
<debug>true</debug>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>2.5</version>
<configuration>
<encoding>UTF-8</encoding>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.2</version>
<configuration>
<webResources>
<resource>
<directory>${basedir}/src/main/resources/META-INF</directory>
<filtering>true</filtering>
<targetPath>META-INF</targetPath>
<includes>
<include>context.xml</include>
</includes>
</resource>
</webResources>
<archive>
<addMavenDescriptor>false</addMavenDescriptor>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addClasspath>true</addClasspath>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>yuicompressor-maven-plugin</artifactId>
<version>1.3.0</version>
<executions>
<execution>
<phase>process-resources</phase>
<configuration>
<excludes>
<exclude>**/*</exclude>
</excludes>
<aggregations>
<aggregation>
<output>${project.build.directory}/${project.build.finalName}/js/commons-pack.js</output>
<includes>
<include>${project.build.sourceDirectory}/../webapp/js1.js</include>
<include>${project.build.sourceDirectory}/../webapp/js2.js</include>
...
What should I do to make mvn tomcat:run to also pick up my generated files?

Use warSourceDirectory:
<warSourceDirectory>${project.build.directory}/${project.build.finalName}</warSourceDirectory>
Instead of this configuration property (warDirectory) for the tomcat-maven-plugin:
<warDirectory>${project.build.directory}/${project.build.finalName}</warDirectory>
According to the tomcat-maven-plugin documentation, warSourceDirectory is where the web resources get picked up, and its default value is ${basedir}/src/main/webapp. This means that if you don’t set that property, you need to generate your unified/minified JavaScript file under ${basedir}/src/main/webapp.
If you set warSourceDirectory to the output folder, this means you need to generate this file before starting Tomcat.

Alternatively, you can also use the run-war goal instead of run, e.g. mvn tomcat6:run-war. This wil use the exploded war in your build directory (and thus filtered resources). See this site. There is also run-war-only which skips the packaging phase.

Note the plugin is now maintained at Apache (so upgrade a bit :-) ) see http://tomcat.apache.org/maven-plugin-2.0/.
Even it works using install I'm not sure it's the optimum solution (regarding io and build time).
The tomcat run must be able to use resources from more than one directory (I'm not sure it's possible with the current tomcat embeded api).
Can you add a feature request here https://issues.apache.org/jira/browse/MTOMCAT
Thanks

Add subversion revision to war manifest using maven2

I want to find a maven native (i.e. without calling external programs) to inject the svn revision in the war manifest.
Does anybody know a way to do that?
I found mention to how to add the subversion revision to manifests in jar files but not with war files.
I searched SO but could not find this issue specifically.

I want to find a maven native (i.e. without calling external programs) to inject the svn revision in the war manifest.
This is possible with the Build Number Maven Plugin using the svnjava provider:
If you need to execute the plugin on
machine without any svn in the path
you can configure the mojo to use the
svnjava provider.
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>buildnumber-maven-plugin</artifactId>
<version>1.0-beta-3</version>
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>create</goal>
</goals>
</execution>
</executions>
<configuration>
<doCheck>true</doCheck>
<doUpdate>true</doUpdate>
<providerImplementations>
<svn>javasvn</svn>
</providerImplementations>
</configuration>
</plugin>
</plugins>
</build>
The Build Number Maven Plugin sets the build number in the ${buildNumber} property that you can then use in your POM.
I found mention to how to add the subversion revision to manifests in jar files but not with war files.
Then, to add the build number in the MANIFEST of a war, configure the plugin as mentioned in the Usage page:
<build>
...
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.0.2</version>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
</manifest>
<manifestEntries>
<Implementation-Build>${buildNumber}</Implementation-Build>
</manifestEntries>
</archive>
</configuration>
</plugin>
</plugins>
</build>

Try this. About halfway down, look for maven-war-plugin
<build>
...
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.0.2</version>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
</manifest>
<manifestEntries>
<Implementation-Build>${buildNumber}</Implementation-Build>
</manifestEntries>
</archive>
</configuration>
</plugin>
</plugins>
</build>