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maven dependency not properly compile into war

I am using the Eclipse IDE and in the past, I have been developing a maven project depending on local sources (from github (sap-olingo)) as well as maven dependencies loaded as jar. I have now updated the github source and also all the dependencies which seems to break standard eclipse export functionalities (right click porject -> export -> war)
The webproject is working fine when using the maven install functionality and is loading all sources into the META-INF/lib classes, but when using the export as war from eclipse (which I did previously) it is missing to compile a proper dependency. Missing in the sense of that the jar is still present in the META-INF/lib directory of the war, but the content is empty and the size is only 1kb
When comparing the mvn clean install to the exported, there are rarely any differences. Except for the projects that are to be compiled during the runtime. Sizes of the libs in the mvn created war and the exported war roughly matches except for that one jar.
Is there a way to root cause that issue? I am using solely the maven integrated into the IDE which is why I doubt differences in the maven versions and or jdk.
Unfortunately I have no idea in where to start and what info you require
Thanks for your input
EDIT:
My projects 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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.test</groupId>
<artifactId>odata</artifactId>
<packaging>war</packaging>
<version>4.0.0</version>
<name>odataMaven Webapp</name>
<url></url>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.sap.olingo</groupId>
<artifactId>odata-jpa-processor</artifactId>
<version>0.3.7-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>com.microsoft.sqlserver</groupId>
<artifactId>mssql-jdbc</artifactId>
<version>6.1.0.jre8</version>
</dependency>
<dependency>
<groupId>org.eclipse.persistence</groupId>
<artifactId>javax.persistence</artifactId>
<version>2.1.0</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<version>2.5</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.eclipse.persistence</groupId>
<artifactId>eclipselink</artifactId>
<version>2.6.2</version>
</dependency>
</dependencies>
<build>
<finalName>odata</finalName>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.17</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>${project.build.source}</source>
<target>${project.build.source}</target>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.build.source>1.8</project.build.source>
</properties>
</project>
The odata-jpa-processor source/project is pulled from here. The problem exists solely with the olingo-jpa-metadata jar which is empty. All other maven dependencies are exported correctly.

JDK sources in Eclipse using maven

I have some Maven projects that I develop under Eclipse. When I want to see the source of a third party class, if the sources were published, I can simply read them:
However when I try to do the same with any of the default classes, those that are part of the JDK, I see a "Source not found" screen:
One of my pom.xml contains this:
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
<version>4.0</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
</plugins>
</build>
I was looking for a way to put the JDK in as a dependency, but I can't find a clue, how. I'm not even sure, if that would solve the problem, because my project compiles fine. I also am also aware that I can simply attach the sources through Eclipse, but again I'm not sure, if that would be a nice solution, as Maven can download the other sources.
Do you have any idea what could cause this, and how to solve the problem?

Spark related jars cannot be resolved in Eclipse

I'm new to Spark so am trying to setup a project from the book Learning Spark: Lightning-Fast Big Data Analysis. The book uses version 1.3 but I've only got 2.1.1 so am trying to work around a few differences.
All the Spark related jars that I'm importing into my Java project have a "import org.apache cannot be resolved". I know it's because the project cannot find the jar files specified.
I can manually add each by going to Build Path > Configure Build path and adding them to the Libraries section but I think I shouldn't need to do this. The project uses Maven so I believe if I have the Spark dependencies configured correctly in my pom.xml it should work. Is this correct?
I also set the following environment variables:
export SPARK_HOME=/Users/mymac/spark-2.1.1-bin-hadoop2.7/
export PATH="$SPARK_HOME/bin/:$PATH"
Are there any others I should be aware of?
Here's the contents of my pom.xml:
<project>
<groupId>com.oreilly.learningsparkexamples.mini</groupId>
<artifactId>learning-spark-mini-example</artifactId>
<modelVersion>4.0.0</modelVersion>
<name>example</name>
<packaging>jar</packaging>
<version>0.0.1</version>
<dependencies>
<dependency> <!-- Spark dependency -->
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
<version>2.1.1</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>2.11.8</version>
</dependency>
</dependencies>
<properties>
<java.version>1.8</java.version>
</properties>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.5</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
</project>

This should be setup as a Maven project, not a Java project. In my case to resolve deleted the project from my workspace, re-created it in the workspace as a general project, then converted it to a Maven project. I probably should have just set it up as a Maven project at the start.

Error Updating Maven Configuration

I downloaded this project(to convert docs to Pdf as the project name say) https://github.com/yeokm1/docs-to-pdf-converter on github then I tried to import in Eclipse but something is wrong. I got this error.
Could not calculate build plan: Plugin org.apache.maven.plugins:maven-resources-plugin:2.6 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-resources-plugin:jar:2.6
I also have errors(I have a red cross on this file) in my pom.xml but this is my first project with maven, I'm not able to detect the problem. Here the code:
<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>docs-to-pdf-converter</groupId>
<artifactId>docs-to-pdf-converter</artifactId>
<version>1.8</version>
<build>
<sourceDirectory>src</sourceDirectory>
<resources>
<resource>
<directory>src</directory>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</resource>
</resources>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>args4j</groupId>
<artifactId>args4j</artifactId>
<version>2.32</version>
</dependency>
<dependency>
<groupId>org.docx4j</groupId>
<artifactId>docx4j</artifactId>
<version>3.2.1</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>3.12</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>3.12</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-scratchpad</artifactId>
<version>3.12</version>
</dependency>
<dependency>
<groupId>fr.opensagres.xdocreport</groupId>
<artifactId>org.apache.poi.xwpf.converter.pdf</artifactId>
<version>1.0.5</version>
</dependency>
<dependency>
<groupId>com.itextpdf</groupId>
<artifactId>itextpdf</artifactId>
<version>5.5.6</version>
</dependency>
<dependency>
<groupId>fr.opensagres.xdocreport</groupId>
<artifactId>org.odftoolkit.odfdom.converter.pdf</artifactId>
<version>1.0.5</version>
</dependency>
<dependency>
<groupId>fr.opensagres.xdocreport</groupId>
<artifactId>fr.opensagres.xdocreport.itext.extension</artifactId>
<version>1.0.5</version>
</dependency>
</dependencies>
</project>
I tried to see many other questions with a lot of solutions, but no one worked for me.
1) I tried to delete the .m2 folder : Not Worked
2) Try to make right click on the project and then Maven-Update Project: same error. Not Worked
3)I tried to go to WINDOW-PREFERENCE-MAVEN-INSTALLATION and then I changed Embedded with the folder that contains Maven, in my case C:\Maven Not Worked
4)I tried to go to WINDOW-PREFERENCE-JAVA-INSTALLED JREs where at the begin I just had C:\Program Files\Java\jre1.8.0_65, then I have read somewhere that I need Jdk 7, so I downloaded and install it but it doesn't work too. So, Now I have these two C:\Program Files\Java\jdk1.7.0_79 and C:\Program Files\Java\jre1.8.0_65
I also post a picture( I have not enough reputation to post two, in ordert to see also the Path Environment Variable) about the Environment variable, maybe I don't see something obvious. enter image description here
I'm sorry in advance because it could be a very easy question, but as I said above this is my first project with maven/eclipse and I'm not expert in this field.

I downloaded this project, and it compiled fine using Eclipse Mars.
It sounds like your Maven installation does not know how to go out to the internet to find artifacts. Could there be a firewall in the way?
Also, in Eclipse go to Window/Preferences/Maven/User settings. Make sure the settings.xml is the same one as used by your external Maven installation (assuming you are using an external Maven engine). For instance, I have set both the global and user config files to C:\development\tools64\apache-maven-3.3.3\conf\settings.xml
I checked my settings.xml, and there is no configuration that points to the maven central repository - Maven 3 must just know where to find it.
On the first compile, you should see lots of info messages saying that Maven is downloading artifacts. The next time you compile, these messages will not appear, as the dependencies are now cached in your local repository.

Tomcat Jersey Eclipse ClassNotFound org.glassfish.jersey.servlet.ServletContainer

I am running the hello world example.
However, I am using version 2.7.
on maven pom.xml I have
<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.mydomain.restful</groupId>
<artifactId>AdvertServer</artifactId>
<version>0.0.1-SNAPSHOT</version>
<name>Advert Server</name>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.glassfish.jersey</groupId>
<artifactId>jersey-bom</artifactId>
<version>2.7</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>2.2.4</version>
</dependency>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-web-api</artifactId>
<version>6.0</version>
</dependency>
<dependency>
<groupId>javax.ws.rs</groupId>
<artifactId>javax.ws.rs-api</artifactId>
<version>2.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.core</groupId>
<artifactId>jersey-client</artifactId>
<version>2.7</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.containers</groupId>
<artifactId>jersey-container-servlet-core</artifactId>
<version>2.7</version>
<!-- use the following artifactId if you don't need servlet 2.x compatibility -->
<!-- artifactId>jersey-container-servlet</artifactId -->
</dependency>
</dependencies>
<build>
<sourceDirectory>src</sourceDirectory>
<resources>
<resource>
<directory>src</directory>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</resource>
</resources>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.0</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
</plugins>
</build>
</project>
I tried running the servlet from command line and from withing the Server plugin on Eclipse. I get the same error:
java.lang.ClassNotFoundException: org.glassfish.jersey.servlet.ServletContainer
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1678)
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1523)
at org.apache.catalina.core.DefaultInstanceManager.loadClass(DefaultInstanceManager.java:525)
at org.apache.catalina.core.DefaultInstanceManager.loadClassMaybePrivileged(DefaultInstanceManager.java:507)
at org.apache.catalina.core.DefaultInstanceManager.newInstance(DefaultInstanceManager.java:126)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1099)
at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1043)
at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4957)
at org.apache.catalina.core.StandardContext$3.call(StandardContext.java:5284)
at org.apache.catalina.core.StandardContext$3.call(StandardContext.java:5279)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:722)
The weird thing is that I can see the class among the .jar files. The class is there.
I have even tried adding the jar skipping maven, but Tomcat won't see the class.

From
Eclipse + tomcat - ClassNotFound exception on deploy
If you have installed both the Maven Eclipse Plugin and the Maven WTP Plugin this is automatic. If you don't have these installed, go ahead and install them and then once Eclipse restarts right-click on the project and do a Maven > Update project.... This will internally change the project configuration so the Maven dependencies are copied to the /WEB-INF/lib folder on your deployment target.
If you don't want to use any of these plug-ins, then you have to go to the Project properties > Deployment Assembly configuration and add your dependencies manually, but again, this is done automatically by these plug-ins.

Just a hint...
At the end, what you are creating are good old war files... which should have your libraries under WEB-INF/lib. Have you checked if it is happening? I mean, you can create your war (Export/WAR file right clicking on the project in the project explorer), and then, through your zip application, go to that WEB-INF/lib folder in the war file, and checking that your jar files are there.
If they are not there, Eclipse is not exporting your libraries into the war file correctly.
Have you added them to your build path(java build path / Libraries and java build path / Order and export)?

Add
<packaging>war</packaging>
in your pom.xml, I experienced this problem when I momentarily change the packing to jar when by using the library via
mvn clean install
which compile it to jar and can be referenced by your other projects, which is not possible to do when your packaging is war.
When you forgot to change the packing back to war I see that exact error stacktrace comes up