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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.

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.

Why does "WEB-INF/lib" folder appear to be empty after a Maven project is built within Eclipse?

i followed this spring-mvc-tutorial using eclipse, but after i call Maven / Update Projects my WEB-INF/lib directory remains empty.
this is how my project explorer looks:
i also see no mistake in my Deployment Assembly settings:
this is the pom.xml file i use:
<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>CrunchifySpringMVCTutorial</groupId>
<artifactId>CrunchifySpringMVCTutorial</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>war</packaging>
<dependencies>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>4.2.0.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-aop</artifactId>
<version>4.2.0.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
<version>4.2.0.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
<version>4.2.0.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>4.2.0.RELEASE</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>jstl</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>1.2</version>
</dependency>
</dependencies>
<build>
<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>2.4</version>
<configuration>
<warSourceDirectory>WebContent</warSourceDirectory>
<failOnMissingWebXml>false</failOnMissingWebXml>
</configuration>
</plugin>
</plugins>
</build>
i even switched to a new workspace as suggested in this link, but nothing helped
EDIT:
when i start the server i get the error:
java.lang.ClassNotFoundException: org.springframework.web.servlet.DispatcherServlet

Eclipse virtually hides the files from the view that displays the WEB-INF/lib folder in a Maven-managed Dynamic Web-Project project. As your first screenshot indicates, the "Maven Dependencies" library entry has been successfully added to your classpath in the background by Eclipse - it contains every dependency referenced in your pom.xml.
The intention behind this behavior for that is/might be: You - as a developer - are not supposed to copy any .jar files manually to WEB-INF/lib, cause that way you would kind of cheat around the idea behind a (Maven-) managed project.
In a certain way, this makes sense as Maven performs any dependency management for you and thus resolves and "bundles" any third-party (or your own) artifacts.
If you run a mvn with the goals clean package (or even: clean install) it will produce a .war file for you in the "target" folder of your project. If you extract that .war file you should find a WEB-INF/lib folder that contains all dependencies bundled into your deployable artifact.

I think it is correct.
Libraries are copied into target after build, not into project itself.
Also Step 8 in the tutorial you pasted shows the same (empty lib folder)

Maven JAR - class not found exception

I created a maven war project and added javaEE API and openCSV.
in eclipse I can see both jars, import classes and use them without any compilation errors.
but when I run the app using tomcat and trying to save a CSV file I get this exception:
java.lang.NoClassDefFoundError: au/com/bytecode/opencsv/CSVWriter
JavaEE api works fine.
I tryed to add compile but it didn't do any good.
this is my pom:
<modelVersion>4.0.0</modelVersion>
<groupId>com.training</groupId>
<artifactId>DevProject</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>war</packaging>
<dependencies>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-api</artifactId>
<version>7.0</version>
</dependency>
<dependency>
<groupId>net.sf.opencsv</groupId>
<artifactId>opencsv</artifactId>
<version>2.3</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
</configuration>
</plugin>
</plugins>
</build>
This is the code that throws the exception:
CSVWriter writer = new CSVWriter(new FileWriter("file.csv"));
Any ideas?

The default java ee api's are um...messed up.
They are not meant to actually run stuff but only to compile stuff, they don't actually have any content because of some copyright or whatever issue that I forgot about.
So when you define the dependency you should state:
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-api</artifactId>
<version>7.0</version>
<scope>provided</scope>
</dependency>
Note that additional "scope" and add an actual implementation to your runtime.
Alternatively (what I often do to allow for testcases) you could include an actual implementation like that of jboss.

Try this:
Right click on the eclipse project containing your pom
Click on Properties
Click on Deployment Assembly
Then check that your Maven Dependencies are in the list and that the deploy path in front of them is WEB-INF/lib
Click the Add... button if necessary then Click Apply and OK buttons.