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Jenkins meven Java Import working giving differnt path

I have a a java class looking for another project using an import.
import this.is.the.java.file.im.looking.for
I run off a pom.xml file using a maven build in eclipse and it's working fine using the m2e plugin. When i try to run it on jenkins using the maven integration plugin it says it can't find the file because it's looking into the same project folder instead of the dependency project.

Maven configured on jenkins also requires appropriate settings.xml to fetch dependencies it required. There might be possibility that due to inappropriate settings.xml file , maven won't be able to fetch dependencies.
Please make sure settings.xml at in jenkins installation directory e.g. /var/lib/jenkins for ubuntu.
also check whether settings.xml under .m2 folder in your jenkins installation directory.
and finally validate whether there is jar file fetched in local maven repository under .m2 directory.

project will treat maven dependency as a folder instead of a jar file and on run time gives ClassNotFoundError

In my maven project, I have this dependency which is my own project that is installed in my local maven (through cmd mvn install):
<dependency>
<groupId>com.myproject</groupId>
<artifactId>api-core</artifactId>
<version>1.0.0</version>
</dependency>
However when I start the tomcat server, I will get ClassDefNotFoundError on the classes within this project.
I tried to add the jar to the deployment assembly through the project's properties, however when I add this jar file, it is taken as a folder and will always be placed into the Deploy path of "WEB-INF/lib/core.api.1.0.0.jar" which is then a folder inside the lib, therefore tomcat isn't able to locate the jar file. I also noticed in the Web Deployment Assembly, the Maven Dependencies are deployed to WEB-INF/lib. Apparently my own jar file is not considered Maven Dependencies when it is being deployed. When I further look into the Maven Dependencies from Eclipse, the jar file is packed inside as "core" folder and it is not treated as a jar file. Therefore on run time, the web app has trouble locating the jar file and is giving me complain.
Further investigation shows that in Eclipse, I have the core project imported, and Eclipse is "smart" to recognize that project is the one generating the dependency, and therefore automatically convert the jar to the folder. If I remove the core project, the maven dependencies will then successfully added as a jar file, and then the deployment to tomcat issue not problem at all!
So, my question is, is it a way to keep the dependency in folder structure, while I can still have to core project imported to my workspace?

Yes, there is one: Show up the contextual menu of the web project, go to the Maven tab and uncheck the Resolve dependencies from workspace projects option: In this way, Eclipse will not interfere in Maven's dependency resolution chain.

Why isn't my war file containing all of the contents?

I have a web application. I have created a war file out of the "export" option from Eclipse. However, the war file only contains the META-INF and the WEB-INF folders. There are no .java or .class files at all.
I also tried another method using the Maven "clean install" goals. This one also gives me the exact problem as above. Where am I going wrong? Can someone help me out?
Thanks.

Please chcek if you have your code in default src path for maven (src\main\java)

If your project is an Eclipse project you need to make sure you created it as a 'Dynamic Web Project' so Eclipse attaches the right Facets so it knows how to build the .war.
If it's a maven project, you at least include
<packaging>war</packaging>
so Maven knows how to package your app.
If you run 'mvn package', assuming your pom.xml is configured correctly, you should get a .war file created in the target dir.
Sounds like something is not configured right - can you share more info about your source project structure and how it is configured?

Java Dynamic Web project with Maven and Eclipse

I have several questions about creating a Java Web application with Maven and Eclipse:
How do I create a Java web project with servlets, jsp, and other classes with Maven?
It creates a simple directory structure, src->main->java. Where and how do I put the web-inf folder?
Do I need to add the jdbc-drivers manually to the folder inside the web-inf/lib, or is it ok just to point out the dependency?
Is there a way to test the servlets with junit?

Wow that's a lot of questions at once. I admit that setting up a webapp project with Maven and Eclipse can be tricky, so I'll try to answer them all.
Creating a Web application project with Maven
How do I create a java web project with servlets jsp and other classes with maven? It creates a simple directory structure, src->main->java.
When you are creating a Java web project, the final product should be a WAR or EAR file. WAR and EAR files are JAR files with a specific structure that can be deployed in an application server or servlet container.
As mentioned, the easiest way to set up a Maven project for web applications is to use archetypes:
mvn archetype:generate -DarchetypeArtifactId=maven-archetype-webapp
If we create a project with this archetype then a simple directory structure and pom.xml are generated. This project follows the standard Maven directory layout you mention, with /src/main/java/, /src/test/java, etc. Maven generates the WAR file from this structure with the war:war goal.
Note that this archetype is for a very simple (outdated) web application, but it's the best available starting point. You probably want to discard the web.xml file and create a new one that supports Servlet 3.0.
WEB-INF location
Where and how do I put the web-inf folder?
By default, Maven expects resources that should go in the root of the WAR file -- such as images, html pages and the WEB-INF directory -- to reside in /src/main/webapp/. So the WEB-INF folder should be located at /src/main/webapp/WEB-INF/. If you use the maven-archetype-webapp this directory is automatically created, along with a sample web.xml file.
Eclipse integration
You mentioned Eclipse in the question title, and it is indeed possible to develop Mavenized web applications in Eclipse with the m2eclipse plugin. Eclipse has good support for Web applications through WTP (Web Tools Platform).
Although many guides on the internet (wrongly) recommend it, you should not use the mvn eclipse:eclipse command to create the Eclipse project. This plugin can only generate WTP projects for very old Eclipse versions (WTP 2.0 is the maximum). Instead, use the m2eclipse plugin as described here.
Dependencies
Do I need to add the jdbc-drivers manually to the folder inside the web-inf/lib, or is it ok just to point out the dependency?
There is no need to do this manually, since one of the key strengths of Maven is dependency management. If you add a dependency in the pom.xml with a scope of compile or runtime, the JAR file will be automatically included in the WEB-INF/lib/ directory of the WAR file. For example to add the Postgresql JDBC driver dependency, add this to your pom.xml:
<dependency>
<groupId>postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>9.1-901.jdbc4</version>
</dependency>
Since the scope is unspecified Maven will assume it is in the the default scope compile. The result is that Maven will include WEB-INF/lib/postgresql-9.1-901.jdbc4.jar in the WAR file.
Testing
Is there a way to test the servlets with junit?
This question has been asked (and answered) on Stackoverflow:
Unit testing a Java servlet
Unit testing servlets
References
Hello World with JSF 2.0, Glassfish 3, Maven, SVN and Eclipse.

You should create a project based on the webapp Maven archetype, not the default one you're using.
I'm using SpringSource Tool Suite, which, for this exercise, is the same as Eclipse with m2e. Create a new Maven project and make sure you select the following archetype:
The Maven the command-line way of doing this is:
mvn archetype:generate -DgroupId=com.mycompany.app -DartifactId=my-webapp -DarchetypeArtifactId=maven-archetype-webapp
This archetype will put the WEB-INF folder in the correct location (under src/main/webapp).
You can find more information at http://maven.apache.org/guides/mini/guide-webapp.html

Just create a normal "Dynamic Web Project". Then right click the project name and select Configure > Convert To Maven Project. It can take up to a minute to complete the conversion, so be patient. See the following article:
http://aykutakin.wordpress.com/2013/12/04/create-eclipse-dynamic-web-project-with-maven-2/
If that doesn't work, try this:
http://crunchify.com/how-to-create-dynamic-web-project-using-maven-in-eclipse/

Step 1: create your web app folder.
Step 2: Move to that folder in command prompt.
Step 3: use following command:
mvn archetype:generate -DgroupId=com.helloworld -DartifactId=HelloWorldDemo -DarchetypeArtifactId=maven-archetype-webapp -DinteractiveMode=false
DarchetypeArtifactId=maven-archetype-webapp will create a maven web project.
Step 4: Now on command prompt go inside the project folder and use this command:
mvn eclipse:eclipse -Dwtpversion=2.0 to make your project a dynamic web project for eclipse, now import this newly created project as an "Ëxisting project"
Use m2eclipse plugin of eclipse to enable MAVEN in eclipe.
Web.xml will be at \src\main\webapp\WEB-INF

How to have tomcat use folder with extension .jar as jar files?

I have in Eclipse web application project that depends from other projects.
When I run debug on embedded Tomcat in lib folder that Eclipse copied not jars, but folders with names like:
dependent_lib1.jar
dependent_lib2.jar
dependent_lib3.jar
....................
So web application don't start because didn't found some files. When I manually deleted all these folders and manually copy jar files - all works.
Does it possible ask Eclipse (or maven - this is maven project) to copy jars or ask Tomcat use folders like jars?
Thanks.

Here is how I think it should be done with maven:
If the other projects are also maven projects, export them as maven artifacts in your local repository. A nice article is Maven Deploy Plugin - If they are not maven projects you should manually generate the jar files and add them to the repository, some information can be found at Best way to create a maven artifact from existing jar
Add the exported artifacts as dependencies to your project. A lot of details can be found at Introduction to the Dependency Mechanism
Hope this helps.

Eclipse cannot do it as its just an IDE, you would need use A BUILD SCRIPT using ANT(Copy tag should do it) and run it before you start your server.
Check this for more details:
http://www.javabeat.net/tips/103-writing-simple-ant-build-script.html