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How do I package this maven project or Java Application?

I'm creating a new project that run as a Java application(.jar), but I am confused about how to package the lib folder into the final jar file.
And I try to use Maven, but did not found some eligable plugins.
The project structure is here
first, I try to package with IDEA's build Artifact. it will extract all jar file into final jar and create a MANIFEST file, but the impact is there are some file like "*.SF, *.RSA", it destory the java -jar xxx.jar, But we can solve it by delete these .sf/.rsa file. Next problem occur, cause I use some springframework dependency, when extract these jar file, they will create a file like spring.handles, but its not complete.
second, I try to use MAVEN. I use the maven-jar-plugin maven-compiler-plugin maven-dependency-plugin to copy all jar file into final jar, and create the correct MANIFEST file. BUT a java.lang.NoClassDefFoundError occur, I am DEAD!!!
So, the actual question is how can I package the lib folder into final executable jar???

Java export running jar w/ project

So, I've added a git repo to my project (sjxlsx). I've then right-clicked the repo and imported into the package explorer. I then went to Project->Build path in order to make sure it's on "Required projects on the build path".
When I debug on Eclipse, works just fine.
I'm now trying to export as a running jar and when I execute it outside of Eclipse, it somehow is giving an error (empty.xlsx not found). That is, because in the XLSXWriterSupport, the open method is fetching this empty.xlsx file. On debug, it's working as expected but on converting to a running jar, it's giving me this error.
This is due to this 'empty.xlsx' file being on the resources of the other project. How can I solve this?
https://github.com/davidpelfree/sjxlsx/blob/master/src/main/java/com/incesoft/tools/excel/support/XLSXWriterSupport.java

This is because a resource on the class path is not a File on the file system.
Here it is packed in a jar (zip format).
The wrong code:
if (getClass().getResource("/empty.xlsx") == null) {
throw new IllegalStateException("no empty.xlsx found in classpath");
}
workbook = new SimpleXLSXWorkbook(new File(getClass().getResource("/empty.xlsx").getFile()));
As SimpleXLSXWorkbook has only a File constructor (AFAIK), you need to create a temporary file.
Path tempPath = Files.createTempFile("sjxlsx-", ".xlsx");
Files.copy(getClass().getResourceAsStream("/empty.xlsx"), tempPath);
workbook = new SimpleXLSXWorkbook(tempPath.toFile());
Better have some provision to delete temp files, for instance creating them in a specific directory, see Files.

You probably have the Eclipse Project build path configured to use absolute library references. When you try to run your runnable jar, the jvm cannot find the required dependencies.
Edit:
If you want to export your software as a RUNNABLE jar file, then the jar must contain a MANIFEST file which specifies the dependencies and main class. Example:
Manifest-Version: 1.0
Main-Class: com.example.Main
Class-Path: lib1.jar lib2.jar
(assuming your main class is com.example.Main)
In order to run your runnable jar file, place lib1 and lib2 on the same directory as your runnable jar and run:
java -jar myJar.jar
Otherwise you could just compile your main class and run it like this (assuming lib1 and lib2 are copied into a lib/ dir on your main class root path):
java -cp '.:/libs/*.jar' com.example.Main
You could also use a dependency manager tool such as maven and configure your build to create an "uberJar":https://maven.apache.org/plugins/maven-shade-plugin/examples/includes-excludes.html
uberJars contain all your software dependencies in one heavy runnable jar file.
Hope this helps.

How to resolve classes with source src-jar library in Eclipse?

I have added this jar file to my project's build path under "libraries":
http://sunet.dl.sourceforge.net/project/jeplite/jeplite/jeplite-0.8.7/jeplite-0.8.7a-src.jar
and cannot get Eclipse to resolve ANY of the included classes.
Packages are visible, but no classes.
Error message is:
"JEP cannot be resolved to a type"

In eclipse, it should be on the build path if its a source tree .... Remember , a jar is just a glorified zip file, so be sure that the binaries are actually in your jar file. The steps to test are
1) unzip the jar file
2) if its source : then either try adding it to your build path, or just directly import the source folders into your project
3) if you see class files in the jar, then it should be okay to add them to "libraries"

This is only a jar containing the source code. You need a jar with the compiled classes in it. Try the jeplite-0.8.7a-bin.jar.

Making a JAR file which includes all files of a cetain type from any subdirectory

So this is a simplified version of my package structure
Project 1
-folder1
-folder2
-folder21
-folder211
-test3.java
-folder22
-folder3
-test4.java
-Project2
-folder1
-folder11
-folder111
-Test.java
-folder2
-.properties
-Test2.java
-folder3
What I want to find is command that will create a jar and take the paths to project1 and project2 and recursively add the folder structure and java files without adding the .properties files.
What i've tried so far is
jar cvf test.jar "pathtoproject1/.java" "pathtoproject2/.java"
That only works for java files in the base project directories not the subfolders.
Anyone know how to do this?
edit
This is for a batch script on windows

Frankly I'm not sure that jar handles this out of the box.
I suggest using ant - with an ant jar task, using a fileset.

Java - jar with librairies included

I am currently trying to make a Jar with all my libraries included.
What I have done.
I have created folders like this :
main folder
class (which contain all my classes)
ressources (containing all my libraries : mongo, jedis...)
MANIFEST.MF
My main class is named process.
My manifest is like this:
Main-Class: process
Class-Path: ressources\commons-pool-1.5.6.jar ressources\jedis-2.0.0.jar resources\mongo-2.6.3.jar class
I have generated the JAR with this command :
jar cvmf MANIFEST.MF process.jar class/*.class ressources/*.jar
My problem : When executing the JAR I have still the message
Exception in thread "main" java.lang.NoClassDefFoundError: process
Any ideas ?

Are you using eclipse? If yes, it have an option in export to export libraries together with jar..
with netbeans, I dont know how to do it.

You could build your jar with Ant using zipfilesets to copy in the content of the other jars (rather than the jars themselves), or you could take a look at jarjar which does that and more.

Eclipse: You have to add the external jar files to the build.properties, otherwise they are no tpart of the generated jar file.
Ar the libraries included in the jar file, you have generated?