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Maven project not treated as a java project in eclipse

I have maven plugin installed for my eclipse of version (Oxygen).
I have the following added to my pom.xml -
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<configuration>
<downloadSources>true</downloadSources>
<downloadJavadocs>true</downloadJavadocs>
</configuration>
</plugin>
I can go to my project and click Maven -> Update Project and it updates it.
Still it is not treated as a java project though. When I am trying add a new package or a class, I get the error "Source folder is not a Java project.". Could someone please provide me pointers? Appreciate any help in advance!

You can first create a java project and right-click the project at Package-Explorer view, select Configure>Convert to Maven Project, then you can use maven dependency.

Setting classpath for a java project with many libraries and external resources in command line

I have the following project. It has some property files in the conf folder, some data in the data folder, some jar files in the lib folder and also some external libraries that are not shown in the photo due to size limitation. Imagine I want to run the RecDriver class. How exactly should I set the classpath so that I can run it in command line? This is how I did it but it does not work as it cannot fine some other files in the project.
C:\Users\myUserName\Downloads\librec-2.0.0\librec-2.0.0\core\src\main\java\net\librec\tool\driver> javac RecDriver.java
The project can be downloaded here:
https://github.com/guoguibing/librec

You can use bin/librec or bin/librec.cmd to run it from commandline.
If you want to build your launch command you can see those start scripts and adapt them for your purposes.

To run your app through command line, once you have the .class files in some dir (usually build) all you have to do is run your application with java -cp "path where jvm can find every .class that you project needs" MainClass.
The -cp flag only tells where to look for compiled .class files, since you are using IntellIJ you can see the command it runs when executing your program, there is a class path that it uses.
Class Path points to where your .class files are, they can be in separate folders, but you need to include every dir when giving the class path, separated by ";"
Example taken from another question in SO.
java -cp "Test.jar;lib/*" my.package.MainClass

Three things to do:
Use the Maven Shade Plugin to create a fat jar (jar with dependencies)
Use the Maven-Jar-Plugin to make the Jar executable
Set <project><build><finalName> to ${artifactId}
Now, after your build ran successfully, you can run your app with
java -jar target/YourArtifactId.jar
(Substitute your project's artifactId for "YourArtifactId")
Okay, here's the full setup.
Add a build section like this to your pom.xml (merge it with any existing one).
<build>
<plugins>
<!-- number 1 -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.0.0</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<minimizeJar>true</minimizeJar>
</configuration>
</execution>
</executions>
</plugin>
<!-- number 2 -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>fully.qualified.MainClass</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
<!-- number 3 -->
<finalName>${project.artifactId}</finalName>
</build>

replace classes with library classes

I have a quite large amount of java sources (an open Source Project), where i want to "patch" some class files with my own for debugging pruposes, without touching the original code.
So I made Patch-Project where i altered eg. com.package.abc.java
Now i want to tell eclipse and/or maven to build the original Project, but overwirte its own (original) com.package.abc.java from /src with the patched abc.java from my second Project, which i exported as a library.jar and added to /libs in the original Project.
The Stucture looks like this
Original:
/src
com/package/
abc.java
def.java
/libs
patch.jar
patch:
/src
com/package/
abc.java
How do i do this with eclipse and maven plugin?

Side-Node: This would be a perfect case for Dependency injection.
But to solve your problem, use the maven compiler plugin and edit the pom of the open source project:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<excludes>
<exclude>**/src/main/java/com/package/abc.java</exclude>
</excludes>
</configuration>
</plugin>
Edit: If you don't want to edit the pom of the original project (this is a bit hacky in my opinion):
Create a profile in your ~/.m2/settings.xml which contains the plugin configuration:
<profiles>
<profile>
<id>ig</id>
<plugins>
<!-- snippet from above -->
</plugins>
</profile>
</profiles>
and then build the open source project with this profile:
mvn -Pig verify

creating jar file of maven projects with netbeans

I am using netbeans to work on a project. I am using svn, so that I can commit to newer versions and revert to an older version in case I mess up. Now I want to create a jar file of this project but the build tab in the project properties does not display the packaging option, it only displays one option and that is of 'compile'.
If I create a new project (Java Application) it does show the packaging option and then I can easily create a jar file, but this maven project that I am working on does not work like this.
Please suggest me a way to create jar file out of my maven project.
Thanks,

Based on #yatskevich answer, you could go to your NetBeans Project Properties > Actions and add package to the Execute Goals of the following Actions:
Build project
Clean and Build project
Build with dependencies
Plus any other you feel should also package
I did this on NetBeans 7.2.1
PS: this will create the JAR on every change you make, so choose wisely where to add package. I don't mind it building a JAR for small projects on every build.

Open cmd (if you are on Windows) or any shell (if you are on Linux)
Navigate to your project directory (use cd command)
Run mvn clean package there.
Your jar will be in <project dir>/target.

Include maven-assembly-plugin plugin in your .pom file. It will instruct Maven to assemble your application with all it's dependencies.
Later when you will build your Netbeans project you will see your newly builded jar with all it's dependencies.
<build>
<sourceDirectory>src</sourceDirectory>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.4</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>com.my.class</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
Check out to learn more about creating Jar file with Maven: https://javatutorial.net/create-java-jar-file-with-maven

create eclipse groovy-java project with maven

I have a Java-Groovy Eclipse project that I build with Maven. I have added the Maven Groovy plugin to the pom.xml such that I can build/test the Java and Groovy sources on the command-line using Maven.
I would like to have some way to automatically generate the Eclipse .project and .classpath files from my pom.xml. If I run mvn eclipse:eclipse it seems to assume that it's a Java project, so there's no way to (for example) run the tests in src/main/groovy from within Eclipse.
I'm using the STS Eclipse distribution, which includes support for Groovy/Grails. All I'm missing is a way to automatically create the appropriate .classpath and .project files.
Thanks!
P.S. I know IntelliJ is better, but I don't have a license

Here is configuration I found that works when Java calls Groovy code
and when Groovy calls Java code fitting good within groovy eclipse IDE plugin (nature).
There is no need for additional source folders for groovy. It just works!
Using:
mvn clean install eclipse:clean eclipse:eclipse
<dependencies>
<dependency>
<groupId>org.codehaus.groovy</groupId>
<artifactId>groovy-all</artifactId>
<version>2.0.4</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
<compilerId>groovy-eclipse-compiler</compilerId>
<verbose>true</verbose>
<extensions>true</extensions>
</configuration>
<dependencies>
<dependency>
<groupId>org.codehaus.groovy</groupId>
<artifactId>groovy-eclipse-compiler</artifactId>
<version>2.7.0-01</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<version>2.9</version>
<configuration>
<additionalProjectnatures>
<projectnature>org.eclipse.jdt.groovy.core.groovyNature</projectnature>
</additionalProjectnatures>
<sourceIncludes>
<sourceInclude>**/*.groovy</sourceInclude>
</sourceIncludes>
</configuration>
</plugin>
</plugins>
</build>

You should try the Groovy-Eclipse m2eclipse integration. It is available here:
http://dist.codehaus.org/groovy/distributions/greclipse/snapshot/e3.6/
With this installed, your maven projects will be automatically configured as groovy-eclipse projects when you import them into your workspace.

If you would like to create a Groovy project just by calling mvn eclipse:eclipse you have to configure your project. As follows a snippet how you configure your maven eclipse plugin so that your project becomes a Groovy project in Eclipse. That snippet must go into your projects pom.xml by the way.
...
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<configuration>
<additionalProjectnatures>
<projectnature>org.eclipse.jdt.groovy.core.groovyNature</projectnature>
</additionalProjectnatures>
<sourceIncludes>
<sourceIncludes>**/*.groovy</sourceIncludes>
</sourceIncludes>
</configuration>
</plugin>
</plugins>
</build>
...
When you now call mvn eclipse:eclipse maven creates the .project and .classpath files. .project contains the new project nature what makes it a Groovy project and .classpath contains the */*.groovy* what makes Eclipse treating any file that ends on .groovy as a source file.
Please see also http://maven.apache.org/plugins/maven-eclipse-plugin/examples/provide-project-natures-and-build-commands.html

There is another best way to create maven groovy project. Please follow below steps:
Navigate to https://start.spring.io/ from your browser.
Select project as maven and language as groovy as shown below.
Select other options as per your build requirement like packaging, java version and project name.
Now click on Generate radio button at the bottom and a maven groovy project will be downloaded.
Open Eclipse and import the downloaded maven project and it's ready to use for your groovy scripting with maven integration.