Maven: Files missing under classes in maven build

Bear with me, am new to Maven. So, I have this project checked in with the following structure-

-WebContent
-src
-pom.xml

When I build this project through the command line, using the command-

mvn clean
mvn package

and I get a target folder with a .war file which I deployed to the tomcat server. My project UI is displayed but no APIs get called. But when I import the same project to Eclipse IDE and build it, I notice there are an extra set of files and folders-

• build
• .classpath
• ImportedClasses
• .project
• .settings

As well as an extra set of .xmls under classes in the target dir.

This is my pom.xml-

<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>GenericApp</groupId>
<artifactId>GenericApp</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>war</packaging>

<dependencies>

    <dependency>
        <groupId>org.glassfish.jersey.media</groupId>
        <artifactId>jersey-media-json-jackson</artifactId>
        <version>2.22.1</version>
    </dependency>
    <dependency>
        <groupId>asm</groupId>
        <artifactId>asm</artifactId>
        <version>3.3.1</version>
    </dependency>
    <dependency>
        <groupId>org.glassfish.jersey.core</groupId>
        <artifactId>jersey-server</artifactId>
        <version>2.22.1</version>
    </dependency>
    <dependency>
        <groupId>org.glassfish.jersey.containers</groupId>
        <artifactId>jersey-container-servlet</artifactId>
        <version>2.22.1</version>
    </dependency>
    <dependency>
                   <groupId>javax.servlet</groupId>
                   <artifactId>javax.servlet-api</artifactId>
                   <version>3.0.1</version>
                   <scope>provided</scope>
           </dependency>
    <dependency>
        <groupId>org.glassfish.jersey.media</groupId>
        <artifactId>jersey-media-multipart</artifactId>
        <version>2.22.1</version>
    </dependency>

    <dependency>
        <groupId>com.google.code.gson</groupId>
        <artifactId>gson</artifactId>
        <version>2.8.0</version>
    </dependency>
    <dependency>
        <groupId>mysql</groupId>
        <artifactId>mysql-connector-java</artifactId>
        <version>5.1.6</version>
    </dependency>
    <dependency>
        <groupId>org.mybatis</groupId>
        <artifactId>mybatis</artifactId>
        <version>3.4.2</version>
    </dependency>
    <dependency>
        <groupId>commons-logging</groupId>
        <artifactId>commons-logging</artifactId>
        <version>1.2</version>
    </dependency><!-- https://mvnrepository.com/artifact/commons-net/commons-net -->
    <dependency>
        <groupId>commons-net</groupId>
        <artifactId>commons-net</artifactId>
        <version>2.0</version>
    </dependency>

    <dependency>
        <groupId>com.fasterxml.jackson.core</groupId>
        <artifactId>jackson-databind</artifactId>
        <version>2.8.2</version>
    </dependency>

    <!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.core/jackson-annotations -->
    <dependency>
        <groupId>com.fasterxml.jackson.core</groupId>
        <artifactId>jackson-annotations</artifactId>
        <version>2.8.4</version>
    </dependency>


    <dependency>
        <groupId>io.jsonwebtoken</groupId>
        <artifactId>jjwt</artifactId>
        <version>0.7.0</version>
    </dependency>


    <!-- https://mvnrepository.com/artifact/log4j/log4j -->
    <dependency>
        <groupId>log4j</groupId>
        <artifactId>log4j</artifactId>
        <version>1.2.17</version>
    </dependency>
    <!-- https://mvnrepository.com/artifact/javax.json/javax.json-api -->
    <dependency>
        <groupId>javax.json</groupId>
        <artifactId>javax.json-api</artifactId>
        <version>1.1.2</version>
    </dependency>
    <!-- https://mvnrepository.com/artifact/org.json/json -->
    <dependency>
        <groupId>org.json</groupId>
        <artifactId>json</artifactId>
        <version>20171018</version>
    </dependency>


</dependencies>

<build>
    <sourceDirectory>src</sourceDirectory>
    <plugins>
        <plugin>
            <artifactId>maven-compiler-plugin</artifactId>
            <version>3.5.1</version>
            <configuration>
                <source>1.8</source>
                <target>1.8</target>
            </configuration>
        </plugin>
        <plugin>
            <artifactId>maven-war-plugin</artifactId>
            <version>3.0.0</version>
            <configuration>
                <warSourceDirectory>WebContent</warSourceDirectory>
            </configuration>
        </plugin>
    </plugins>
</build>

Why does both builds produce seperate results from the same set of files? How do I resolve and understand this problem?

By default, maven package adds the default src by compiling and packaging them and adding default resource into the war file.

The default location for resources in maven based web-apps is: src/main/resources If your resources are at other location it will not be added to a war file.

If you wish to include another resource like any .xml file or image etc. you can mention that explicitly in pom.xml for the same.

Example: inside your build tag of add below:

<resources>
 <resource>
   <directory>[your folder here]</directory>
 </resource>

The above instruction will add the resources to the root of the folder in war WEB-INF. If you wish to add them to a specific location then you can add

<resources>
 <resource>
   <directory>[your folder here]</directory>
   <targetPath>[you target path in WEB_INF/classes</targetPath>
 </resource>

Example:

 <resource>
    <directory>src/com/ekagga/ga/config/</directory>
    <targetPath>com/ekagga/ga/config</targetPath>
    <filtering>true</filtering>
  </resource>
</resources>

Default it will add all the files like .java etc, you may need to add a filter to remove such file.