Maven Clean doesn't clean the old class and generate new class - maven

Question

I am having strange issue in Maven. After doing Maven clean install, when I opened the jar file by 7 zip, inside the jar file, I can see two class files instead of one, which are an old class file and a newly compiled class file with current timestamp as per attached image.
I have tried troubleshooting such as clearing the target folder and trying to recompile, fixing a known issue of Maven compiler 3.1 (useIncrementalCompilation -yes (true)).
However it is still the same and I ran out of ideas. I am also new to Java and it's quite important to me. Any kind of help and idea from you is highly appreciated.
Trans
Classes
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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>Some Content here</groupId>
<artifactId>alert</artifactId>
<version>1</version>
<dependencies>
<dependency>
<groupId>Some Content Here</groupId>
<artifactId>processing</artifactId>
<version>2.2</version>
</dependency>
<dependency>
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
<version>1.5.6</version>
</dependency>
<dependency>
<groupId>javax.activation</groupId>
<artifactId>activation</artifactId>
<version>1.1.1</version>
</dependency>
<dependency>
<groupId>com.sun.mail</groupId>
<artifactId>javax.mail</artifactId>
<version>1.5.6</version>
</dependency>
<dependency>
<groupId>sax</groupId>
<artifactId>sax</artifactId>
<version>2.0.1</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.6</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<version>2.5</version>
</dependency>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-api</artifactId>
<version>6.0</version>
</dependency>
</dependencies>
<build>
<sourceDirectory>src/main/java</sourceDirectory>
<resources>
<resource>
<directory>src/main/resources</directory>
</resource>
</resources>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>
</build>
</project>
Log
[INFO] javax/transaction/UserTransaction.class already added, skipping
[INFO] META-INF/maven/ already added, skipping
[INFO] META-INF/maven/javax.javaee.api/ already added, skipping
[INFO] META-INF/maven/javax.javaee.api/javaee.api-compact/ already added, skipping
[INFO] META-INF/maven/javax.javaee.api/javaee.api-compact/pom.xml already added, skipping
[INFO] META-INF/maven/javax.javaee.api/javaee.api-compact/pom.properties already added, skipping
[INFO] DBConnect.properties already added, skipping
[INFO] EmailSetting.properties already added, skipping
[INFO] SourceConnect.properties already added, skipping
[INFO]
[INFO] --- maven-install-plugin:2.4:install (default-install) # alert ---
[INFO] Installing C:\AA\alert\target\alert-1.jar to C:\Users\AA\.m2\repository\com\bb\automation\alert\1\alert-1.jar
[INFO] Installing C:\AA\alert\pom.xml to C:\Users\AA\.m2\repository\com\bb\automation\alert\1\alert-1.pom
[INFO] Installing C:\AA\alert\target\alert-1-jar-with-dependencies.jar to C:\Users\AA\.m2\repository\com\bb\automation\alert\1\alert-1-jar-with-dependencies.jar
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 5.371 s
[INFO] Finished at: 2018-03-13T10:47:07+08:00
[INFO] Final Memory: 39M/404M
[INFO] ------------------------------------------------------------------------
Effective POM
<?xml version="1.0"?>
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<modelVersion>4.0.0</modelVersion>
<groupId>Some Content Here</groupId>
<artifactId>alert</artifactId>
<version>1</version>
<dependencies>
<dependency>
<groupId>Some Content Here</groupId>
<artifactId>processing</artifactId>
<version>2.2</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
<version>1.5.6</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>javax.activation</groupId>
<artifactId>activation</artifactId>
<version>1.1.1</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.sun.mail</groupId>
<artifactId>javax.mail</artifactId>
<version>1.5.6</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>sax</groupId>
<artifactId>sax</artifactId>
<version>2.0.1</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.6</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<version>2.5</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-api</artifactId>
<version>6.0</version>
<scope>compile</scope>
</dependency>
</dependencies>
<repositories>
<repository>
<snapshots>
<enabled>false</enabled>
</snapshots>
<id>central</id>
<name>Central Repository</name>
<url>https://repo.maven.apache.org/maven2</url>
</repository>
</repositories>
<pluginRepositories>
<pluginRepository>
<releases>
<updatePolicy>never</updatePolicy>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
<id>central</id>
<name>Central Repository</name>
<url>https://repo.maven.apache.org/maven2</url>
</pluginRepository>
</pluginRepositories>
<build>
<sourceDirectory>C:\AA\alert\src\main\java</sourceDirectory>
<scriptSourceDirectory>C:\AA\alert\src\main\scripts</scriptSourceDirectory>
<testSourceDirectory>C:\AA\alert\src\test\java</testSourceDirectory>
<outputDirectory>C:\AA\alert\target\classes</outputDirectory>
<testOutputDirectory>C:\AA\alert\target\test-classes</testOutputDirectory>
<resources>
<resource>
<directory>C:\AA\alert\src\main\resources</directory>
</resource>
</resources>
<testResources>
<testResource>
<directory>C:\AA\alert\src\test\resources</directory>
</testResource>
</testResources>
<directory>C:\AA\alert\target</directory>
<finalName>alert-1</finalName>
<pluginManagement>
<plugins>
<plugin>
<artifactId>maven-antrun-plugin</artifactId>
<version>1.3</version>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.2-beta-5</version>
</plugin>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.8</version>
</plugin>
<plugin>
<artifactId>maven-release-plugin</artifactId>
<version>2.3.2</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.2-beta-5</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</execution>
</executions>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<version>2.5</version>
<executions>
<execution>
<id>default-clean</id>
<phase>clean</phase>
<goals>
<goal>clean</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>2.6</version>
<executions>
<execution>
<id>default-testResources</id>
<phase>process-test-resources</phase>
<goals>
<goal>testResources</goal>
</goals>
</execution>
<execution>
<id>default-resources</id>
<phase>process-resources</phase>
<goals>
<goal>resources</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<executions>
<execution>
<id>default-jar</id>
<phase>package</phase>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<executions>
<execution>
<id>default-compile</id>
<phase>compile</phase>
<goals>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>default-testCompile</id>
<phase>test-compile</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.12.4</version>
<executions>
<execution>
<id>default-test</id>
<phase>test</phase>
<goals>
<goal>test</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-install-plugin</artifactId>
<version>2.4</version>
<executions>
<execution>
<id>default-install</id>
<phase>install</phase>
<goals>
<goal>install</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-deploy-plugin</artifactId>
<version>2.7</version>
<executions>
<execution>
<id>default-deploy</id>
<phase>deploy</phase>
<goals>
<goal>deploy</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-site-plugin</artifactId>
<version>3.3</version>
<executions>
<execution>
<id>default-site</id>
<phase>site</phase>
<goals>
<goal>site</goal>
</goals>
<configuration>
<outputDirectory>C:\AA\alert\target\site</outputDirectory>
<reportPlugins>
<reportPlugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
</reportPlugin>
</reportPlugins>
</configuration>
</execution>
<execution>
<id>default-deploy</id>
<phase>site-deploy</phase>
<goals>
<goal>deploy</goal>
</goals>
<configuration>
<outputDirectory>C:\AA\alert\target\site</outputDirectory>
<reportPlugins>
<reportPlugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
</reportPlugin>
</reportPlugins>
</configuration>
</execution>
</executions>
<configuration>
<outputDirectory>C:\AA\alert\target\site</outputDirectory>
<reportPlugins>
<reportPlugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
</reportPlugin>
</reportPlugins>
</configuration>
</plugin>
</plugins>
</build>
<reporting>
<outputDirectory>C:\AA\alert\target\site</outputDirectory>
</reporting>
</project>

Answer 1

I have fixed the issue by Purging local repository dependencies of the project. As per plugin documentation,
The default behaviour of the plugin is to first resolve the entire dependency tree, then delete the contents from the local repository, and then re-resolve the dependencies from the remote repository.
It's working well now!! Cheers!!
https://snag.gy/qvzoAL.jpg
https://maven.apache.org/plugins/maven-dependency-plugin/examples/purging-local-repository.html
mvn dependency:purge-local-repository
Credit:
A guy from other community called Martijn advised me to remove .m2 repo, but as i am afraid to delete .m2 repo, instead i used that plugin to remove dependencies from local repo of the project after reading multiple online resources.
https://snag.gy/FcdBqz.jpg