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maven war plugin does not forget about old files and dependencies and creates a war that contains removed files and dependencies

Hello I'm having a weird problem about war creation.
I use maven-war-plugin (tried with 3.1.0, 3.2.0, and 2.6). When I run war:war (or mvn clean package, or similars) the war is created but I noticed that it is like it always packages all the files and dependencies it encountered in the history of the project. I noticed this because the war file is always getting bigger and by opening it I see there are a lot of dependencies that I declared on the pom but now they are removed, and most importantly there are classes I deleted from the project! I even tried to start a new project and the result does not change.
I guess I'm using this badly... Is there something I should do to let him "forget" about the history and force it to consider the project "as it is" when creating a war?
Thanks for the help!
PS:
I always clean and compile before running war:war;
I work with IntelliJ IDEA Community 2017.3
using jdk 1.7 because of technical constraints.
Just for completeness, there is my pom.xml:
<?xml version="1.0" encoding="UTF-8"?>
<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>sduca-consumer-listener</groupId>
<artifactId>sduca-consumer-listener</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>war</packaging>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<build>
<sourceDirectory>src/main/java</sourceDirectory>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.6.0</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>3.2.0</version>
<configuration>
<webappDirectory>/sduca</webappDirectory>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<!-- Using Spring 4 because of jdk 1.7 -->
<!-- https://mvnrepository.com/artifact/org.springframework/spring-webmvc -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
<version>4.3.18.RELEASE</version>
</dependency>
<!-- https://mvnrepository.com/artifact/log4j/log4j -->
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.17</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>3.1.0</version>
</dependency>
</dependencies>
</project>
EDIT1: I tried to change versions of maven-war-plugin, maven-compiler-plugin, and Maven itself, but nothing changes.
EDIT2: I tried changing the output directory, no changes. I tried to change version of the dependencies and as "expected" now the war includes both versions, becoming bigger and bigger...
EDIT3: I reinstalled IntelliJ IDEA, upgrading to the latest version. Nothing changes, it has only reset the content of the package, but it still "keep track" of the content and dependencies and still includes removed stuff on the package when creating a new one.
EDIT4: I've started using mvn clean compile war:war instead of mvn clean package and at first things started working, but then the problem of the existing old files returned. However, I find out that if I manually remove the exceding resources and *.class from the war it looks it works (at least it's deployed).

It's just a trick worked for me many times,
Backup your dependencies from pom.xml and delete it.
Do a clean build, it will show errors in all Java classes. Also delete the previous war.
Now, replace those backed up dependencies and clean build the webapp again. All errors will be disappeared and war file will be as expected.

Maven Read properties plugin doesn't substitute values for dependencies

Following is my project structure.
test-proj
|_ src
|_main
| |_java
|_test
|_java
|_prop.properties
|_pom.xml
And 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>com.sample</groupId>
<artifactId>test</artifactId>
<version>1.0-SNAPSHOT</version>
<build>
<!-- The resources tag will be used if prop file is under src location. -->
<!-- <resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources> -->
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>properties-maven-plugin</artifactId>
<version>1.0.0</version>
<executions>
<execution>
<phase>initialize</phase>
<goals>
<goal>read-project-properties</goal>
</goals>
<configuration>
<files>
<file>${basedir}/prop.properties</file>
</files>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
<version>${spring-version}</version>
</dependency>
</dependencies>
</project>
Prop.properties file has
spring-version=3.1.0.RELEASE
I have tried to use maven-read properties plugin to read the properties and substitute the same in the place of spring version. But it throws up error saying 'dependencies.dependency.version' for org.springframework:spring-beans:jar must be a valid version but is '${spring-version}'.
I tried to use validate phase instead of initialize in the maven execution phase. But still the problem persists. Instead of context path, i tried replacing the property file location to be an absolute path D:\test-proj\prop.properties in configuration which didnt help me either. I am using maven compiler plugin version 2.3.2. Am I missing something? Please let me know if its feasible to substitute dependency versions by some other plugin as well.
Note: I will not be able to use parent-child pom relationship as all my projects are modular and they don't depend on the same parent

If you want multiple unrelated project share dependecies version you can use Bill of Material concept http://howtodoinjava.com/maven/maven-bom-bill-of-materials-dependency/
Create unrelated BOM project with packaging pom. Add shared dependencies to the project
Each your project must import the BOM project
Below is snippet from the example page
How to add BOM [Bill Of Materials] dependency
Maven provides a tag dependencyManagement for this purpose. You need to add the bom information in this tag as follows. I am taking the example of Spring bom file.
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-framework-bom</artifactId>
<version>4.0.1.RELEASE</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>
An added benefit of using the BOM is that you no longer need to specify the version attribute when depending on Spring Framework artifacts. So it will work perfectly fine.
<dependencies>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
</dependency>

I cannot imagine that this is going to work. AFAIU Maven has to resolve dependencies prior to any build execution since how should it be able to create a proper classpath for executions otherwise?
Re:
I will not be able to use parent-child pom relationship as all my projects are modular and they don't depend on the same parent.
I think you are able. Establish a super-parent POM that contains appropriate setting(s) to be inherited by all and make all your projects' parents childs of this:
+- super-parent
+- pom.xml ... containing setting(s) for all
+- parent-project-1
+- ...
+- parent-project-2
+- ...
+- ...

Classloader with Maven built jar

I am working on a project which contains a number of subprojects. The structure is something like Project 1, Project 2 and ProjectClassLoader.
Using separate configuration files, I pass in the binary names of the classes from Projects 1 and 2 that need to be loaded each time as arguments to the ProjectClassLoader project.
The ProjectClassLoader gets a handle to the system classloader
ClassLoader loader = ClassLoader.getSystemClassLoader();
which in theory allows it to load any classes which are contained in the classpath.
I'm using Maven to build the projects and handle their associated dependences. Thus each project has it's own individual pom.xml file. The ProjectClassLoader defines a parent pom.xml over Projects 1 and 2 which inherit from this. The parent pom contains dependency entries for both Project 1 and 2.
My understanding was that any dependencies specified in the pom.xml files of these projects would get added to the classpath at runtime. However when trying to load classes using the system classloader, I'm getting class not found execptions.
I have tried using the mvn:exec plugin which I understand includes the dependencies in the classpath when executing jars on the command line but this has not worked.
I'd grately appreciate any help in furthering my understanding of why I can load the classes even though the dependencies are defined in the pom...Thanks in advance

Can you check if your pom matches this configuration a bit?
<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">
...
<properties>
...
<exec.maven.plugin.version>1.2.1</exec.maven.plugin.version>
...
</properties>
<build>
<plugins>
...
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
</plugin>
...
</plugins>
<pluginManagement>
<plugins>
...
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>${exec.maven.plugin.version}</version>
<configuration>
<executable>java</executable>
<arguments>
<argument>-classpath</argument>
<!-- automatically creates the classpath using all project dependencies, also adding the project build directory -->
<classpath />
<argument>com.example.Main</argument><!-- your mainClass -->
</arguments>
</configuration>
</plugin>
...
</plugins>
</pluginManagement>
</build>
<dependencies>
...
<dependency>
<groupId>groupId.for.project1</groupId>
<artifactId>project1</artifactId>
</dependency>
<dependency>
<groupId>groupId.for.project2</groupId>
<artifactId>project2</artifactId>
</dependency>
...
</dependencies>
<dependencyManagement>
<dependencies>
...
<dependency>
<groupId>groupId.for.project1</groupId>
<artifactId>project1</artifactId>
<version>${project1.version}</version>
</dependency>
<dependency>
<groupId>groupId.for.project2</groupId>
<artifactId>project2</artifactId>
<version>${project2.version}</version>
</dependency>
...
</dependencies>
</dependencyManagement>
...
</project>
Where you fill them with the correct artifacts.
You should then be able to start it with:
mvn exec:exec
Can you post your configuration for your pom plz if it doesn't match, that way it's easier to understand what exactly you currently have in your pom.

Maven compilation error for android Project "error: package R does not exist "

I am trying to set up a MAVEN project with Android application.
I have this pom file
<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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.myproject</groupId>
<artifactId>userprofile</artifactId>
<packaging>jar</packaging>
<version>1.0-SNAPSHOT</version>
<name>userprofile</name>
<url>http://maven.apache.org</url>
<dependencies>
<dependency>
<groupId>com.google.android</groupId>
<artifactId>android</artifactId>
<version>4.1.1.4</version>
<scope>provided</scope>
</dependency>
</dependencies>
</project>
and during MAVEN compile I get this error (about 100 times, ie as many times as it is used in my methods)
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
src\main\java\com\myproject\userprofile\BaseActivity.java:[52,43] error: package R does not exist
Process finished with exit code 1
Any idea about this error? On the web I either find unanswered questions about similar error output. I have no experience on MAVEN, so I believe I am missing something here.

R class is build by your IDE during compilation. MAVEN cannot find the R class because by default the class can be found under build folder. You need to add something like this
<sourceDirectory>build</sourceDirectory>
<outputDirectory>target</outputDirectory>
telling MAVEN that you have some resource files under build folder and you want to make them available to compile so add them under the target folder which will be under your project.
so now I have
build
|----res
|----src
src
|----main
|----java
|----res
target

After a quick look, I believe you're missing the build element. Maven is building the project with current sources, R and other gen classes have not been generated yet. At least you need something like (after dependencies tag):
<build>
<finalName>${project.artifactId}</finalName>
<sourceDirectory>src</sourceDirectory>
<pluginManagement>
<plugins>
<plugin>
<groupId>com.jayway.maven.plugins.android.generation2</groupId>
<artifactId>android-maven-plugin</artifactId>
<version>3.7.0</version>
<extensions>true</extensions>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>com.jayway.maven.plugins.android.generation2</groupId>
<artifactId>android-maven-plugin</artifactId>
<configuration>
<sdk>
<!-- platform or api level (api level 16 = platform 4.1)-->
<platform>16</platform>
</sdk>
</configuration>
</plugin>
</plugins>
</build>
Also the packaging must be apk:
<packaging>apk</packaging>
I would strongly recommend to start reading the Android Maven documentation along with samples.

This error might happen if you had modify the package name that generate by archetype:generate, for me, I use android-quickstart to generate the module structure :
mvn archetype:generate \
-DarchetypeArtifactId=android-quickstart \
-DarchetypeGroupId=de.akquinet.android.archetypes \
-DarchetypeVersion=1.0.11 \
-DgroupId=com.yy.android.gameLibs \
-DartifactId=sample
akquient recommend me to use "com.yy.android.gameLibs" as package name and I accepted, I compile this module successful and worked. After that, I change the package name as "com.yy.android.sample" also change the Androidmenifest.xml package attribute, therefore the module report that error, I follow back the generate command and choice package name myself to solve this.

Modify packaging to apklib, like this:
<packaging>apklib</packaging>
And add build goal at end of pom.xml like this:
<dependencies>
<!--Android deps -->
<dependency>
<groupId>com.google.android</groupId>
<artifactId>android</artifactId>
<version>4.0.1.2</version>
<scope>provided</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>com.jayway.maven.plugins.android.generation2</groupId>
<artifactId>android-maven-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<sdk>
<platform>17</platform>
</sdk>
</configuration>
<extensions>true</extensions>
</plugin>
</plugins>
</build>

I'm having troubles to compile a maven project

I've imported my project into Eclipse (Helios + m2eclipse), and also into Netbeans (7.0) and in both IDEs one of the troubles is:
This is what I get in Netbeans when I try to build.
The project com.miCompany:myProject:1.0 (.....) has 1 error
Unresolveable build extension: Plugin
org.apache.axis2:axis2-wsdl2code-maven-plugin:1.3
or one of its dependencies could not
be resolved: Failed to collect
dependencies for
org.apache.axis2:axis2-wsdl2code-maven-plugin:jar:1.3
(): Failed to read artifact descriptor
for
org.apache.woden:woden:jar:1.0-incubating-M7b:
Could not transfer artifact
org.apache.woden:woden:pom:1.0-incubating-M7b
from/to jibx
(http://jibx.sourceforge.net/maven):
No connector available to access
repository jibx
(http://jibx.sourceforge.net/maven) of
type legacy using the available
factories
WagonRepositoryConnectorFactory ->
[Help 2]
This is what I get in Eclipse:
Project build error: Unresolveable build extension: Plugin
org.apache.axis2:axis2-wsdl2code-maven-plugin:1.3
or one of its dependencies could not
be resolved: Failed to collect
dependencies for
org.apache.axis2:axis2-wsdl2code-maven-plugin:jar:1.3
() pom.xml /myProject line 1 Maven
Problem
In Eclipse I've downloaded this: http://www.apache.org/dyn/mirrors/mirrors.cgi/axis/axis2/java/core/1.5.4/axis2-eclipse-service-plugin-1.5.4.zip unzipped and copied the file: "org.apache.axis2.eclipse.codegen.plugin_1.5.4.jar" into the directory "plugins" of my Eclipse instalation. And I still getting the same error.
I am running Netbeans over Win XP and Eclipse over Win XP and also over Mac, allways the same error.
Does somebody have any idea what can I do?
Here goes my pom.xml
<?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>
<parent>
<artifactId>MyParent</artifactId>
<groupId>com.mycompany</groupId>
<version>1.0</version>
</parent>
<groupId>com.mycompany</groupId>
<artifactId>myModule</artifactId>
<version>1.0</version>
<name>myModule</name>
<url>http://maven.apache.org</url>
<build>
<plugins>
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<configuration>
<filesets>
<fileset>
<directory>src/main/java</directory>
<includes>
<include>com/mycompany/client/*.java</include>
</includes>
</fileset>
</filesets>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.axis2</groupId>
<artifactId>axis2-wsdl2code-maven-plugin</artifactId>
<version>1.3</version>
<extensions>true</extensions>
<executions>
<execution>
<phase>generate-sources</phase>
<goals>
<goal>wsdl2code</goal>
</goals>
</execution>
</executions>
<configuration>
<packageName>com.mycompany.client</packageName>
<wsdlFile>src/main/axis2/MyWsdl.wsdl</wsdlFile>
<outputDirectory>.</outputDirectory>
<targetResourcesFolderLocation>target/main/axis2</targetResourcesFolderLocation>
<targetSourceFolderLocation>src/main/java</targetSourceFolderLocation>
<namespaceURIs>
<namespaceURI>
<uri>http://schema.mycompany.com/Esb</uri>
<packageName>com.mycompany.services.Esbsrv.schema</packageName>
</namespaceURI>
<namespaceURI>
<uri>http://wsdl.mycompany.com/Esb</uri>
<packageName>com.mycompany.services.Esbsrv.schema</packageName>
</namespaceURI>
<namespaceURI>
<uri>http://schema.mycompany.com/Global/WSException</uri>
<packageName>com.mycompany.schema.global.wsexception</packageName>
</namespaceURI>
</namespaceURIs>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<!--
<dependency>
<groupId>wsdl4j</groupId>
<artifactId>wsdl4j</artifactId>
<version>1.6.2</version>
<scope>compile</scope>
</dependency>
-->
<dependency>
<groupId>org.apache.axis2</groupId>
<artifactId>axis2-adb</artifactId>
<version>1.3</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.apache.axis2</groupId>
<artifactId>axis2-kernel</artifactId>
<version>1.3</version>
<scope>compile</scope>
</dependency>
<!--
<dependency>
<groupId>org.apache.axis2</groupId>
<artifactId>axis2-xmlbeans</artifactId>
<version>1.3</version>
<scope>compile</scope>
</dependency>
-->
</dependencies>
</project>

Well, I can only offer suggestions as I"m not much of a maven expert, but I did just have to do this today and it was pretty straightforward for me -
set up the maven project to be eclipse friendly : mvn eclipse:eclipse
make sure eclipse can see the libs. this meant going to the projectsetup/buildpath/libraries editor in eclipse and adding the variable M2_REPO to point to your local maven repository (e.g. something like /home/nacho3d/.m2/repository)
Your error, actually, looks to me like maven can't find a dependency for axis. The specifics for that should be on the axis website,

I think you're using maven 3.0+, right?
That pom(org.apache.woden:woden:jar:1.0-incubating-M7b) isn't compatible with maven 3 yet.
If you use maven 2.2.1 to build ESB 4.3.0-03 source, then it would be successfully.

If you have the jar of the missing dependency you can:
1) deploy it on your maven repository, if you have one
2) declare the dependency in your pom with a scope of 'system': check this out

I have also faced the same problem and fixed it by following below step...
In you project directory do the command: mvn eclipse:eclipse
In eclipse project right click->Maven->Update Project.
Again right click->Maven->Disable Maven Nature
Restart eclipse.
Right click on project->Configure->Convert to Maven Project.
Finish. Error will gone.
Thanks