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How to embed maven modules as .class dependencies as opposed to jars?

I have a multi-module maven project that is used to produce a single spring boot fat jar. My project looks something like this.
- Parent Module Aggergator
- A
- B
- C
- app <-- app.jar is the only thing I want to publish
In my case module A, B, C are only ever used by app and should not be published into maven repo. I have split up the app into multi-module project because it's a lot of code in the app and it's to work with that way.
Currently the app.jar will contain inside it a.jar, b.jar c.jar.
Is there a way to tell maven that the compiled classes from module A, B, C should just be inserted into app.jar classes folder without ever producing A.JAR, B.JAR, C.JAR?

I use the Maven Shade Plugin for my multi-module project; it creates a single JAR and extracts each module into it rather than creating multiple JAR files:
Parent 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>
<properties>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
</properties>
<groupId>...</groupId>
<artifactId>pipeline</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>pom</packaging>
<modules>
<module>firehose</module>
<module>gson</module>
<module>lambda</module>
<module>mapper</module>
<module>model</module>
<module>receiver</module>
<module>redshift</module>
<module>reloader</module>
<module>s3</module>
<module>sns</module>
<module>sqs</module>
<module>systemstests</module>
<module>transaction</module>
<module>utility</module>
</modules>
<dependencies>
...
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.1.1</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
Child pom.xml (the JAR):
<?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>
<parent>
<groupId>...</groupId>
<artifactId>pipeline</artifactId>
<version>1.0-SNAPSHOT</version>
</parent>
<artifactId>lambda</artifactId>
<dependencies>
...
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<finalName>MyJar</finalName>
</configuration>
</plugin>
</plugins>
</build>
</project>

Here is a non answer.
Is there a way to tell maven that the compiled classes from module A,
B, C should just be inserted into app.jar classes folder without ever
producing A.JAR, B.JAR, C.JAR?
You could use the repackage goal of the spring boot maven plugin that flatten the dependencies into classes in the uber jar.
In my case module A, B, C are only ever used by app and should not be
published into maven repo.
Adding the modules in a local repository is really wanted to have a efficient and standard build.
Without that, you will need to compile systematically each module at each time you want to run your spring boot app.
While actually sometimes you need to build dependencies, but other times you don't need because these are already updated.
Or else you will be constraint to twist the default Maven way of work by adding manual tasks to compile from the spring boot module the other modules and to move the compiled classes into the spring boot module. Really not a gift for the people that will have to read/maintain this configuration.

Why is OSGI bundle module getting built twice

I am building this multi-module project with Maven. The folder structure of the project at root is as follows:
core (dir)
|--- pom.xml
|--- pom (dir)
|---com.loc.dist.core.msp.osgi.pom (dir)
|---pom.xml
|--- com.lgc.dist.core.msp.example.helloservice.client (dir)
|---pom.xml
Project com.lgc.dist.core.msp.example.helloservice.client is packaged as OSGI bundle and it is a child module of com.loc.dist.core.msp.osgi.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>
<parent>
<groupId>com.lgc.dist</groupId>
<artifactId>com.lgc.dist.core.msp.osgi.pom</artifactId>
<relativePath>../pom/com.lgc.dist.core.msp.osgi.pom</relativePath>
<version>0.1</version>
</parent>
<artifactId>com.lgc.dist.core.msp.example.helloservice.client</artifactId>
<packaging>bundle</packaging>
<dependencies>
<dependency>
<groupId>com.lgc.dist</groupId>
<artifactId>com.lgc.dist.core.msp.service</artifactId>
<version>0.1</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<configuration>
<instructions>
<Export-Package>com.lgc.dist.core.msp.example.helloservice.client.*;version=${project.version}</Export-Package>
<Private-Package>com.lgc.dist.core.msp.example.helloservice.client.internal</Private-Package>
<Import-Package>*</Import-Package>
</instructions>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-scr-plugin</artifactId>
</plugin>
</plugins>
</build>
</project>
The pom.xml in top level shows pom folder and com.lgc.dist.core.msp.example.helloservice.client are in the reactor list.
<modules>
<module>pom</module>
<module>com.lgc.dist.core.msp.example.helloservice.client</module>
</modules>
When I ran mvn clean install from the root, it tends to build com.lgc.dist.core.msp.example.helloservice.client back to back twice. It is ok to install twice, but it will cause trouble when I run mvn deploy. All other submodules just built once. It is only the child modules of com.loc.dist.core.msp.osgi.pom are being built twice. I guess osgi builds all the bundle modules by default. But if I comment it out in pom.xml, the osgi bundle modules won't get built at all. What should I do to build these OSGI bundles just once?
EDIT It works fine if I change the packaging mode from bundle to jar, but that negates the purpose of having OSGI bundles.

Since the project "com.lgc.dist.core.msp.example.helloservice.client" is not a direct child of top level pom.xml, remove it from there.
So, in top level pom.xml, the entries should be :
<modules>
<module>pom/com.loc.dist.core.msp.osgi.pom</module>
</modules>
And pom.xml in pom/com.loc.dist.core.msp.osgi.pom should be having :
<modules>
<module>com.lgc.dist.core.msp.example.helloservice.client</module>
</modules>

After some research, it turns out maven-bundle-plugin 2.5.4 deploys the bundles by default. According to one of the answers of When using “bundle” packaging with maven-bundle-plugin goals are executed twice
(I'm surprised it did not get any up votes), you need to stop deploying by adding the execution block
<executions>
<execution>
<id>default-deploy</id>
<phase>no-execute</phase>
<goals>
<goal>deploy</goal>
</goals>
</execution>
</executions>
It is working now.
EDIT, based on the comment of this answer, it is resolved in 2.5.5. Haven't tried it though.

mvn process-resources doesn't pull down uber jar created with shade plugin

Goal: Create an executable uber jar with maven shade plugin that can be executed during the mvn compile of another pom.
Repro steps:
Create a pom.xml for the "publisher" component using below pom.
Use a Jenkins build to mvn deploy it (mvn install will work as well)
Add dependency to pom.xml for "consumer" (pom below)
mvn compile the consumer
Expected behavior:
Uber jar for publisher is downloaded somewhere in consumer/target directories
Actual:
Uber jar does not appear in consumer directory
Component 1: Publisher
<?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>com.mec.experiment</groupId>
<artifactId>publisher</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>
<dependencies>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>5.2.6.Final</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifestFile>src/main/resources/META-INF/MANIFEST.mf</manifestFile>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
Component 2: Consumer
<?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>com.mec.experiment</groupId>
<artifactId>consumer</artifactId>
<version>1.0-SNAPSHOT</version>
<dependencies>
<dependency>
<groupId>com.mec.experiment</groupId>
<artifactId>publisher</artifactId>
<version>1.0-SNAPSHOT</version>
</dependency>
</dependencies>

The answer from the possible duplicate I linked to in the comments has a link to a dead example page. Here's a supplement for you. The plugin configuration would belong inside the consumer pom.
exec:java
Full name:
org.codehaus.mojo:exec-maven-plugin:1.5.0:java
Description:
Executes the supplied java class in the current VM with the enclosing project's dependencies as classpath.
Attributes:
Requires a Maven project to be executed.
Requires dependency resolution of artifacts in scope: test.
The goal is thread-safe and supports parallel builds.
Since version: 1.0.
See especially executableDependency for your use case. That looks like it will allow you to reference producer according to its group id and artifact instead of hard-coding a path.

How do you replace the class of a Maven dependency?

There is a class in a maven dependency that is incompatible with Java 8.
How do you properly fix that problem?
Right now I'm doing the following:
Create a package with the same name
Create a class with the same name in that package
Copy and paste the code
Fix the incompatible API call
The problem is that this class contains API calls to restricted classes and although I changed the Eclipse compiler settings (Window -> Preferences -> Java -> Compiler -> Error/Warnings -> Deprecated and restricted API -> Forbidden reference (access rule): Error -> Warning) to allow access the project will only compile sometimes. If it doesn't compile I'll get a "can't find symbol" error.
Edit:
Here are the details you asked for:
Dependency: http://mvnrepository.com/artifact/com.sun.xml.wss/xws-security/3.0
Class: EncryptionProcessor
Necessary change:
// Change line 1053 FROM:
// _dataEncryptor = XMLCipher.getInstance(dataEncAlgo, _dataCipher);
// TO:
_dataEncryptor = XMLCipher.getInstance(dataEncAlgo);
Edit-2:
Maven build error:
[ERROR] symbol: class XMLCipher
[ERROR] location: class com.sun.xml.wss.impl.apachecrypto.EncryptionProcessor
[ERROR] /C:/Users/{name}/development/eclipse_workspace/git/xws-security/src/main/java/com/sun/xml/wss/impl/apachecrypto/EncryptionProcessor.java:[1482,98] cannot find symbol

Here is a detailed guide describing what I did exactly:
Create new Maven project in Eclipse
Configure Maven settings of new project (Important: Use the same group and artifact ID and only change the version number)
<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.sun.xml.wss</groupId>
<artifactId>xws-security</artifactId>
<version>3.0-java8-fix</version>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<java.version>1.8</java.version>
</properties>
</project>
Add dependency of bugged JAR
<dependencies>
<dependency>
<groupId>com.sun.xml.wss</groupId>
<artifactId>xws-security</artifactId>
<version>3.0</version>
<exclusions>
<exclusion>
<artifactId>xmldsig</artifactId>
<groupId>javax.xml.crypto</groupId>
</exclusion>
<exclusion>
<artifactId>activation</artifactId>
<groupId>javax.activation</groupId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
Create Java file in the same package of class that needs to be fixed
package com.sun.xml.wss.impl.apachecrypto;
public class EncryptionProcessor {
// The FIX goes here
}
Add Maven shade build plug in to handle creation of patched JAR file (this is not the only plug in to handle this kind of task - e.g. dependency:unpack)
<build>
<plugins>
<!-- plug in for creation of patched JAR file -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.1</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<filters>
<filter>
<artifact>com.sun.xml.wss:xws-security:3.0</artifact>
<includes>
<include>**/*.class</include>
<include>**/*.xml</include>
</includes>
<excludes>
<exlude>
com/sun/xml/wss/impl/apachecrypto/EncryptionProcessor.class
</exlude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
Include patched JAR in other projects as necessary (Note: If you experience ClassNotFoundExceptions or similar errors do this: Right-click on the project -> Properties -> Maven -> "Resolve dependencies from Workspace projects":false)
In case you are not familiar with Maven. Here is the complete pom.xml: http://pastebucket.com/88444

Similar to Steven S.'s answer, but using the maven-dependency-plugin. Based on this blog post.
I changed the name of the patched library (not the version), but it depends on your needs what works better for you.
The dependency on the original library should be marked as <optional>true</optional>. Otherwise, the projects that depend on your patched library will also depend on the original library, which means that both the patched and the original version will be on the classpath, which can lead to all kinds of problems.
If your project is a child project, you can still use a completely different groupId and version than your parent pom. Doesn't matter.
You can exclude the classes you patch from unpacking, but it's probably not necessary, because Maven will first unpack the original library and then compile your new version, which means that the original classes are overwritten. Nice!
<?xml version="1.0"?>
<project xmlns="http://maven.apache.org/POM/4.0.0">
<modelVersion>4.0.0</modelVersion>
<!-- remove this if you don't have a parent pom -->
<parent>
<groupId>my.company</groupId>
<artifactId>my.company</artifactId>
<version>1.2.3</version>
<relativePath>../pom.xml</relativePath>
</parent>
<groupId>com.foo</groupId>
<artifactId>foo-bar-patched</artifactId>
<version>4.5.6</version>
<build>
<plugins>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>unpack</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>com.foo</groupId>
<artifactId>foo-bar</artifactId>
<outputDirectory>${project.build.directory}/classes</outputDirectory>
<!-- excludes are probably not necessary -->
<!-- <excludes>**/Foo.class,**/Bar.class</excludes> -->
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>com.foo</groupId>
<artifactId>foo-bar</artifactId>
<version>4.5.6</version>
<optional>true</optional>
</dependency>
</dependencies>
</project>

General solution:
download all project sources
apply your modification
use version control so that change isn't lost
change version in pom.xml, for example from 3.0 to 3.0-patched
launch maven build
copy generated artifacts to you repository/Artifactory, if you use one
change dependency version in your own project

How to reference a non-maven project (in eclipse workspace) from a maven project?

I am working on a new project which is a plugin for a product.
I use maven to build my plugin (zip) but I need to reference the source code of the product which is defined in my Eclipse workspace. But this source code is not managed by Maven and I do not want to migrate it.
Is it possible to refers this workspace project by any way? (maven plugins, workaround welcome).
The dependency is just needed for the compilation inside Eclipse but will not be packaged in the plugin itself (provided scope).
I have also m2e in Eclipse and I want to keep this configuration when I make a "Maven Update".
UPDATE: I am looking for a solution which will work with a mvn clean install on a command line because I want to be able to execute the build from a CI platform (e.g. Jenkins)

Simply use Project -> Properties -> Java Build Path -> Projects -> Add
If you need to compile it outside Eclipse you can add a dependency to physical jar location:
<dependency>
<groupId>test</groupId>
<artifactId>test</artifactId>
<version>1.0</version>
<scope>system</scope>
<systemPath>${basedir}/lib/test.jar</systemPath>
</dependency>

You might consider using the antrun plugin to trigger the compilation of your source code in the external project linked to your compile phase. You could even copy your .class files into your target folder so the runtime classpath finds them

Because I have already the compiled source and I do not need to recompile them (or to modify anything) I decided to package them using the pom assembly.
I made a separate project (under the same parent's than my plugins developement projects) called like openemm-src:
Parent project (openemm-plugin-dev)
|- plugin-1
|- plugin-2
|- openemm-src
|- pom.xml
The pom.xml for the openemm-src project looks like:
<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>
<parent>
<groupId>openemm.plugin.dev</groupId>
<artifactId>plugin</artifactId>
<version>1.0.0-SNAPSHOT</version>
</parent>
<artifactId>openemm-src</artifactId>
<version>1.0.0</version>
<packaging>pom</packaging>
<name>OpenEMM Source Code Library</name>
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<descriptors>
<descriptor>src/assembly/src-plugin.xml</descriptor>
</descriptors>
</configuration>
<executions>
<execution>
<id>make-assembly</id> <!-- this is used for inheritance merges -->
<phase>package</phase> <!-- bind to the packaging phase -->
<goals>
<goal>single</goal>
</goals>
<xecution>
</executions>
</plugin>
</plugins>
</build>
</project>
and the file src/assembly/src-plugin.xml:
<assembly>
<formats>
<format>jar</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
<fileSets>
<fileSet>
<directory>build/classes</directory>
<outputDirectory></outputDirectory>
</fileSet>
</fileSets>
</assembly>
After this, I refers the jar from the siblings projects like this:
<dependency>
<groupId>openemm.plugin.dev</groupId>
<artifactId>openemm-src</artifactId>
<version>1.0.0</version>
<scope>provided</scope>
</dependency>
This solution is looking more like a workaround, but this is because the OpenEMM project does not have any "Plugin Template Project" to be managed with Maven.
Note this is just a partial configuration and I had also to refers to the Agnitas libraries which did not contains all the source code (both were necessary to compile my code).