I am new to maven and spent ~3 days in generating the zip file with assembly plugin refering to http://www.petrikainulainen.net/programming/tips-and-tricks/creating-a-runnab
The basic thing you should change is to create a separate module where you do the packaging which will look like this.
+-- root (pom.xml)
+--- mod-1 (pom.xml)
+--- mod-2 (pom.xml)
+--- mod-assembly (pom.xml)
The pom in the mod-assembly
will look like this:
<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>org.test.parent</groupId>
<artifactId>root</artifactId>
<version>1.0.0-SNAPSHOT</version>
</parent>
<artifactId>dist</artifactId>
<packaging>pom</packaging>
<name>Packaging Test : Distribution</name>
<dependencies>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>module-one</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>module-two</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<id>make-bundles</id>
<goals>
<goal>single</goal>
</goals>
<phase>package</phase>
<configuration>
<descriptors>
<descriptor>proj1-assembly.xml</descriptor>
</descriptors>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
That will solve the problem with running maven-assembly-plugin in every child and the problem with the dummy descriptor. Here you can find a real example of such structure.
Furthermore having the modules in one folder and the dependencies in an other folder you can use a assembly descriptor like this:
<id>bin</id>
<formats>
<format>zip</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
<dependencySets>
<dependencySet>
<useProjectArtifact>false</useProjectArtifact>
<useTransitiveDependencies>true</useTransitiveDependencies>
<outputDirectory>lib</outputDirectory>
<unpack>false</unpack>
<excludes>
<exclude>${project.groupId}:*:*</exclude>
</excludes>
</dependencySet>
</dependencySets>
<moduleSets>
<moduleSet>
<useAllReactorProjects>true</useAllReactorProjects>
<binaries>
<outputDirectory>modules</outputDirectory>
<unpack>false</unpack>
</binaries>
</moduleSet>
</moduleSets>
I think the post How to Assemble Multi-Module Project with Maven might answer your question with an example.
My answers to your questions:
1) You should add the Assembly plugin in the parent pom within the build and pluginManagement tags to reuse it in the modules; the post mentioned above is a good example on how to do it. You can also take a look at 8.6 Best Practise chapter, topic 8.6.2, of the online book 'Maven: The Complete Reference'.
2) The exclusion tag might be tricky. Again, take a look at 8.5 Controlling the Contents of an Assembly chapter of the online book 'Maven: The Complete Reference'. For example, the subtopic 8.5.4, about dependencySets mentions how to fine tune dependency includes and excludes for dependencySets; again, the subtopic 8.5.5, now about moduleSets, shows how to use it in that context.