java.lang.RuntimeException: java.lang.ClassNotFoundException: Cannot find implementation about mapstruct.org

[agudian]

That is most probably a problem with how the pom is set up - the classes should only be generated once. I bet the mapstruct-processor module ended up on the compile classpath, which is then picked up automatically by the java compiler. My tip would be to set up your pom like it's described in our latest docs: http://mapstruct.org/documentation/1.1/reference/html/index.html#setup

...
<properties>
    <org.mapstruct.version>1.1.0.Beta1</org.mapstruct.version>
    <m2e.apt.activation>jdt_apt</m2e.apt.activation>
</properties>
...
<dependencies>
    <dependency>
        <groupId>org.mapstruct</groupId>
        <artifactId>mapstruct-jdk8</artifactId>
        <version>${org.mapstruct.version}</version>
    </dependency>
</dependencies>
...
<build>
    <plugins>
        <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-compiler-plugin</artifactId>
            <version>3.5.1</version>
            <configuration>
                <source>1.8</source>
                <target>1.8</target>
                <annotationProcessorPaths>
                    <path>
                        <groupId>org.mapstruct</groupId>
                        <artifactId>mapstruct-processor</artifactId>
                        <version>${org.mapstruct.version}</version>
                    </path>
                </annotationProcessorPaths>
            </configuration>
        </plugin>
    </plugins>
</build>
...

If you then also have the latest Eclipse m2e-apt plugin installed, then the annotation processor within Eclipse will be configured correctly and you won't have any trouble either in maven or in eclipse.

Regarding your other points, I don't get what you mean with 1) and hence can't see what's missing in the docs or the examples. Could you give us some more information on what you have and what you want to accomplish?
Point 3) is by design - used mappers are not propaged transitively. But you can define commonly used mappers in an @MappingConfig annotated class and reference it in your mapper.
Finally, the MapStruct Eclipse Plugin is not supposed to set up the eclipse compiler settings based on your pom - that's what m2e-apt is for. Perhaps we should make that more clear in readme of the plugin.

I'm closing this issue now. If you want to continue discussing your points, please open up a mail thread in our mapstruct-users mailing list. For actual issues or feature requests, https://github.com/mapstruct/mapstruct/issues is the right place for them. This repository / issue tracker is for the pages and documentation on mapstruct.org only.
Thanks!