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Maven deploy two jars with different classifiers from two separate pom.xml

I want to deploy two jar artifacts with different classifiers, but at the moment that fails because both supply their own version of pom.xml. How can I fix that, so that both pom.xmls can be uploaded along with their artifacts?
Example - I have com.test.company.somelib-1.0.0-cmp1.jar and com.test.company.somelib-1.0.0-cmp2.jar, where cmpX is a classifier. Both packages contain (logically) the same code and classes (of the same version), they only differ slightly in the way they were preprocessed. The classifier annotation is there due to backwards compatibility we need to maintain.
Long story short, first artifact uploads fine, second one fails with Forbidden, because our repository does not allow overwriting artifacts (and I want to keep it that way).
There is a slightly different pipeline that creates both the packages, so it is easier to have their builds separate. I just want to deploy them as two packages of the same name and different classifier.
Thanks for help
Edit: it has been suggested to use Maven profiles. I can see that they would work, but they would not be ideal.
Consider the setup I have depicted on the picture below - there is a CI server (TeamCity).
There is a "starter" build (Sources). This build checkouts all required source files.
From this starter build several other builds are triggered (processing using x.x.x/compile). Each of those builds adjusts a template-pom.xml (fills in particular classifier and other info), and then builds and deploys its artifact to our Artifactory.
With the setup I want to achieve if I decide to add another processing-build, all I need to do is add another "branch". If I was using profiles, I would need to also add a new profile to the pom.xml file.
Correct me if I am wrong please. Profiles seem to be able to achieve the goal, but not ideally, at least in my case.

I strongly discourage having 2 (or more) different pom files with the same GAV.
But I understand your need is raised by legacy reasons.
I have not tried this myself but it could be working:
Leave one build (= maven project) as you have it now. On the other build skip the normal deployment and manually invoke the deploy-file goal of the deploy plugin like so:
<build>
<plugins>
<!-- skip normal execution of deploy plugin -->
<plugin>
<artifactId>maven-deploy-plugin</artifactId>
<executions>
<execution>
<id>default-deploy</id>
<configuration>
<skip>true</skip>
</configuration>
</execution>
</executions>
</plugin>
<!-- invoke with goal: deploy-file -->
<plugin>
<artifactId>maven-deploy-plugin</artifactId>
<executions>
<execution>
<id>someId</id>
<phase>deploy</phase>
<goals>
<goal>deploy-file</goal>
</goals>
<inherited>false</inherited>
<configuration>
<file>path-to-your-artifact-jar</file>
<generatePom>false</generatePom>
<artifactId>xxx</artifactId>
<groupId>xxx</groupId>
<version>xxx</version>
<classifier>xxx</classifier>
<packaging>xxx</packaging>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>

How to generate separate jar files for application, source, and documentation (for central.sonatype.org)

Sonatype has a repository that I want to deploy a jar file to, and they ask for separate files for application, sources, and javadocs:
Example:
example-application-1.4.7.pom
example-application-1.4.7.jar
example-application-1.4.7-sources.jar
example-application-1.4.7-javadoc.jar
In Scala SBT, I have a command called "package" that generates the jar file for the project, but that only generates "example-application-1.4.7.jar".
Question: What should I do to generate the other two jar files?

In Maven, in order to get the additional -sources and -javadoc artifacts, add to your POM file the following:
<build>
<plugins>
<!-- additional plugin configurations, if any.. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.0.0</version>
<executions>
<execution>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.10.3</version>
<executions>
<execution>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
Note the snippet above:
We are invoking the Maven Source Plugin to create an additional jar files for sources
We are invoking the Maven Javadoc Plugin to create an additional jar files for javadoc
Executing
mvn clean package
You will find these two additional jars in the target folder.
The .pom file instead is generated during the install phase, but it is not placed under the target folder. Basically, it is a copy of your pom.xml file, with a different extension and used by Maven during the dependency mediation process to check which transitive dependencies are required by the concerned artifact.
Executing
mvn clean install
Maven will install the artifact in your local cache (in your machine), under path_to_cache/.m2/repository/your_groupId/your_artifactId/your_version/. In this folder, you will also find the .pom file, which normally you don't need to distribute (it is created automatically by Maven).
Further note: you probably don't want to generate these additional jar files at each and every build, so to speed up normal builds and have them only on demand, you could wrap the snippet above in a Maven profile.
You can achieve this by removing the snippet above from your build section and add a further section at the end of your pom:
<profiles>
<profile>
<id>prepare-distribution</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.0.0</version>
<executions>
<execution>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.10.3</version>
<executions>
<execution>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
So that normal builds would not create these jars anymore, but when executing the following:
mvn clean install -Pprepare-distribution
You would instead get them back. the -P option is actually activating on demand the profile defined with the id prepare-distribution.
With Maven 3 a default profile already comes as part of the super pom which perform exactly the same actions (sources and javadoc artifact), hence no need to add anything to your existing project. Simply run:
mvn clean install -Prelease-profile
Or, to activate it via a property
mvn clean install -DperformRelease=true
However, as also specified in the super pom, this profile may be removed in future releases (although there since first Maven 3 version till version 3.3.9 so far)
NOTE: The release profile will be removed from future versions of the super POM
The main reason behind this warning is most probably to push for the usage of the Maven Release Plugin, which indirectly makes use of this profile via the useReleaseProfile option of the release:perform goal.
As highlighted by comments, if you are not familiar with maven (especially via console) I would definitely recommend to
Go through the official Maven in 5 minutes documentation for a quick but worthy look.
Play with Maven from the command line, is there where Maven gives you its best. IDE integrations are great, but command line is the real turning point.
Then play with the POM customization above, to get familiar with some concepts and behaviors, first directly as part of your default build, then moved to a profile.
Then, and only then, move to the Maven Release Plugin usage. I recommend it as last step because you would already have acquired more confidence and understanding and see it as less magic and more reasonable approach.

Maven release plugin fails : source artifacts getting deployed twice

We are using the maven release plugin on hudson and trying to automate the release process.
The release:prepare works fine. When we try to do the release:perform , it fails because it tries to upload a source artifact twice to the repository.
Things that I tried,
removing the profile which does include the maven source plugin from the super pom ( did not work)
specifying the goals on hudson for release as -P!attach-source release:prepare release:perform. Which I thought will exclude the source plugin from getting executed. (did not work).
tried specifying the plugin phase to some non existent phase in the super pom.(Did not work)
tried specifying the plugin configuration, forReleaseProfile as false. ( guess what?? Did not work too)
It still spits out this error.
[INFO] [DEBUG] Using Wagon implementation lightweight from default mapping for protocol http
[INFO] [DEBUG] Using Wagon implementation lightweight from default mapping for protocol http
[INFO] [DEBUG] Checking for pre-existing User-Agent configuration.
[INFO] [DEBUG] Adding User-Agent configuration.
[INFO] [DEBUG] not adding permissions to wagon connection
[INFO] Uploading: http://xx.xx.xx.xx:8081/nexus/content/repositories/releases//com/yyy/xxx/hhh/hhh-hhh/1.9.40/hhh-hhh-1.9.40-sources.jar
[INFO] 57K uploaded (xxx-xxx-1.9.40-sources.jar)
[INFO] [DEBUG] Using Wagon implementation lightweight from default mapping for protocol http
[INFO] [DEBUG] Using Wagon implementation lightweight from default mapping for protocol http
[INFO] [DEBUG] Checking for pre-existing User-Agent configuration.
[INFO] [DEBUG] Adding User-Agent configuration.
[INFO] [DEBUG] not adding permissions to wagon connection
[INFO] Uploading: http://xx.xxx.xx.xx:8081/nexus/content/repositories/releases//com/xxx/xxxx/xxx/xxx-xxx/1.9.40/xxx-xxx-1.9.40-sources.jar
[INFO] [DEBUG] Using Wagon implementation lightweight from default mapping for protocol http
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [ERROR] BUILD ERROR
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] Error deploying artifact: Authorization failed: Access denied to: http://xx.xxx.xx.xx:8081/nexus/content/repositories/releases/com/xxx/xxx/xxx/xxx-config/1.9.40/xxx-xxx-1.9.40-sources.jar
Any help regarding this will be really appreciated.

Try running mvn -Prelease-profile help:effective-pom.
You will find that you have two execution sections for maven-source-plugin
The output will look something like this:
<plugin>
<artifactId>maven-source-plugin</artifactId>
<version>2.0.4</version>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
<execution>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
To fix this problem, find everywhere you have used maven-source-plugin and make sure that you use the "id" attach-sources so that it is the same as the release profile. Then these sections will be merged.
Best practice says that to get consistency you need to configure this in the root POM of your project in build > pluginManagement and NOT in your child poms. In the child pom you just specify in build > plugins that you want to use maven-source-plugin but you provide no executions.
In the root pom.xml:
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<executions>
<execution>
<!-- This id must match the -Prelease-profile id value or else sources will be "uploaded" twice, which causes Nexus to fail -->
<id>attach-sources</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
</build>
In the child pom.xml:
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
</plugin>
</plugins>
</build>

I know this question is old but it was google hit #1 today so I'll add my answer appropriate for recent versions of maven 3.
The symptom is that sources and javadoc jars are deployed twice when doing a release build with some versions of maven 3. If you're using maven to deploy your artifacts to a Sonatype Nexus repository that only allows a release artifact to be uploaded once (which is totally reasonable behavior), the build fails when the second upload attempt is rejected. Argh!
Maven versions 3.2.3 thru 3.3.9 have bugs - see https://issues.apache.org/jira/browse/MNG-5868 and https://issues.apache.org/jira/browse/MNG-5939. Those versions generate and deploy sources and javadoc jars twice when doing a release.
If I read the Maven issue tracker correctly, those bugs are not scheduled for fix as of this writing (the burned 3.4.0 release probably affected these).
Instead of a complex tweak to my pom, my simple workaround was to fall back to Maven version 3.2.1.

Just having hit the same problem, I analyzed it a bit. mvn release:perform evaluates the release.properties file, then checks out the tag in a temporary directory and invokes there something like
/usr/bin/mvn -D maven.repo.local=... -s /tmp/release-settings5747060794.xml
-D performRelease=true -P set-envs,maven,set-envs deploy
I tried to reproduce this – manually checked out the tag produced by release:prepare and invoked this:
mvn -D performRelease=true -P set-envs,maven,set-envs deploy
I got the same result: It was trying to upload the -sources.jar twice.
As noted by qualidafial in a comment, setting performRelease=false instead omits one of the two attachments of the same file.
I don't really have an idea how the deploy plugin (or any other plugin) uses this property.
We can provide this parameter as a configuration to the maven-relase-plugin:
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<useReleaseProfile>false</useReleaseProfile>
</configuration>
</plugin>
</plugins>
</build>
I now added the <useReleaseProfile>false</useReleaseProfile> line to all the POMs, and it looks like releasing now works without an error message.

I have been struggeling with this issue for a while and have finally been able to resolve it in our infrastructure. The answers here didn't help me, as we didn't have multiple executions of the source plugin goals and the configuration seemed fine to us.
What we did miss out was to bind the execution of the source plugin to a phase. Extending the example by Bae, including the line <phase>install</phase> to the execution resolved the issue for us:
<plugin>
<artifactId>maven-source-plugin</artifactId>
<version>2.0.4</version>
<executions>
<execution>
<id>attach-sources</id>
<phase>install</phase>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
I suspect the solution lies in this answer here; different plugins seem to be invoking the jar goal / the attach-sources execution. By binding our execution to a certain phase, we force our plugin only to be run in this phase.

This was happening to me when running
mvn install deploy
I avoided the problem by instead running
mvn deploy
(which implies install). In my case only one artifact was being attempted to be uploaded twice, and that was a secondary artifact (maven-jar-plugin was setup to build a secondary jar in addition to the one built by the default-jar execution).

TL;DR
Disable execution with id attach-sources fixes this problem, if you cannot modify your parent poms.
--
This answer is a supplementary for #Bae's answer:
https://stackoverflow.com/a/10794985/3395456
My problem is the same, when running mvn -Prelease-profile help:effective-pom, I have two execution sections for maven-source-plugin
<plugin>
<artifactId>maven-source-plugin</artifactId>
<version>2.0.4</version>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
<execution>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
The top voted answer just recommends a best practice to remove unnamed (anonymous) execution to avoid duplicated binding. But what if I cannot remove it, because I cannot change the parent pom?
There is one way to disable one execution, not the anonymous one, but the one with id attach-source. And it also works for uploading xx-javadoc.jar twice.
So under my pom.xml, I can explictly override the plugins settings, by disabling the execution with id attach-source.
<!-- Fix uploading xx-source.jar and xx-javadoc.jar twice to Nexus -->
<!-- try to disable attach-sources, attach-javadocs execution (bind its phase to none) -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<executions>
<execution>
<id>attach-sources</id>
<phase>none</phase>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<executions>
<execution>
<id>attach-javadocs</id>
<phase>none</phase>
</execution>
</executions>
<inherited>true</inherited>
</plugin>
References:
Is it possible to override executions in maven pluginManagement?

I don't think the probem is in the release plugin, I think you've got the xxx-sources.jar attached two times - that's why the duplicate upload. Why is there a duplicate attachment is hard to tell without seeing the POM. Try running mvn -X and checking the log for who attaches xxx-source.jar another time.
In any case, a good workaround on Nexus would be having a staging repository where you can upload releases several times - and when everything's ready you just close/promote the staging repo. Check the Sonatype OSS setup for an example.

I had the same problem. Basically, the error message is issued when an artifacts is sent to Nexus twice. This may be twice to the same Nexus repository or even across different repositories within the same Nexus.
However, the reasons for such a misconfiguration may vary. In my case, the artifacts were uploaded correctly during a mvn clean deploy build step in Jenkins, but then failed when a second deploy had been attempted. This second deploy had been configured in a Jenkins post build step "Publish artifacts in Maven repository".

Maven plugins in parent and child poms should not have execution. As per standard convention, define all plugin with execution/goals in parent pom in plugin management section. Child pom should not redefine above details, but mention only the plugin (with artifactId, and version) that needs to be executed.
I had similar issue with maven-assembly-plugin with parent pom as below:
<build>
<pluginManagement>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.6</version>
<configuration>
<descriptors>
<descriptor>src/assembly/assembly.xml</descriptor>
</descriptors>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
</build>
And Child pom had maven-assembly-plugin as below:
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.2-beta-5</version>
<configuration>
<finalName>xyz</finalName>
<descriptors>
<descriptor>src/assembly/assembly.xml</descriptor>
</descriptors>
</configuration>
<executions>
<execution>
<id>xyz-distribution</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
Removing the <executions> from child pom rectified the issue.
The effective pom had 2 executions performed causing the duplicate install to Nexus repo.

FWIW this issue was breaking our build for a while and the answer was none-of-the-above.
Instead I had foolishly set the seemingly innocuous appendAssemblyId to false in a maven-assembly-plugin for an artifact that gets attached (read deployed, released) with our main artifact. E.g.:
<execution>
<id>ci-groovy-distrib</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<descriptorRefs>
<descriptorRef>my-extra-assembly</descriptorRef>
</descriptorRefs>
<!-- This is the BUG: the assemblyID MUST be appended
because it is the classifier that distinguishes
this attached artifact from the main one!
-->
<appendAssemblyId>false</appendAssemblyId>
<!-- NOTE: Changes the name of the zip in the build target directory
but NOT the artifact that gets installed, deployed, releaseed -->
<finalName>my-extra-assembly-${project.version}</finalName>
</configuration>
</execution>
In summary:
the assembly plugin uses the assemblyId as the classifier for the artifact, hence an essential part of it's unique GAV coordinates in maven terms (actually it's more like GAVC coordinates - C is the classifier).
the name of the file installed, deployed, or released is actually built from these coordinates. It is not the same as the filename you see in your target directory. That's why your local build looks good, but your release will fail.
The stupid element only determines the local build artifact name and plays no part in the rest of it. It's a complete red-herring.
Summary of the summary:
The 400 error from Nexus was because our extra attached artifact was being uploaded over top of the main artifact, since it had the same name as the main artifact, because it had the same GAVC coordinates as the main artifact, because I removed the only distinguishing coordinate: the classifier derived automatically from the assemblyId.
The investigation to find this was a long and tortuous path the answer was right there all along in the docs for maven-assembly:
appendAssemblyId
boolean
Set to false to exclude the assembly id
from the assembly final name, and to create the resultant assembly
artifacts without classifier. As such, an assembly artifact having the
same format as the packaging of the current Maven project will replace
the file for this main project artifact.
Default value is: true.
User property is: assembly.appendAssemblyId.
From http://maven.apache.org/plugins/maven-assembly-plugin/single-mojo.html#attach
The extra bold is mine. The docs should have a big flashing warning here: "Set this to false and abandon all hope"
I got some help from this answer about a different problem maven-assembly-plugin: How to use appendAssemblyId
The explanation there from tunaki really helped.

I faced similar issue. Artifacts were getting deployed twice and the resultant build was failing.
Checked and found that the issue was in Jenkins Script. The settings.xml was called twice. Like:
sh "mvn -s settings.xml clean deploy -s settings.xml deploy -U .....
which caused the issue.
Updated this line and it worked like a charm:
sh "mvn clean deploy -s settings.xml -U .....

with nexus thix configuratio nworked for me
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<configuration>
<useReleaseProfile>false</useReleaseProfile>
</configuration>
</plugin>

I configured the maven release plug-in with releaseProfile=false and dont execute the source artifacts profile. Which did the trick.
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.1</version>
<configuration>
<arguments>-P!source-artifacts</arguments>
<useReleaseProfile>false</useReleaseProfile>
<goals>-Dmaven.test.skip=true deploy</goals>
</configuration>
</plugin>
</plugins>
</build>

maven yui compression on war:war

I'm trying to automatically compress both CSS and JS using maven and this plugin. I want to compress when the goal war is executed but I'm not figuring how:
<build>
<finalName>${artifactId}-${version}-production</finalName>
<plugins>
<plugin>
<groupId>net.sf.alchim</groupId>
<artifactId>yuicompressor-maven-plugin</artifactId>
<executions>
<execution>
<configuration>
<gzip>true</gzip>
<nosuffix>true</nosuffix>
</configuration>
<goals>
<goal>compress</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>

You need to bind the execution to a phase so it will be executed when you run the war packaging. These are the available phases you can bind to for war packaging.
<plugin>
<groupId>net.sf.alchim</groupId>
<artifactId>yuicompressor-maven-plugin</artifactId>
<executions>
<execution>
<id>compress</id>
<phase>process-resources</phase>
...<!--rest of config is fine-->
Update: Are the js.gz files not being generated or just not included in the war?
One additional thing to check if you're still not seeing the content in the war is that the resources should be under src/main/resources, not src/main/webapp.
The yuicompressor plugin will process the js files in src/main/webapp, but they won't be included in the final war.
Update 2: reread your question after seeing your answer, I'd misread the goal you were running. To avoid running two goals you can do one of these:
Try instead of running the war goal, run install or package, this will invoke the standard lifecycle, and the yuicompressor plugin will be invoked in the process-resources phase.
Alternatively change the phase the yuicompressor goal is bound to in the example above to package so it is activated when you run the war:war goal.

for some weird reason war:war doesn't call the plugin in the phase process-resources: I just added a custom menu on nb 6.7 that call first compile, then war:war

Generating a maven site including a Cobertura Report

I've got some projects that are already doing site generation via maven, and I want to integrate cobertura reports in them, but no maven goal I seem to run will generate a local preview for me to look at that includes the Cobertura reports in the site. I want to be sure they're generating correctly before I commit the pom changes to the repo and have broken site generated.
Below is what I've added to the maven poms (parent and module), but the site I see when I run mvn site:run does not include the cobertura reports:
<project>
...
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>cobertura-maven-plugin</artifactId>
<configuration>
<check>
<haltOnFailure>false</haltOnFailure>
<regexes>
<regex>
<pattern>parent-package-name-here.*</pattern>
<branchRate>80</branchRate>
<lineRate>80</lineRate>
</regex>
</regexes>
</check>
<instrumentation>
<includes>
<include>parent-package-name-here/**/*.class</include>
</includes>
</instrumentation>
</configuration>
<executions>
<execution>
<id>clean</id>
<phase>pre-site</phase>
<goals>
<goal>clean</goal>
</goals>
</execution>
<execution>
<id>instrument</id>
<phase>site</phase>
<goals>
<goal>instrument</goal>
<goal>cobertura</goal>
<goal>check</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
...
<reporting>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>cobertura-maven-plugin</artifactId>
</plugin>
</plugins>
</reporting>
...
</project>
What maven command should I use to generate the site with cobertura reports? Or, what should I add (additionally) to get the site generation to include the cobertura reports?

Should do:
mvn site
To elaborate, running mvn a:b runs the goal b in plugin a. Saying mvn c means to run the lifecycle phase c, which runs all of the bound goals in all of the phases up to c. As a result, this will trigger a lot more things to happen (such as doing the necessary preparation to produce cobertura reports).

I figured out how to do this.
It seems there are a lot of bugs in the link generation within the maven site generation plugin.
The only way I've found to make maven generate a local copy of the site with working module links is to modify the distributionManagement/site tag to point to some local directory instead of the real-live deploy directory, then use maven site:deploy.
Every attempt to use mvn site:stage generates broken links. Same goes for mvn site:run.
The report links work with mvn site:run / mvn site:stage but the links to modules do not.

mvn site
should do what you are looking for. You configure the plugin to run in the pre-site and site phases of the life cycle but your are then executing the site:run goal not site. We are doing similar things with clover (commercial coverage tool) and mvn site does the trick.

site:stage module links don't work in my experience either for multi module builds but site:deploy does. Try this:
Use a property for the site URL in the parent pom, e.g. ${site.url}. Then call this
mvn clean site site:deploy -Dsite.url=file://`pwd`/target/site-deployed
The pwd is a -nix command that will substitute the current directory. This is because the URL that you use must be absolute.

We use
mvn site-deploy
This builds the site and deploys it (copies it to the place we have configured).

mvn site:site should produce what you are after, in the target directory, there will be a site directory containing all reports linked with an index.html in that directory.