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https://jira.codehaus.org/browse/JXR-69?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=314863#comment-314863
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Malachi de AElfweald commented on JXR-69:
-----------------------------------------

malachi@methe:~$ mvn --version
Apache Maven 3.0.4 (r1232337; 2012-01-17 00:44:56-0800)
Maven home: /usr/local/maven
Java version: 1.8.0-ea, vendor: Oracle Corporation
Java home: /usr/local/jdk1.8.0/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "3.2.0-3-rt-amd64", arch: "amd64", family: "unix"

Here's the commands I was running:
mvn clean install site:site
mvn site:stage -DstagingDirectory=/home/malachi/work/test/jxr-site

I just tried with and without aggregation.  If I use aggregation, the source is 
at the top-level instead of the module level; but the linkage is the same.
                
> fails to create cross links in multi-module project
> ---------------------------------------------------
>
>                 Key: JXR-69
>                 URL: https://jira.codehaus.org/browse/JXR-69
>             Project: Maven JXR
>          Issue Type: Bug
>          Components: maven2 jxr plugin
>    Affects Versions: 2.1
>            Reporter: Giovanni Azua
>             Fix For: 2.3
>
>         Attachments: jxrtest.jar
>
>
> My build pulls jxr 2.1. Although I set the aggregate parameter to true, I 
> still don't get linked cross module references say e.g.
> Module A
>     Interface X
> Module B (depends on A)
>     Class Y implements X
> In the aggregate reports Class Y will not link to X.

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