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https://jira.codehaus.org/browse/MSITE-669?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=315817#comment-315817
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Lukas Theussl commented on MSITE-669:
-------------------------------------

The problem here is that the site plugin needs one top-level base url that 
serves as reference for relative links of all sub-projects. The current 
assumption is that this base url is the one defined in the top-level reactor 
project. In your project layout this is not the case, some modules get deployed 
'above' the top reactor project, i.e. 'beyond root'. So it's not the module 
directory layout per se that causes the trouble, but the relative deployment 
location of the sub-projects. If you can re-define the urls such that all 
modules get deployed to sub-urls of the top project, everything should work.

As a fix for the site plugin, the only solution I can see for this particular 
problem is to extract the actual top-level url by looping over all modules 
before processing anything. However, first I would encourage you to re-think 
your project layout, I would not be surprised if your setup would lead to all 
kind of other troubles as well.
                
> site:stage creates incorrect structure when module paths contains sets of 
> "../"
> -------------------------------------------------------------------------------
>
>                 Key: MSITE-669
>                 URL: https://jira.codehaus.org/browse/MSITE-669
>             Project: Maven 2.x and 3.x Site Plugin
>          Issue Type: Bug
>          Components: multi module, relative links, site:stage(-deploy)
>    Affects Versions: 3.1, 3.2
>            Reporter: Lennart Jörelid
>            Assignee: Lukas Theussl
>         Attachments: sample.zip
>
>
> Given the module definitions given below, the site:stage goal produces sets 
> of maps relative to the staging directory - i.e. outside of the target 
> directory.
> {code:xml} 
> <modules>
>   <module>../../validation/validation-api</module>
>   <module>../../validation/validation-aspect</module>
>   <module>../parent</module>
> </modules>
> {code}
> The staged site should be fully included within the staging directory. It 
> would appear that relativization of links for site:stage should take special 
> links into consideration.

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