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http://jira.codehaus.org/browse/MECLIPSE-165?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#action_101619
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Brian Fox commented on MECLIPSE-165:
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Applied the patch and updated so it applied cleanly. The resulting classpath 
doesn't match the expected one. Although the resulting one actually has the 
excludes, the format seems curious to me. It's excluding **/*.java from the 
binary resources. The code is applied to a branch here: 
https://svn.apache.org/repos/asf/maven/plugins/branches/maven-eclipse-plugin-MECLIPSE-165

If you can look and provide a patch from this branch, then we can get it 
applied to trunk. Thanks.

> Ability to exclude filtered resources from eclipse's source directories
> -----------------------------------------------------------------------
>
>                 Key: MECLIPSE-165
>                 URL: http://jira.codehaus.org/browse/MECLIPSE-165
>             Project: Maven 2.x Eclipse Plugin
>          Issue Type: New Feature
>          Components: PDE support
>    Affects Versions: 2.3
>            Reporter: Cédric Vidal
>         Attachments: MECLIPSE-165.patch
>
>
> Resources should be in the classpath from Eclipse's point of view because 
> they end up being in the classpath from Maven 2's point of view, but whenever 
> resources are marked as being filtered by M2, Eclipse puts them unfiltered in 
> the classpath thus introducing an inconsistency between Maven 2 and Eclipse.
> Whether or not to include filtered resource directories in eclipse's sources 
> directories is therefore a real dilemna. While I'm sure a consistent solution 
> to this dilemna will eventually be found, it would be great to let the user 
> choose what to do in the meantime.
> The attached patch adresses this issue by adding a parameter, 
> 'excludeFilteredResourcesFromSourceDirs', which when set to true prevents 
> filtered resource directories from being added to eclipse's source 
> directories. The parameter defaults to false to avoid changing current 
> projects' behavior.
> Regards,
> Cédric Vidal
> http://www.B-Process.com
> PS: This parameter could be overriden on a per resource directory basis as 
> mentionned in MECLIPSE-162. This is not adressed by the attached patch though

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