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https://jira.codehaus.org/browse/MCOMPILER-206?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
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Bob Fields closed MCOMPILER-206.
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    Resolution: Not A Bug

I figured out the misconfiguration in the project I was trying to compile, 
sorry it's not a bug.
                
> Buildhelper plugin (add source dir) ignored on compile in site phase
> --------------------------------------------------------------------
>
>                 Key: MCOMPILER-206
>                 URL: https://jira.codehaus.org/browse/MCOMPILER-206
>             Project: Maven 2.x Compiler Plugin
>          Issue Type: Bug
>    Affects Versions: 3.1
>         Environment: Java 1.6.0_43-b01 64 bit Windows7. maven 3.0.4.
>            Reporter: Bob Fields
>         Attachments: mvnsiteFailure.zip
>
>
> mvn install recognizes additional directories from maven-buildhelper-plugin. 
> Running mvn site afterwards does not recognize the additional src 
> directories. This was not a problem until compiler 3.0 plugin changed the way 
> compilation is done, it now recompiles the project every time even when no 
> changes have been made, unfortunately it needs to recompile during the site 
> phase now. Multiple recompilations normally would not be a problem (though 
> preferred not to have to do), if it found all the source directories. I 
> tested the old 2.5.1 plugin by deleting the target/classes files and then 
> running mvn site, and it fails the same way (additional buildhelper 
> directories not added to compilation path), so this issue also exists in the 
> plugin v2.x. Attached a debug log output, it shows that the buildhelper dirs 
> were added when that plugin was run under 'Source directories' but were not 
> passed to the javac command line when the compiler plugin was run. Running 
> the same under mvn install shows both sourcepath values passed to the javac 
> compiler. I'm hoping there's a simple solution to this, otherwise I'll build 
> the SNAPSHOT version of the compiler-plugin and attempt to troubleshoot 
> (probably easier than duplicating the problem in a very small project). 
> Because it is such a large project, I have to run the install phase 
> separately from the site phase (memory constraints).

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