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https://issues.apache.org/jira/browse/UIMA-1169?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13224325#comment-13224325
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Mike Barborak commented on UIMA-1169:
-------------------------------------

For anyone looking for a workaround, when run from the Component Descriptor 
Editor in Eclipse, JCasGen uses the project's first folder resource as it 
output folder. So to change the output folder, open the project's properties, 
go to Java Build Path, go to the Order and Export tab, and move the desired 
output folder above all other folder resources.

That didn't quite fulfill my needs as I have a project with two type systems: a 
"real" one for which JCasGen should output to src and a "test" one for which 
I'd like JCasGen to output to test. The test type system imports the real one. 

When I run JCasGen on the test type system, I first move my test source folder 
to the top of the order list as described above. Then I run JCasGen. This puts 
the generated Java classes in the test folder. Yay. But it also generates the 
Java classes for the imported type system and puts them in the test folder even 
though those classes already exist in the src folder. This creates various 
compiler issues but they're easily resolved by deleting the extra Java files.

So I guess a complete fix for me would be to allow specifying an output folder 
for each type system to JCasGen or an option to not generate Java classes for 
imported type systems.
                
> Specify source directory for JCAsGen
> ------------------------------------
>
>                 Key: UIMA-1169
>                 URL: https://issues.apache.org/jira/browse/UIMA-1169
>             Project: UIMA
>          Issue Type: Improvement
>          Components: Eclipse plugins
>    Affects Versions: 2.3
>            Reporter: Julien Nioche
>
> By default JCASGen generates java code in the src/ directory (or maybe in the 
> first source directory available). It would be nice to have the possibility 
> to specify an alternative source directory

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