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https://issues.jenkins-ci.org/browse/JENKINS-9250?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=162827#comment-162827
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Henrik Skupin commented on JENKINS-9250:
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We hit this issue too in our ci system. abayer, given that you are assigned do 
you have any news about a possible fix?
                
> Clone workspace does not work well with multiple scm plugin
> -----------------------------------------------------------
>
>                 Key: JENKINS-9250
>                 URL: https://issues.jenkins-ci.org/browse/JENKINS-9250
>             Project: Jenkins
>          Issue Type: Improvement
>          Components: clone-workspace
>            Reporter: Michael Pisula
>            Assignee: abayer
>
> Currently the plugin will clean the destination workspace before the cloned 
> workspace is copied there. This is problematic when the job uses the Multiple 
> SCM plugin in to get another set of sources, even if set up correctly this 
> leads to a complete checkout of all of the other sources for each invokation 
> of the build.
> I guess allowing the user to choose to unzip the cloned workspace into a 
> directory and to only clear this directory before copying might solve the 
> problem.
> While one might argue that such an option might be better located in the 
> multiple SCM plugin, other SCM plugins like SVN offer such an option. 
> (Besides this option could be useful if cloning workspaces from more than one 
> job will be possible)

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