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https://issues.jenkins-ci.org/browse/JENKINS-13267?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
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Henrik Skupin resolved JENKINS-13267.
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    Resolution: Not A Defect

As it has been turned out it was really an issue on our side. Sorry for the 
false alarm.
                
> Wrong working dir used on Windows if executed command is in a subfolder
> -----------------------------------------------------------------------
>
>                 Key: JENKINS-13267
>                 URL: https://issues.jenkins-ci.org/browse/JENKINS-13267
>             Project: Jenkins
>          Issue Type: Bug
>          Components: xshell
>    Affects Versions: current
>         Environment: Any Windows platform
>            Reporter: Henrik Skupin
>
> If a build step with XShell calls a command which is not in the current 
> working dir but in a sub folder, the sub folder is used as current working 
> dir. This issue only persists on Windows and cannot be seen on Linux or Mac.
> Just take a command (which is a wrapper script) like:
> scripts/run hg clone https://hg.mozilla.org/qa/mozmill-automation
> It should clone the given repository into the nodes working dir, but right 
> now it will end up as 'scripts/mozmill-automation'. So the wrapper scripts 
> working dir is used.
> Calling the wrapper script from outside Jenkins it works fine, so it has to 
> be a XShell bug.
> As reference of a problematic job see:
> https://github.com/whimboo/mozmill-ci/blob/master/jenkins-master/jobs/functional-test/config.xml#L78
> Steps to reproduce:
> 1. Clone https://github.com/whimboo/mozmill-ci/
> 2. Follow the readme and setup the system
> 3. Add a node for Windows
> 4. Run 'Build Now' on the functional testrun (Branch: mozilla-central, 
> Platform: win32, Locale: en-US, BuildId: 20120328115525, Nodes: win_xp, 
> Env-Platform: Windows)
> 5. Check the working dir of the project and notice that the hg clone is not 
> ending up in the root working dir
> There is also no difference with executeFromWorkingDir enabled or disabled.
> 5. 

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