I solved this problem on Windows by adding this as a buildstep before the SCM 
runs:

git.exe config --global credential.helper wincred

it is specifically needed for sub-modules. The local cred store does not handle 
sub-modules (I think)

From: jenkinsci-users@googlegroups.com 
[mailto:jenkinsci-users@googlegroups.com] On Behalf Of Pratik Dhandharia
Sent: Monday, August 24, 2015 3:46 PM
To: Jenkins Users
Subject: Get Jenkins Working with Private Repo

Hi All,

I am comparatively new to Jenkins and I am trying to troubleshoot a Jenkins 
issue where we are trying to fetch a public repository which has multiple 
private sub-modules. It is due to legal reasons we cannot keep the private 
sub-modules public.

So I have most of the plugin's installed in Jenkins. I have configured Jenkins 
to store the jenkins user credential using the credential plugin.

What I am really trying to do is, fetching the private sub-modules using 
credentials (username and password). I don't want to switch to using SSH key of 
the jenkins user for pulling the private sub-modules. And here is the error 
that I get:

 > /usr/bin/git submodule sync # timeout=10

 > /usr/bin/git config --get remote.origin.url # timeout=10

 > /usr/bin/git submodule update --init --recursive

FATAL: Command "/usr/bin/git submodule update --init --recursive" returned 
status code 1:

stdout:

stderr: fatal: Authentication failed

Unable to fetch in submodule path

Can someone please help point out if the Jenkins Git Client Plugin, work with 
fetching private repositories using credentials(username and password)?

Thanks
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