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I found it was possible to fix by disabling and re-enabling submodules. It seems that the <extensions/> configuration starts out empty. After the disable, I had this diff between the backed up config.xml and new one:
31,37c31
< <extensions>
< <hudson.plugins.git.extensions.impl.SubmoduleOption>
< <disableSubmodules>true</disableSubmodules>
< <recursiveSubmodules>false</recursiveSubmodules>
< <trackingSubmodules>false</trackingSubmodules>
< </hudson.plugins.git.extensions.impl.SubmoduleOption>
< </extensions>
—
> <extensions/>