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I seem to have a similar problem. The plugin seems to fail to use GIT_SSH when a "Recursively update submodules" is used. So basically, the parent module is checked out correctly then I get the following failure for for submodule checkout. Note I can use hte plugin to directly check the submodule out (hence the crednetials are correct) :
> /usr/bin/git submodule update --init --recursive
FATAL: Command "/usr/bin/git submodule update --init --recursive" returned status code 1:
stdout: Initialized empty Git repository in /export/Apps/srater_recognizer.15.1/SRaterHome/SRater/ASR_Files/files/ELTeach/expunct/.git/
...
stderr: Permission denied (publickey).
fatal: The remote end hung up unexpectedly
Clone of 'ssh://git@xxx:7999/foo/bar.git' into submodule path 'Foo/bar' failed
hudson.plugins.git.GitException: Command "/usr/bin/git submodule update --init --recursive" returned status code 1:
stdout: Initialized empty Git repository in /somewhere/.git/
stderr: Permission denied (publickey).
fatal: The remote end hung up unexpectedly
Clone of 'ssh://git@xxx:7999/foo/bar.git' into submodule path 'Foo/bar' failed