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I'm disappointed to report that I can still reproduce this issue. I have Jenkins 1.585, git plugin 2.2.7, and git client plugin 1.11.0. The last comment here says it's fixed in git plugin 2.3, but that was three months ago. Is 2.3 on the way?
In any case, I have been using the same test project as mentioned earlier, configured with a 240 minute timeout on submodules. The output is below. You can see the timeouts in the output, but it seems like they are commented out.
{{
Building in workspace C:\Jenkins\jobs\git-test\workspace
Cloning the remote Git repository
Cloning repository g...@github.com:stimulant/IMR4.git
> C:\Program Files (x86)\Git\cmd\git.exe init C:\Jenkins\jobs\git-test\workspace # timeout=10
Fetching upstream changes from g...@github.com:stimulant/IMR4.git
> C:\Program Files (x86)\Git\cmd\git.exe --version # timeout=10
> C:\Program Files (x86)\Git\cmd\git.exe fetch --tags --progress g...@github.com:stimulant/IMR4.git +refs/heads/:refs/remotes/origin/ # timeout=240
> C:\Program Files (x86)\Git\cmd\git.exe config remote.origin.url g...@github.com:stimulant/IMR4.git # timeout=10
> C:\Program Files (x86)\Git\cmd\git.exe config remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10
> C:\Program Files (x86)\Git\cmd\git.exe config remote.origin.url g...@github.com:stimulant/IMR4.git # timeout=10
Fetching upstream changes from g...@github.com:stimulant/IMR4.git
> C:\Program Files (x86)\Git\cmd\git.exe fetch --tags --progress g...@github.com:stimulant/IMR4.git +refs/heads/:refs/remotes/origin/ # timeout=240
> C:\Program Files (x86)\Git\cmd\git.exe rev-parse "refs/remotes/origin/dev^{commit}" # timeout=10
> C:\Program Files (x86)\Git\cmd\git.exe rev-parse "refs/remotes/origin/origin/dev^{commit}" # timeout=10
Checking out Revision 696e4dea88730d445406e6a7dd5101b00be2d751 (refs/remotes/origin/dev)
> C:\Program Files (x86)\Git\cmd\git.exe config core.sparsecheckout # timeout=10
> C:\Program Files (x86)\Git\cmd\git.exe checkout -f 696e4dea88730d445406e6a7dd5101b00be2d751 # timeout=240
> C:\Program Files (x86)\Git\cmd\git.exe rev-list 696e4dea88730d445406e6a7dd5101b00be2d751 # timeout=10
> C:\Program Files (x86)\Git\cmd\git.exe remote # timeout=10
> C:\Program Files (x86)\Git\cmd\git.exe submodule init # timeout=10
> C:\Program Files (x86)\Git\cmd\git.exe submodule sync # timeout=10
> C:\Program Files (x86)\Git\cmd\git.exe config --get remote.origin.url # timeout=10
> C:\Program Files (x86)\Git\cmd\git.exe submodule update --init --recursive
ERROR: Timeout after 10 minutes
FATAL: Command "C:\Program Files (x86)\Git\cmd\git.exe submodule update --init --recursive" returned status code -1:
}}