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I am also seeing this happening. My setup is as follows:
If I log into any build slave and use the "lsof" command to see what processes have files open, I see that the java instance of the build slave has files open in the .git/objects/pack/ directory of several jobs.
I have to restart all build-slaves that have files open before I can run the job again.
EDIT: I also want to say that I'm seeing this even when the branch specifier is explicit: "origin/master". no wildcard is being used...