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Could you also try running the test with your gitblit repository, but using jenkins.war with its self-contained HTTP server, rather than tomcat? I'd like to confirm that it is not related to your use of tomcat.
Once that is started, install the git plugin in the Jenkins at http://localhost:10101/, define a job and confirm that it behaves the same as your tomcat configured Jenkins. I expect it will, and that will give further credence to the issue being somehow related to the gitblit browser code in the git plugin, rather than being related to your tomcat configuration.