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Our build process is a little unusual. It is made up of two components:
1) The setup script, which determines the branch to actually build (this information is published in a JSON file) and then creates a branch locally called "jenkins" pointed at this branch. This script runs in the Pre-SCM phase.
This can be seen in the above output - "Branch jenkins set up to track remote branch master from origin".
2) The primary build phase.
The Git plugin is invoked between component #1 and #2.
Does this help?