update documentation

All Submissions:

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• [YES] Have you added an explanation of what your changes do and why you'd like us to include them?
• [YES] I have updated the documentation accordingly.
• [YES] My code follows the code style of this project.

Current Behavior or Linked Issues

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• Fix broken link in the documentation.
• Made GIT_REPO variable optional in common_prepare.sh script to support optional flux repository.
• Related to #318

Does this introduce a breaking change?

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• [NO]