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CentOS / Redhat: Protect Yum Repo's Packages

How do I protect my yum repo's packages from certain repositories getting replaced / updated via yum command itself under CentOS / RHEL / Redhat Enterprise Linux?
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Q. Why does my yum command fail with an error that a repo is listed more than once under Fedora / RHEL / CentOS Linux? This error occurs when I type yum clean command

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Repository xen-repo is listed more than once in the configuration

How do I fix this problem?

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