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The install command microdnf does not use -q list to query installed packages. The command used is repoquery. This is a problem in the common-utils/main.sh:install_redhat_packages() function as all the conditionals checking if a package is not installed will evaluate to true and attempt to install the package.
An example from the function:
# Install EPEL repository if needed (required to install 'jq' for CentOS)if!${install_cmd} -q list jq >/dev/null 2>&1;then${install_cmd} -y install epel-release
remove_epel="true"fi
This particular example causes a problem for me as my base container doesn't have the epel-release package defined, but does have jq installed.