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propagate MutuallyExclusiveFlags persistent flags to subcommands

propagate MutuallyExclusiveFlags persistent flags to subcommands: a task in repo2rlenv-commit-runtime-test: repo2rlenv-commit-runtime (Harbor dataset). Title: propagate MutuallyExclusiveFlags persistent flags to subcommands

The task

**Title:** propagate MutuallyExclusiveFlags persistent flags to subcommands

Part of AdithyaSK/repo2rlenv-commit-runtime-test.