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motivation: The issue is caused by indexStoreMode: Bool? so it's set to nil when running --help on any subcommand. It can be solved by setting to either true or false, but by choosing either true or false we lose auto which is our default. Using an enum solves the issue of having a nil value by using the case autoIndexStoreand preserves the ability to use auto as our default.
changes: move indexStoreMode to an enum
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